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Parallel execution javascript evaluation error
See original GitHub issueExpected Behavior
Jobs execute in parallel
Actual Behavior
Jobs executed in parallel but an expression evaluation error caused successful workflow steps to fail. This error tends to occur when multiple steps finished together.
Workflow Code
workflow.cwl
cat hisat2-6.cwl
#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
requirements:
ScatterFeatureRequirement: {}
MultipleInputFeatureRequirement: {}
StepInputExpressionRequirement: {}
InlineJavascriptRequirement: {}
inputs:
threads: int
genomeDir: Directory
annotation: File
subject_name1: string
subject_name2: string
subject_name3: string
subject_name4: string
subject_name5: string
subject_name6: string
fastq1: File[]
fastq2: File[]
fastq3: File[]
fastq4: File[]
fastq5: File[]
fastq6: File[]
outputs:
hisat2_align_out:
type: Directory
outputSource: hisat2_align_folder/out
steps:
hisat2_align_1:
run: /data/rnaseq/RNASeq/cwl-tools/docker/hisat2_align.cwl
in:
threads: threads
index_directory: genomeDir
first_pair:
source: fastq1
valueFrom: $(self[0])
second_pair:
source: fastq1
valueFrom: $(self[1])
sam_name:
source: subject_name1
valueFrom: $(self + '.sam')
out: [sam_output, hisat2_align_out]
hisat2_align_2:
run: /data/rnaseq/RNASeq/cwl-tools/docker/hisat2_align.cwl
in:
threads: threads
index_directory: genomeDir
first_pair:
source: fastq2
valueFrom: $(self[0])
second_pair:
source: fastq2
valueFrom: $(self[1])
sam_name:
source: subject_name2
valueFrom: $(self + '.sam')
out: [sam_output, hisat2_align_out]
hisat2_align_3:
run: /data/rnaseq/RNASeq/cwl-tools/docker/hisat2_align.cwl
in:
threads: threads
index_directory: genomeDir
first_pair:
source: fastq3
valueFrom: $(self[0])
second_pair:
source: fastq3
valueFrom: $(self[1])
# single_file: fastq3
sam_name:
source: subject_name3
valueFrom: $(self + '.sam')
out: [sam_output, hisat2_align_out]
hisat2_align_4:
run: /data/rnaseq/RNASeq/cwl-tools/docker/hisat2_align.cwl
in:
threads: threads
index_directory: genomeDir
first_pair:
source: fastq4
valueFrom: $(self[0])
second_pair:
source: fastq4
valueFrom: $(self[1])
# single_file: fastq4
sam_name:
source: subject_name4
valueFrom: $(self + '.sam')
out: [sam_output, hisat2_align_out]
hisat2_align_5:
run: /data/rnaseq/RNASeq/cwl-tools/docker/hisat2_align.cwl
in:
threads: threads
index_directory: genomeDir
first_pair:
source: fastq5
valueFrom: $(self[0])
second_pair:
source: fastq5
valueFrom: $(self[1])
# single_file: fastq4
sam_name:
source: subject_name5
valueFrom: $(self + '.sam')
out: [sam_output, hisat2_align_out]
hisat2_align_6:
run: /data/rnaseq/RNASeq/cwl-tools/docker/hisat2_align.cwl
in:
threads: threads
index_directory: genomeDir
first_pair:
source: fastq6
valueFrom: $(self[0])
second_pair:
source: fastq6
valueFrom: $(self[1])
# single_file: fastq4
sam_name:
source: subject_name6
valueFrom: $(self + '.sam')
out: [sam_output, hisat2_align_out]
hisat2_align_folder:
run: /data/rnaseq/RNASeq/cwl-tools/folder.cwl
in:
item:
- hisat2_align_1/hisat2_align_out
- hisat2_align_2/hisat2_align_out
- hisat2_align_3/hisat2_align_out
- hisat2_align_4/hisat2_align_out
- hisat2_align_5/hisat2_align_out
- hisat2_align_6/hisat2_align_out
name:
valueFrom: "hisat2"
out: [out]
hisat2_align.cwl
#!usr/bin/env cwl-runner
cwlVersion: v1.0
class: CommandLineTool
baseCommand:
hints:
ShellCommandRequirement: {}
DockerRequirement:
dockerPull: quay.io/biocontainers/hisat2:2.1.0--py27h2d50403_2
requirements:
InlineJavascriptRequirement: {}
arguments:
- position: 1
valueFrom: "mkdir"
- position: 2
valueFrom: $(inputs.sam_name.split('.')[0])
- position: 3
shellQuote: False
valueFrom: '&& cd'
- position: 4
valueFrom: $(inputs.sam_name.split('.')[0])
- position: 5
shellQuote: False
valueFrom: '&& hisat2'
inputs:
input_type:
type: string
default: "-q"
inputBinding:
position: 6
index_directory:
type: Directory
inputBinding:
position: 7
prefix: "-x"
valueFrom: "${return inputs.index_directory.path + '/'
+ inputs.index_directory.listing[0].nameroot.split('.').slice(0,-1).join('.')}"
first_pair:
type: File?
