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Function not implemented

See original GitHub issue

Hi, I used HiC dbg2olc40x -i /scratch/waterhouse_team/benth/dbg2olc-40x/snakepipes/snakePipes/workflows/HiC/hic-fq -o /scratch/waterhouse_team/benth/dbg2olc-40x/snakepipes/snakePipes -c defaults.yaml but I got this error:

Failed to create temp dir under temp path prefix (/data/extended/)! Try fallback: /scratch/waterhouse_team/benth/dbg2olc-40x/snakepipes/snakePipes/ ...
Building DAG of jobs...
Using shell: /bin/bash
Provided cluster nodes: 5
Job counts:
        count   jobs
        4       FASTQ
        1       all
        2       build_matrix
        2       call_tads
        2       compute_thresholds
        2       correct_matrix
        2       diagnostic_plot
        4       map_fastq_single_end
        1       multiQC
        20

[Wed Oct 31 11:18:00 2018]
localrule FASTQ:
    input: /scratch/waterhouse_team/benth/dbg2olc-40x/snakepipes/snakePipes/workflows/HiC/hic-fq/N_Ben_HiC4.R1.fastq.gz
    output: FASTQ/N_Ben_HiC4.R1.fastq.gz
    jobid: 5
    wildcards: sample=N_Ben_HiC4.R, read=1


[Wed Oct 31 11:18:00 2018]
localrule FASTQ:
    input: /scratch/waterhouse_team/benth/dbg2olc-40x/snakepipes/snakePipes/workflows/HiC/hic-fq/N_Ben_HiC4.R2.fastq.gz
    output: FASTQ/N_Ben_HiC4.R2.fastq.gz
    jobid: 11
    wildcards: sample=N_Ben_HiC4.R, read=2


[Wed Oct 31 11:18:00 2018]
localrule FASTQ:
    input: /scratch/waterhouse_team/benth/dbg2olc-40x/snakepipes/snakePipes/workflows/HiC/hic-fq/N_Ben_HiC2.R1.fastq.gz
    output: FASTQ/N_Ben_HiC2.R1.fastq.gz
    jobid: 9
    wildcards: sample=N_Ben_HiC2.R, read=1


[Wed Oct 31 11:18:00 2018]
localrule FASTQ:
    input: /scratch/waterhouse_team/benth/dbg2olc-40x/snakepipes/snakePipes/workflows/HiC/hic-fq/N_Ben_HiC2.R2.fastq.gz
    output: FASTQ/N_Ben_HiC2.R2.fastq.gz
    jobid: 17
    wildcards: sample=N_Ben_HiC2.R, read=2

touch: touch: touch: touch: setting times of 'FASTQ/N_Ben_HiC4.R1.fastq.gz'setting times of 'FASTQ/N_Ben_HiC2.R1.fastq.gz'setting times of 'FASTQ/N_Ben_HiC2.R2.fastq.gz'setting times of 'FASTQ/N_Ben_HiC
4.R2.fastq.gz': Function not implemented: Function not implemented: Function not implemented: Function not implemented

What did I miss?

Thank you in advance,

Michal

Issue Analytics

State:
Created 5 years ago
Comments:18 (10 by maintainers)

Top GitHub Comments

2reactions

steffenheynecommented, Oct 31, 2018

it seems the touch option “-r --reference=FILE” flag is implemented on SUSE as well, so we might switch to this more generic one and use as file e.g. the config.yaml inside the output directory

0reactions

steffenheynecommented, Nov 28, 2018

we released version 1.1.1 that should fix all of the issues