NameError: name 'remove' is not defined

[gwidme01]

Hi, thanks for writing transIndel and making it available to the community. I am trying to identify indels in a set of sequence reads originating from a Cryptosporidium isolate. I noticed this error:

(htseq) [gwidme01@c1cmp063 transIndel]$ python transIndel_build_DNA.py -i /cluster/tufts/gwidme01/transIndel/UK12_v1.bam  -o /cluster/tufts/gwidme01/transIndel/UK12_v1_build.bam
transIndel build starts running: 2022-12-23 13:41:09
Checking for 'samtools': found /opt/shared/samtools/1.9/bin/samtools

[bam_sort_core] merging from 3 files and 1 in-memory blocks...
Traceback (most recent call last):
  File "transIndel_build_DNA.py", line 239, in <module>
    main()
  File "transIndel_build_DNA.py", line 231, in main
    remove('{}.temp.bam'.format(output))
NameError: name 'remove' is not defined

[cauyrd]

I have updated the transIndel_build_DNA.py file and this bug is fixed. Please download the latest file and re-run your program with transIndel_build_DNA.py. Let me know if you have additional questions.

[gwidme01]

Hi Rendong, thanks for the quick action. I was wondering what the most likely cause might be if the output vcf file from this command is empty:

python transIndel_call.py -i /cluster/tufts/gwidme01/transIndel/UK12_v1_build.bam -o /cluster/tufts/gwidme01/transIndel/UK12_v1.vcf

content of vcf output file:

fileformat=VCFv4.1

source=transIndel v2.0

ALT=

ALT=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

FORMAT=

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT /cluster/tufts/gwidme01/transIndel/UK12_v1.vcf

The input file is 334 MB in size.

thanks for your help,

Giovanni

From: Rendong Yang @.> Sent: Friday, December 23, 2022 9:41 PM To: cauyrd/transIndel @.> Cc: Widmer, Giovanni F. @.>; Author @.> Subject: [External] Re: [cauyrd/transIndel] NameError: name 'remove' is not defined (Issue #10)

I have updated the transIndel_build_DNA.py file and this bug is fixed. Please download the latest file and re-run your program with transIndel_build_DNA.py. Let me know if you have additional questions.

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[cauyrd]

You may need to adjust the paraters to allow transindel to detect low allele frequency variants. you can use -c 1 -d 1 -f 0.001 instead of the default values. This should allow you to call all potential variants but also the false positive rate will be high. After you have output in the VCF file, you may need to adjust the parameters, for examples -c 2 -d 5, -f 0.01 to call less and more likely to be true positives.