inputBinding:
position: 8
prefix: "-1"
second_pair:
type: File?
inputBinding:
position: 9
prefix: "-2"
single_file:
type: File[]?
inputBinding:
position: 10
prefix: -U
sra_acc:
type: string?
inputBinding:
position: 11
prefix: --sra-acc
sam_name:
type: string
inputBinding:
position: 12
prefix: -S
threads:
type: int
inputBinding:
position: 13
prefix: -p
XSTag:
type: string?
default: --dta-cufflinks
inputBinding:
position: 14
log:
type: string
default: "log.txt"
inputBinding:
position: 15
prefix: --summary-file
outputs:
hisat2_align_out:
type: Directory
outputBinding:
glob: $(inputs.sam_name.split('.')[0])
sam_output:
type: File
outputBinding:
glob: $(inputs.sam_name.split('.')[0] + '/' + inputs.sam_name)
Full Traceback
Full traceback too long for issue, a txt log file is attacked below
[2019-02-20 15:51:31] [workflow ] starting step hisat2_align_2
[2019-02-20 15:51:31] [job step hisat2_align_2] job input {
"file:///data/rnaseq/test/plas/hisat2-6.cwl#hisat2_align_2/first_pair": [
{
"class": "File",
"location": "file:///data/rnaseq/test/plas/SRR3584107_1.fastq.gz",
"size": 1060958478,
"basename": "SRR3584107_1.fastq.gz",
"nameroot": "SRR3584107_1.fastq",
"nameext": ".gz"
},
{
"class": "File",
"location": "file:///data/rnaseq/test/plas/SRR3584107_2.fastq.gz",
"size": 1096917576,
"basename": "SRR3584107_2.fastq.gz",
"nameroot": "SRR3584107_2.fastq",
"nameext": ".gz"
}
],
"file:///data/rnaseq/test/plas/hisat2-6.cwl#hisat2_align_2/index_directory": {
"class": "Directory",
"location": "file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index",
"basename": "HISAT2Index",
"listing": [
{
"class": "File",
"location": "file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.1.ht2",
"basename": "P.yoelii.1.ht2"
},
{
"class": "File",
"location": "file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.2.ht2",
"basename": "P.yoelii.2.ht2"
},
{
"class": "File",
"location": "file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.3.ht2",
"basename": "P.yoelii.3.ht2"
},
{
"class": "File",
"location": "file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.4.ht2",
"basename": "P.yoelii.4.ht2"
},
{
"class": "File",
"location": "file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.5.ht2",
"basename": "P.yoelii.5.ht2"
},
{
"class": "File",
"location": "file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.6.ht2",
"basename": "P.yoelii.6.ht2"
},
{
"class": "File",
"location": "file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.7.ht2",
"basename": "P.yoelii.7.ht2"
},
{
"class": "File",
"location": "file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.8.ht2",
"basename": "P.yoelii.8.ht2"
}
]
},
"file:///data/rnaseq/test/plas/hisat2-6.cwl#hisat2_align_2/sam_name": "SRR3584107",
"file:///data/rnaseq/test/plas/hisat2-6.cwl#hisat2_align_2/second_pair": [
{
"class": "File",
"location": "file:///data/rnaseq/test/plas/SRR3584107_1.fastq.gz",
"size": 1060958478,
"basename": "SRR3584107_1.fastq.gz",
"nameroot": "SRR3584107_1.fastq",
"nameext": ".gz"
},
{
"class": "File",
"location": "file:///data/rnaseq/test/plas/SRR3584107_2.fastq.gz",
"size": 1096917576,
"basename": "SRR3584107_2.fastq.gz",
"nameroot": "SRR3584107_2.fastq",
"nameext": ".gz"
}
],
"file:///data/rnaseq/test/plas/hisat2-6.cwl#hisat2_align_2/threads": 12
}
[2019-02-20 15:51:31] [job step hisat2_align_2] evaluated job input to {
"file:///data/rnaseq/test/plas/hisat2-6.cwl#hisat2_align_2/first_pair": {
"class": "File",
"location": "file:///data/rnaseq/test/plas/SRR3584107_1.fastq.gz",
"size": 1060958478,
"basename": "SRR3584107_1.fastq.gz",
"nameroot": "SRR3584107_1.fastq",
"nameext": ".gz"
},
"file:///data/rnaseq/test/plas/hisat2-6.cwl#hisat2_align_2/index_directory": {
"class": "Directory",
"location": "file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index",
"basename": "HISAT2Index",
"listing": [
{
"class": "File",
"location": "file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.1.ht2",
"basename": "P.yoelii.1.ht2"
},
{
"class": "File",
"location": "file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.2.ht2",
"basename": "P.yoelii.2.ht2"
},
{
"class": "File",
"location": "file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.3.ht2",
"basename": "P.yoelii.3.ht2"
},
{
"class": "File",
"location": "file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.4.ht2",
"basename": "P.yoelii.4.ht2"
},
{
"class": "File",
"location": "file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.5.ht2",
"basename": "P.yoelii.5.ht2"
},
{
"class": "File",
"location": "file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.6.ht2",
"basename": "P.yoelii.6.ht2"
},
{
"class": "File",
"location": "file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.7.ht2",
"basename": "P.yoelii.7.ht2"
},
{
"class": "File",
"location": "file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.8.ht2",
"basename": "P.yoelii.8.ht2"
}
]
},
"file:///data/rnaseq/test/plas/hisat2-6.cwl#hisat2_align_2/sam_name": "SRR3584107.sam",
"file:///data/rnaseq/test/plas/hisat2-6.cwl#hisat2_align_2/second_pair": {
"class": "File",
"location": "file:///data/rnaseq/test/plas/SRR3584107_2.fastq.gz",
"size": 1096917576,
"basename": "SRR3584107_2.fastq.gz",
"nameroot": "SRR3584107_2.fastq",
"nameext": ".gz"
},
"file:///data/rnaseq/test/plas/hisat2-6.cwl#hisat2_align_2/threads": 12
}
[2019-02-20 15:51:31] [step hisat2_align_2] start
[2019-02-20 15:51:31] [job hisat2_align_2] initializing from file:///data/rnaseq/RNASeq/cwl-tools/docker/hisat2_align.cwl as part of step hisat2_align_2
[2019-02-20 15:51:31] [job hisat2_align_2] {
"first_pair": {
"class": "File",
"location": "file:///data/rnaseq/test/plas/SRR3584107_1.fastq.gz",
"size": 1060958478,
"basename": "SRR3584107_1.fastq.gz",
"nameroot": "SRR3584107_1.fastq",
"nameext": ".gz"
},
"index_directory": {
"class": "Directory",
"location": "file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index",
"basename": "HISAT2Index",
"listing": [
{
"class": "File",
"location": "file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.1.ht2",
"basename": "P.yoelii.1.ht2"
},
{
"class": "File",
"location": "file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.2.ht2",
"basename": "P.yoelii.2.ht2"
},
{
"class": "File",
"location": "file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.3.ht2",
"basename": "P.yoelii.3.ht2"
},
{
"class": "File",
"location": "file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.4.ht2",
"basename": "P.yoelii.4.ht2"
},
{
"class": "File",
"location": "file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.5.ht2",
"basename": "P.yoelii.5.ht2"
},
{
"class": "File",
"location": "file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.6.ht2",
"basename": "P.yoelii.6.ht2"
},
{
"class": "File",
"location": "file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.7.ht2",
"basename": "P.yoelii.7.ht2"
},
{
"class": "File",
"location": "file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.8.ht2",
"basename": "P.yoelii.8.ht2"
}
]
},
"sam_name": "SRR3584107.sam",
"second_pair": {
"class": "File",
"location": "file:///data/rnaseq/test/plas/SRR3584107_2.fastq.gz",
"size": 1096917576,
"basename": "SRR3584107_2.fastq.gz",
"nameroot": "SRR3584107_2.fastq",
"nameext": ".gz"
},
"threads": 12
}
[2019-02-20 15:51:31] [job hisat2_align_2] path mappings is {
"file:///data/rnaseq/test/plas/SRR3584107_1.fastq.gz": [
