samplot errors out when trying to generate png

Versions: OS: CentOS 7 samplot: 1.0.1 Python: 3.7.7 numpy: 1.19.2 matplotlib: 3.2.1 pysam: 0.16.0.1

Error Output:

Traceback (most recent call last):
  File "/path/to/samplot", line 152, in get_tabix_iter
    itr = tbx.fetch(chrm, max(0, start-1000), end+1000)
  File "pysam/libctabix.pyx", line 509, in pysam.libctabix.TabixFile.fetch
ValueError: could not create iterator for region '6:79785917-79789285'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/path/to/samplot", line 161, in get_tabix_iter
    itr = tbx.fetch(chrm, max(0,start-1000), end+1000)
  File "pysam/libctabix.pyx", line 509, in pysam.libctabix.TabixFile.fetch
ValueError: could not create iterator for region '6:79785917-79789285'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/path/to/samplot", line 3207, in <module>
    current_axis_idx)
  File "/path/to/samplot", line 2830, in plot_annotations
    annotation_plan = get_plot_annotation_plan(ranges, annotation_file)
  File "/path/to/samplot", line 2786, in get_plot_annotation_plan
    itr = get_tabix_iter(r.chrm, r.start, r.end, annotation_file)
  File "/path/to/samplot", line 165, in get_tabix_iter
    ' from ' + datafile)
TypeError: can only concatenate str (not "int") to str
Traceback (most recent call last):
  File "/path/to/samplot", line 152, in get_tabix_iter
    itr = tbx.fetch(chrm, max(0, start-1000), end+1000)
  File "pysam/libctabix.pyx", line 509, in pysam.libctabix.TabixFile.fetch
ValueError: could not create iterator for region '7:70250695-70599526'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/path/to/samplot", line 161, in get_tabix_iter
    itr = tbx.fetch(chrm, max(0,start-1000), end+1000)
  File "pysam/libctabix.pyx", line 509, in pysam.libctabix.TabixFile.fetch
ValueError: could not create iterator for region '7:70250695-70599526'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/path/to/samplot", line 3207, in <module>
    current_axis_idx)
  File "/path/to/samplot", line 2830, in plot_annotations
    annotation_plan = get_plot_annotation_plan(ranges, annotation_file)
  File "/path/to/samplot", line 2786, in get_plot_annotation_plan
    itr = get_tabix_iter(r.chrm, r.start, r.end, annotation_file)
  File "/path/to/samplot", line 165, in get_tabix_iter
    ' from ' + datafile)
TypeError: can only concatenate str (not "int") to str
Traceback (most recent call last):
  File "/path/to/samplot", line 152, in get_tabix_iter
    itr = tbx.fetch(chrm, max(0, start-1000), end+1000)
  File "pysam/libctabix.pyx", line 509, in pysam.libctabix.TabixFile.fetch
ValueError: could not create iterator for region '9:95278469-96418357'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/path/to/samplot", line 161, in get_tabix_iter
    itr = tbx.fetch(chrm, max(0,start-1000), end+1000)
  File "pysam/libctabix.pyx", line 509, in pysam.libctabix.TabixFile.fetch
ValueError: could not create iterator for region '9:95278469-96418357'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/path/to/samplot", line 3207, in <module>
    current_axis_idx)
  File "/path/to/samplot", line 2830, in plot_annotations
    annotation_plan = get_plot_annotation_plan(ranges, annotation_file)
  File "/path/to/samplot", line 2786, in get_plot_annotation_plan
    itr = get_tabix_iter(r.chrm, r.start, r.end, annotation_file)
  File "/path/to/samplot", line 165, in get_tabix_iter
    ' from ' + datafile)
TypeError: can only concatenate str (not "int") to str

Command run: samplot -b 430477.merged.matefixed.sorted.markeddups.recal.bam 430478.merged.matefixed.sorted.markeddups.recal.bam 430479.merged.matefixed.sorted.markeddups.recal.bam -o 5_79786916_79788285.png -c 5 -s 79786916 -e 79788285 -T Homo_sapiens.GRCh37.82.sort.gff3.gz -A wgEncodeDukeMapabilityUniqueness35bp.bed.gz

Expected Output: A PNG is generated

Troubleshooting steps: I really don’t know what this error means. I built and used the most recent version from the master branch (Commited 09/04/2020), and the behavior for that is different (runs and exits 0 but does not generate a png). I am using a hand-built samplot installation instead of a conda-installed samplot.

Any help would be greatly appreciated.

[jbelyeu]

Awesome, glad to be of assistance

[rsolano1-uw]

Thank you for updating the releases page. I downloaded the updated release for 1.0.18 and ran the same command with samplot plot instead of samplot and it generated some PNGs. Thank you