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tf2 / CNest

Copy Number Methods for Detection and Genome Wide Association Tests
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error running step 2 #12

Open pradyumnasagar opened 2 years ago

pradyumnasagar commented 2 years ago

when i try to run step 2 with the following command the CNest.py stops processing.

sudo docker run -v "/data/results/tools/CNest_Analysis:/input" -v "/data/results//tools/CNest_Analysis:/output" -w "/output" -it --rm \
    tomas81/cnest:dev step2 \
    --project test_proj \
    --sample 'bam' \
    --input sample.bam

we have the bam file in "/data/results/tools/CNest_Analysis/" the sequencing technique is single end sequencing in iontorrent.

I got the following error message:

10/20/2022 13:13:01 | INFO: Start step2 for sample bam

10/20/2022 13:13:01 | ERROR: bam-to-rd failed with exit code -11.
b''
Traceback (most recent call last):
  File "/resources/cnest.py", line 355, in <module>
    step2(args.project, args.sample_id, args.input_file, args.debug)
  File "/resources/cnest.py", line 164, in step2
    if process2.returncode == 0:
UnboundLocalError: local variable 'process2' referenced before assignment

Please help me troubleshoot. Thanks

tf2 commented 2 years ago

Hi Pradyumna,

Sure - happy to help here...

First thing thing to check is that "chromosome tags" (i.e. chr1 vs 1) in your BAM files and the "index" files are consistent.

Can you check and let me know - also are these BAMs human alignments or something else?

Cheers,

Tom

On Thu, Oct 20, 2022 at 2:22 PM Pradyumna Jayaram @.***> wrote:

when i try to run step 2 with the following command the CNest.py stops processing.

sudo docker run -v "/data/results/tools/CNest_Analysis:/input" -v "/data/results//tools/CNest_Analysis:/output" -w "/output" -it --rm \ tomas81/cnest:dev step2 \ --project test_proj \ --sample 'bam' \ --input sample.bam

we have the bam file in "/data/results/tools/CNest_Analysis/" the sequencing technique is single end sequencing in iontorrent.

I got the following error message:

10/20/2022 13:13:01 | INFO: Start step2 for sample bam

10/20/2022 13:13:01 | ERROR: bam-to-rd failed with exit code -11. b'' Traceback (most recent call last): File "/resources/cnest.py", line 355, in step2(args.project, args.sample_id, args.input_file, args.debug) File "/resources/cnest.py", line 164, in step2 if process2.returncode == 0: UnboundLocalError: local variable 'process2' referenced before assignment

Please help me troubleshoot. Thanks

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pradyumnasagar commented 2 years ago

Hi thanks for helping, The BAM file consist of chromosome tag (with chr) and the index was created by samtools index function . yes the BAM file is human alignment files.