"/data/rnaseq/test/plas/SRR3584107_1.fastq.gz",
"/var/lib/cwl/stg86c9298c-5c70-48c2-b3dc-d02bf5becf71/SRR3584107_1.fastq.gz",
"File",
true
],
"file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index": [
"/data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index",
"/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index",
"Directory",
true
],
"file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.1.ht2": [
"/data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.1.ht2",
"/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index/P.yoelii.1.ht2",
"File",
false
],
"file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.2.ht2": [
"/data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.2.ht2",
"/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index/P.yoelii.2.ht2",
"File",
false
],
"file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.3.ht2": [
"/data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.3.ht2",
"/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index/P.yoelii.3.ht2",
"File",
false
],
"file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.4.ht2": [
"/data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.4.ht2",
"/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index/P.yoelii.4.ht2",
"File",
false
],
"file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.5.ht2": [
"/data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.5.ht2",
"/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index/P.yoelii.5.ht2",
"File",
false
],
"file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.6.ht2": [
"/data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.6.ht2",
"/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index/P.yoelii.6.ht2",
"File",
false
],
"file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.7.ht2": [
"/data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.7.ht2",
"/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index/P.yoelii.7.ht2",
"File",
false
],
"file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.8.ht2": [
"/data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.8.ht2",
"/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index/P.yoelii.8.ht2",
"File",
false
],
"file:///data/rnaseq/test/plas/SRR3584107_2.fastq.gz": [
"/data/rnaseq/test/plas/SRR3584107_2.fastq.gz",
"/var/lib/cwl/stgbfd0456a-1175-455f-9904-112ae6be51c4/SRR3584107_2.fastq.gz",
"File",
true
]
}
[2019-02-20 15:51:31] [job hisat2_align_2] command line bindings is [
{
"position": [
1,
0
],
"valueFrom": "mkdir"
},
{
"position": [
2,
1
],
"valueFrom": "$(inputs.sam_name.split('.')[0])"
},
{
"position": [
3,
2
],
"shellQuote": false,
"valueFrom": "&& cd"
},
{
"position": [
4,
3
],
"valueFrom": "$(inputs.sam_name.split('.')[0])"
},
{
"position": [
5,
4
],
"shellQuote": false,
"valueFrom": "&& hisat2"
},
{
"position": [
6,
"input_type"
],
"datum": "-q"
},
{
"position": [
7,
"index_directory"
],
"prefix": "-x",
"valueFrom": "${return inputs.index_directory.path + '/' + inputs.index_directory.listing[0].nameroot.split('.').slice(0,-1).join('.')}",
"datum": {
"class": "Directory",
"location": "file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index",
"basename": "HISAT2Index",
"listing": [
{
"class": "File",
"location": "file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.1.ht2",
"basename": "P.yoelii.1.ht2",
"size": 11381890,
"nameroot": "P.yoelii.1",
"nameext": ".ht2",
"path": "/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index/P.yoelii.1.ht2",
"dirname": "/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index"
},
{
"class": "File",
"location": "file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.2.ht2",
"basename": "P.yoelii.2.ht2",
"size": 5357516,
"nameroot": "P.yoelii.2",
"nameext": ".ht2",
"path": "/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index/P.yoelii.2.ht2",
"dirname": "/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index"
},
{
"class": "File",
"location": "file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.3.ht2",
"basename": "P.yoelii.3.ht2",
"size": 17333,
"nameroot": "P.yoelii.3",
"nameext": ".ht2",
"path": "/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index/P.yoelii.3.ht2",
"dirname": "/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index"
},
{
"class": "File",
"location": "file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.4.ht2",
"basename": "P.yoelii.4.ht2",
"size": 5357509,
"nameroot": "P.yoelii.4",
"nameext": ".ht2",
"path": "/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index/P.yoelii.4.ht2",
"dirname": "/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index"
},
{
"class": "File",
"location": "file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.5.ht2",
"basename": "P.yoelii.5.ht2",
"size": 10823785,
"nameroot": "P.yoelii.5",
"nameext": ".ht2",
"path": "/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index/P.yoelii.5.ht2",
"dirname": "/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index"
},
{
"class": "File",
"location": "file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.6.ht2",
"basename": "P.yoelii.6.ht2",
"size": 5446918,
"nameroot": "P.yoelii.6",
"nameext": ".ht2",
"path": "/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index/P.yoelii.6.ht2",
"dirname": "/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index"
},
{
"class": "File",
"location": "file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.7.ht2",
"basename": "P.yoelii.7.ht2",
"size": 12,
"nameroot": "P.yoelii.7",
"nameext": ".ht2",
"path": "/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index/P.yoelii.7.ht2",
"dirname": "/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index"
},
{
"class": "File",
"location": "file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.8.ht2",
"basename": "P.yoelii.8.ht2",
"size": 8,
"nameroot": "P.yoelii.8",
"nameext": ".ht2",
"path": "/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index/P.yoelii.8.ht2",
"dirname": "/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index"
}
],
"path": "/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index",
"dirname": "/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763"
}
},
{
"position": [
8,
"first_pair"
],
"prefix": "-1",
"datum": {
"class": "File",
"location": "file:///data/rnaseq/test/plas/SRR3584107_1.fastq.gz",
"size": 1060958478,
"basename": "SRR3584107_1.fastq.gz",
"nameroot": "SRR3584107_1.fastq",
"nameext": ".gz",
"path": "/var/lib/cwl/stg86c9298c-5c70-48c2-b3dc-d02bf5becf71/SRR3584107_1.fastq.gz",
"dirname": "/var/lib/cwl/stg86c9298c-5c70-48c2-b3dc-d02bf5becf71"
}
},
{
"position": [
9,
"second_pair"
],
"prefix": "-2",
"datum": {
"class": "File",
"location": "file:///data/rnaseq/test/plas/SRR3584107_2.fastq.gz",
"size": 1096917576,
"basename": "SRR3584107_2.fastq.gz",
"nameroot": "SRR3584107_2.fastq",
"nameext": ".gz",
"path": "/var/lib/cwl/stgbfd0456a-1175-455f-9904-112ae6be51c4/SRR3584107_2.fastq.gz",
"dirname": "/var/lib/cwl/stgbfd0456a-1175-455f-9904-112ae6be51c4"
}
},
{
"position": [
12,
"sam_name"
],
"prefix": "-S",
"datum": "SRR3584107.sam"
},
{
"position": [
13,
"threads"
],
"prefix": "-p",
"datum": 12
},
{
"position": [
14,
"XSTag"
],
"datum": "--dta-cufflinks"
},
{
"position": [
15,
"log"
],
"prefix": "--summary-file",
"datum": "log.txt"
}
]
[2019-02-20 15:51:31] [job hisat2_align_2] /tmp/tmpcrt_6qsg$ docker \
run \
-i \
--volume=/tmp/tmpcrt_6qsg:/var/spool/cwl:rw \
--volume=/tmp/tmpstb5kcem:/tmp:rw \
--volume=/data/rnaseq/test/plas/SRR3584107_1.fastq.gz:/var/lib/cwl/stg86c9298c-5c70-48c2-b3dc-d02bf5becf71/SRR3584107_1.fastq.gz:ro \
--volume=/data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index:/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index:ro \
--volume=/data/rnaseq/test/plas/SRR3584107_2.fastq.gz:/var/lib/cwl/stgbfd0456a-1175-455f-9904-112ae6be51c4/SRR3584107_2.fastq.gz:ro \
--workdir=/var/spool/cwl \
--read-only=true \
--user=201808:700 \
--rm \
--env=TMPDIR=/tmp \
--env=HOME=/var/spool/cwl \
quay.io/biocontainers/hisat2:2.1.0--py27h2d50403_2 \
/bin/sh \
-c \
'mkdir' 'SRR3584107' && cd 'SRR3584107' && hisat2 '-q' '-x' '/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index/P.yoelii' '-1' '/var/lib/cwl/stg86c9298c-5c70-48c2-b3dc-d02bf5becf71/SRR3584107_1.fastq.gz' '-2' '/var/lib/cwl/stgbfd0456a-1175-455f-9904-112ae6be51c4/SRR3584107_2.fastq.gz' '-S' 'SRR3584107.sam' '-p' '12' '--dta-cufflinks' '--summary-file' 'log.txt'
[2019-02-20 15:56:27] [job hisat2_align_2] Job error:
Error collecting output for parameter 'hisat2_align_out':
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: Traceback (most recent call last):
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: File "/project/soft/linux64/anaconda/Anaconda3-2018.12-Linux-x86_64/lib/python3.7/site-packages/cwltool/sandboxjs.py", line 377, in execjs
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: return json.loads(stdout)
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: File "/project/soft/linux64/anaconda/Anaconda3-2018.12-Linux-x86_64/lib/python3.7/json/__init__.py", line 348, in loads
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: return _default_decoder.decode(s)
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: File "/project/soft/linux64/anaconda/Anaconda3-2018.12-Linux-x86_64/lib/python3.7/json/decoder.py", line 337, in decode
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: obj, end = self.raw_decode(s, idx=_w(s, 0).end())
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: File "/project/soft/linux64/anaconda/Anaconda3-2018.12-Linux-x86_64/lib/python3.7/json/decoder.py", line 355, in raw_decode
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: raise JSONDecodeError("Expecting value", s, err.value) from None
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: During handling of the above exception, another exception occurred:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: Traceback (most recent call last):
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: File "/project/soft/linux64/anaconda/Anaconda3-2018.12-Linux-x86_64/lib/python3.7/site-packages/cwltool/expression.py", line 293, in do_eval
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: strip_whitespace=strip_whitespace)
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: File "/project/soft/linux64/anaconda/Anaconda3-2018.12-Linux-x86_64/lib/python3.7/site-packages/cwltool/expression.py", line 226, in interpolate
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: debug=debug, js_console=js_console)
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: File "/project/soft/linux64/anaconda/Anaconda3-2018.12-Linux-x86_64/lib/python3.7/site-packages/cwltool/expression.py", line 191, in evaluator
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: debug=debug, js_console=js_console)
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: File "/project/soft/linux64/anaconda/Anaconda3-2018.12-Linux-x86_64/lib/python3.7/site-packages/cwltool/sandboxjs.py", line 381, in execjs
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: err, fn_linenum(), stdout, stderr))
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: cwltool.sandboxjs.JavascriptException: Expecting value: line 1 column 1 (char 0)
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: script was:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 29 "class": "File",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 30 "location": "file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.2.ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 31 "basename": "P.yoelii.2.ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 32 "size": 5357516,
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 33 "nameroot": "P.yoelii.2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 34 "nameext": ".ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 35 "path": "/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index/P.yoelii.2.ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 36 "dirname": "/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index"
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 37 },
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 38 {
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 39 "class": "File",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 40 "location": "file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.3.ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 41 "basename": "P.yoelii.3.ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 42 "size": 17333,
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 43 "nameroot": "P.yoelii.3",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 44 "nameext": ".ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 45 "path": "/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index/P.yoelii.3.ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 46 "dirname": "/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index"
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 47 },
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 48 {
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 49 "class": "File",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 50 "location": "file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.4.ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 51 "basename": "P.yoelii.4.ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 52 "size": 5357509,
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 53 "nameroot": "P.yoelii.4",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 54 "nameext": ".ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 55 "path": "/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index/P.yoelii.4.ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 56 "dirname": "/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index"
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 57 },
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 58 {
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 59 "class": "File",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 60 "location": "file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.5.ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 61 "basename": "P.yoelii.5.ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 62 "size": 10823785,
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 63 "nameroot": "P.yoelii.5",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 64 "nameext": ".ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 65 "path": "/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index/P.yoelii.5.ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 66 "dirname": "/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index"
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 67 },
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 68 {
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 69 "class": "File",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 70 "location": "file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.6.ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 71 "basename": "P.yoelii.6.ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 72 "size": 5446918,
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 73 "nameroot": "P.yoelii.6",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 74 "nameext": ".ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 75 "path": "/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index/P.yoelii.6.ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 76 "dirname": "/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index"
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 77 },
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 78 {
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 79 "class": "File",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 80 "location": "file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.7.ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 81 "basename": "P.yoelii.7.ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 82 "size": 12,
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 83 "nameroot": "P.yoelii.7",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 84 "nameext": ".ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 85 "path": "/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index/P.yoelii.7.ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 86 "dirname": "/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index"
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 87 },
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 88 {
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 89 "class": "File",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 90 "location": "file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.8.ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 91 "basename": "P.yoelii.8.ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 92 "size": 8,
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 93 "nameroot": "P.yoelii.8",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 94 "nameext": ".ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 95 "path": "/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index/P.yoelii.8.ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 96 "dirname": "/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index"
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 97 }
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 98 ],
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 99 "path": "/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 100 "dirname": "/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763"
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 101 },
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 102 "sam_name": "SRR3584107.sam",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 103 "second_pair": {
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 104 "class": "File",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 105 "location": "file:///data/rnaseq/test/plas/SRR3584107_2.fastq.gz",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 106 "size": 1096917576,
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 107 "basename": "SRR3584107_2.fastq.gz",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 108 "nameroot": "SRR3584107_2.fastq",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 109 "nameext": ".gz",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 110 "path": "/var/lib/cwl/stgbfd0456a-1175-455f-9904-112ae6be51c4/SRR3584107_2.fastq.gz",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 111 "dirname": "/var/lib/cwl/stgbfd0456a-1175-455f-9904-112ae6be51c4"
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 112 },
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 113 "threads": 12,
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 114 "XSTag": "--dta-cufflinks",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 115 "input_type": "-q",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 116 "log": "log.txt",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 117 "single_file": null,
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 118 "sra_acc": null
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 119 };
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 120 var self = null;
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 121 var runtime = {
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 122 "cores": 1,
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 123 "ram": 1024,
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 124 "tmpdir": "/tmp",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 125 "outdir": "/var/spool/cwl"
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 126 };
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 127 (function(){return ((inputs.sam_name.split('.')[0]));})()
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: stdout was: ''
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: stderr was: ''
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: During handling of the above exception, another exception occurred:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: Traceback (most recent call last):
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: File "/project/soft/linux64/anaconda/Anaconda3-2018.12-Linux-x86_64/lib/python3.7/site-packages/cwltool/command_line_tool.py", line 648, in collect_output
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: gb = builder.do_eval(gb)
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: File "/project/soft/linux64/anaconda/Anaconda3-2018.12-Linux-x86_64/lib/python3.7/site-packages/cwltool/builder.py", line 425, in do_eval
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: strip_whitespace=strip_whitespace)
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: File "/project/soft/linux64/anaconda/Anaconda3-2018.12-Linux-x86_64/lib/python3.7/site-packages/cwltool/expression.py", line 296, in do_eval
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: raise WorkflowException("Expression evaluation error:\n%s" % e)
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: cwltool.errors.WorkflowException: Expression evaluation error:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: Expecting value: line 1 column 1 (char 0)
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: script was:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 29 "class": "File",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 30 "location": "file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.2.ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 31 "basename": "P.yoelii.2.ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 32 "size": 5357516,
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 33 "nameroot": "P.yoelii.2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 34 "nameext": ".ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 35 "path": "/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index/P.yoelii.2.ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 36 "dirname": "/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index"
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 37 },
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 38 {
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 39 "class": "File",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 40 "location": "file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.3.ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 41 "basename": "P.yoelii.3.ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 42 "size": 17333,
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 43 "nameroot": "P.yoelii.3",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 44 "nameext": ".ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 45 "path": "/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index/P.yoelii.3.ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 46 "dirname": "/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index"
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 47 },
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 48 {
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 49 "class": "File",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 50 "location": "file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.4.ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 51 "basename": "P.yoelii.4.ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 52 "size": 5357509,
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 53 "nameroot": "P.yoelii.4",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 54 "nameext": ".ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 55 "path": "/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index/P.yoelii.4.ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 56 "dirname": "/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index"
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 57 },
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 58 {
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 59 "class": "File",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 60 "location": "file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.5.ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 61 "basename": "P.yoelii.5.ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 62 "size": 10823785,
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 63 "nameroot": "P.yoelii.5",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 64 "nameext": ".ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 65 "path": "/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index/P.yoelii.5.ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 66 "dirname": "/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index"
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 67 },
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 68 {
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 69 "class": "File",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 70 "location": "file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.6.ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 71 "basename": "P.yoelii.6.ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 72 "size": 5446918,
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 73 "nameroot": "P.yoelii.6",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 74 "nameext": ".ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 75 "path": "/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index/P.yoelii.6.ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 76 "dirname": "/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index"
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 77 },
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 78 {
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 79 "class": "File",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 80 "location": "file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.7.ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 81 "basename": "P.yoelii.7.ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 82 "size": 12,
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 83 "nameroot": "P.yoelii.7",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 84 "nameext": ".ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 85 "path": "/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index/P.yoelii.7.ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 86 "dirname": "/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index"
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 87 },
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 88 {
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 89 "class": "File",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 90 "location": "file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.8.ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 91 "basename": "P.yoelii.8.ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 92 "size": 8,
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 93 "nameroot": "P.yoelii.8",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 94 "nameext": ".ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 95 "path": "/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index/P.yoelii.8.ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 96 "dirname": "/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index"
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 97 }
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 98 ],
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 99 "path": "/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 100 "dirname": "/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763"
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 101 },
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 102 "sam_name": "SRR3584107.sam",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 103 "second_pair": {
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 104 "class": "File",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 105 "location": "file:///data/rnaseq/test/plas/SRR3584107_2.fastq.gz",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 106 "size": 1096917576,
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 107 "basename": "SRR3584107_2.fastq.gz",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 108 "nameroot": "SRR3584107_2.fastq",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 109 "nameext": ".gz",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 110 "path": "/var/lib/cwl/stgbfd0456a-1175-455f-9904-112ae6be51c4/SRR3584107_2.fastq.gz",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 111 "dirname": "/var/lib/cwl/stgbfd0456a-1175-455f-9904-112ae6be51c4"
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 112 },
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 113 "threads": 12,
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 114 "XSTag": "--dta-cufflinks",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 115 "input_type": "-q",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 116 "log": "log.txt",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 117 "single_file": null,
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 118 "sra_acc": null
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 119 };
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 120 var self = null;
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 121 var runtime = {
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 122 "cores": 1,
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 123 "ram": 1024,
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 124 "tmpdir": "/tmp",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 125 "outdir": "/var/spool/cwl"
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 126 };
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: 127 (function(){return ((inputs.sam_name.split('.')[0]));})()
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: stdout was: ''
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: stderr was: ''
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: During handling of the above exception, another exception occurred:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: Traceback (most recent call last):
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: File "/project/soft/linux64/anaconda/Anaconda3-2018.12-Linux-x86_64/lib/python3.7/site-packages/cwltool/command_line_tool.py", line 601, in collect_output_ports
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: compute_checksum=compute_checksum)
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: File "/project/soft/linux64/anaconda/Anaconda3-2018.12-Linux-x86_64/lib/python3.7/site-packages/cwltool/command_line_tool.py", line 681, in collect_output
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: raise
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: File "/project/soft/linux64/anaconda/Anaconda3-2018.12-Linux-x86_64/lib/python3.7/site-packages/schema_salad/sourceline.py", line 166, in __exit__
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3: raise self.makeError("\n".join(traceback.format_exception(exc_type, exc_value, tb)))
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:82:3:
cwltool.errors.WorkflowException: ../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: Traceback (most recent call last):
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: File "/project/soft/linux64/anaconda/Anaconda3-2018.12-Linux-x86_64/lib/python3.7/site-packages/cwltool/sandboxjs.py", line 377, in execjs
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: return json.loads(stdout)
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: File "/project/soft/linux64/anaconda/Anaconda3-2018.12-Linux-x86_64/lib/python3.7/json/__init__.py", line 348, in loads
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: return _default_decoder.decode(s)
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: File "/project/soft/linux64/anaconda/Anaconda3-2018.12-Linux-x86_64/lib/python3.7/json/decoder.py", line 337, in decode
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: obj, end = self.raw_decode(s, idx=_w(s, 0).end())
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: File "/project/soft/linux64/anaconda/Anaconda3-2018.12-Linux-x86_64/lib/python3.7/json/decoder.py", line 355, in raw_decode
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: raise JSONDecodeError("Expecting value", s, err.value) from None
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: During handling of the above exception, another exception occurred:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: Traceback (most recent call last):
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: File "/project/soft/linux64/anaconda/Anaconda3-2018.12-Linux-x86_64/lib/python3.7/site-packages/cwltool/expression.py", line 293, in do_eval
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: strip_whitespace=strip_whitespace)
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: File "/project/soft/linux64/anaconda/Anaconda3-2018.12-Linux-x86_64/lib/python3.7/site-packages/cwltool/expression.py", line 226, in interpolate
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: debug=debug, js_console=js_console)
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: File "/project/soft/linux64/anaconda/Anaconda3-2018.12-Linux-x86_64/lib/python3.7/site-packages/cwltool/expression.py", line 191, in evaluator
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: debug=debug, js_console=js_console)
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: File "/project/soft/linux64/anaconda/Anaconda3-2018.12-Linux-x86_64/lib/python3.7/site-packages/cwltool/sandboxjs.py", line 381, in execjs
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: err, fn_linenum(), stdout, stderr))
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: cwltool.sandboxjs.JavascriptException: Expecting value: line 1 column 1 (char 0)
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: script was:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 29 "class": "File",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 30 "location": "file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.2.ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 31 "basename": "P.yoelii.2.ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 32 "size": 5357516,
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../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 51 "basename": "P.yoelii.4.ht2",
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../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 61 "basename": "P.yoelii.5.ht2",
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../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 116 "log": "log.txt",
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../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 120 var self = null;
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 121 var runtime = {
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../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 125 "outdir": "/var/spool/cwl"
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 126 };
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 127 (function(){return ((inputs.sam_name.split('.')[0]));})()
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: stdout was: ''
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: stderr was: ''
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: During handling of the above exception, another exception occurred:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: Traceback (most recent call last):
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: File "/project/soft/linux64/anaconda/Anaconda3-2018.12-Linux-x86_64/lib/python3.7/site-packages/cwltool/command_line_tool.py", line 648, in collect_output
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: gb = builder.do_eval(gb)
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: File "/project/soft/linux64/anaconda/Anaconda3-2018.12-Linux-x86_64/lib/python3.7/site-packages/cwltool/builder.py", line 425, in do_eval
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: strip_whitespace=strip_whitespace)
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: File "/project/soft/linux64/anaconda/Anaconda3-2018.12-Linux-x86_64/lib/python3.7/site-packages/cwltool/expression.py", line 296, in do_eval
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: raise WorkflowException("Expression evaluation error:\n%s" % e)
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: cwltool.errors.WorkflowException: Expression evaluation error:
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: Expecting value: line 1 column 1 (char 0)
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: script was:
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../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 31 "basename": "P.yoelii.2.ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 32 "size": 5357516,
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 33 "nameroot": "P.yoelii.2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 34 "nameext": ".ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 35 "path": "/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index/P.yoelii.2.ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 36 "dirname": "/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index"
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 37 },
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 38 {
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 39 "class": "File",
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../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 41 "basename": "P.yoelii.3.ht2",
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../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 53 "nameroot": "P.yoelii.4",
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../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 60 "location": "file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.5.ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 61 "basename": "P.yoelii.5.ht2",
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../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 63 "nameroot": "P.yoelii.5",
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../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 65 "path": "/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index/P.yoelii.5.ht2",
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../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 69 "class": "File",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 70 "location": "file:///data/rnaseq/GenomeIndex/Plasmodium_Yoelii/HISAT2Index/P.yoelii.6.ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 71 "basename": "P.yoelii.6.ht2",
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../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 81 "basename": "P.yoelii.7.ht2",
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../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 91 "basename": "P.yoelii.8.ht2",
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../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 93 "nameroot": "P.yoelii.8",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 94 "nameext": ".ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 95 "path": "/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index/P.yoelii.8.ht2",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 96 "dirname": "/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index"
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 97 }
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 98 ],
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 99 "path": "/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763/HISAT2Index",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 100 "dirname": "/var/lib/cwl/stg3abbb992-805a-4255-bd2e-a3c3c961a763"
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 101 },
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 102 "sam_name": "SRR3584107.sam",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 103 "second_pair": {
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 104 "class": "File",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 105 "location": "file:///data/rnaseq/test/plas/SRR3584107_2.fastq.gz",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 106 "size": 1096917576,
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 107 "basename": "SRR3584107_2.fastq.gz",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 108 "nameroot": "SRR3584107_2.fastq",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 109 "nameext": ".gz",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 110 "path": "/var/lib/cwl/stgbfd0456a-1175-455f-9904-112ae6be51c4/SRR3584107_2.fastq.gz",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 111 "dirname": "/var/lib/cwl/stgbfd0456a-1175-455f-9904-112ae6be51c4"
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 112 },
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 113 "threads": 12,
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 114 "XSTag": "--dta-cufflinks",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 115 "input_type": "-q",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 116 "log": "log.txt",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 117 "single_file": null,
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 118 "sra_acc": null
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 119 };
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 120 var self = null;
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 121 var runtime = {
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 122 "cores": 1,
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 123 "ram": 1024,
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 124 "tmpdir": "/tmp",
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 125 "outdir": "/var/spool/cwl"
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 126 };
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: 127 (function(){return ((inputs.sam_name.split('.')[0]));})()
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: stdout was: ''
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7: stderr was: ''
../../RNASeq/cwl-tools/docker/hisat2_align.cwl:85:7:
[2019-02-20 15:56:27] [job hisat2_align_2] completed permanentFail
[2019-02-20 15:56:27] [job hisat2_align_2] {}
[2019-02-20 15:56:27] [step hisat2_align_2] Output is missing expected field file:///data/rnaseq/test/plas/hisat2-6.cwl#hisat2_align_2/sam_output
[2019-02-20 15:56:27] [step hisat2_align_2] Output is missing expected field file:///data/rnaseq/test/plas/hisat2-6.cwl#hisat2_align_2/hisat2_align_out
[2019-02-20 15:56:27] [step hisat2_align_2] produced output {}
[2019-02-20 15:56:27] [step hisat2_align_2] completed permanentFail
[2019-02-20 15:56:27] [job hisat2_align_2] Removing input staging directory /tmp/tmpq2ky69zs
[2019-02-20 15:56:27] [job hisat2_align_2] Removing temporary directory /tmp/tmpstb5kcem
Your Environment
- cwltool version: 1.0.20180820141117
Issue Analytics
- State:
- Created 5 years ago
- Comments:9 (6 by maintainers)
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Hey, @tonyyzy,
Thanks for posting such a thorough report. Excuse me if its unreasonable to ask, but would it be possible for you to attach
hisat2_align.cwlandfolder.cwlfiles as well ?Hi @kkarolis Unfortunately, the error still persists. I tried the newest cwltool as well (20190228) and got the same error message. I do not have a local installation of nodejs, so the javascript part would be executed in a docker container. Would this be the cause of error?