pysam.csamtools.AlignedRead' object has no attribute 'has_tag'

[paulhtyang]

Hello Dr. Yang,

We are running ScanNeo pipeline in which the transIndel command was applied below: "transIndel_build_RNA.py -r /data/genome/GRCh38/hg38.fa -g /data/genome/GRCh38/gencode3.annotation.gtf -i Adipose01_R1.HISAT2-2.1.0.aligned.sorted.bwa.bam -o Adipose01_R1.HISAT2-2.1.0.aligned.sort"

The error message was shown as well:

---

indel.bam' returned non-zero exit status 1 transIndel_RNA build starts running: 2020-12-09 21:49:11 Checking for 'samtools': found /data/anaconda3/envs/NeoAg/bin/samtools

Traceback (most recent call last): File "/data/tools/transIndel/transIndel_build_RNA.py", line 304, in main() File "/data/tools/transIndel/transIndel_build_RNA.py", line 296, in main softclipping_realignment(mapq_cutoff, max_del_len, input, output, ref_genome, gtf, splice_bin) File "/data/tools/transIndel/transIndel_build_RNA.py", line 170, in softclipping_realignment if read.mapq >= mapq_cutoff and not read.is_secondary and not read.has_tag('XA'): AttributeError: 'pysam.csamtools.AlignedRead' object has no attribute 'has_tag'

---

Just wondering about the version of Pysam package is v0.16.0.1. Could you please let me know what's going on and how to resolve it? Thank you very much, Paul

[cauyrd]

Dear Paul, This is very likely to be a pysam version issue. someone had a similar problem (https://github.com/hall-lab/svtyper/issues/37 ). Update to the newer version will fix this issue. Tingyou

On Thu, Dec 10, 2020 at 10:55 AM Hsih-Te (Paul) Yang < notifications@github.com> wrote:

Hello Dr. Yang,

We are running ScanNeo pipeline in which the transIndel command was applied below: "transIndel_build_RNA.py -r /data/genome/GRCh38/hg38.fa -g /data/genome/GRCh38/gencode3.annotation.gtf -i Adipose01_R1.HISAT2-2.1.0.aligned.sorted.bwa.bam -o Adipose01_R1.HISAT2-2.1.0.aligned.sort"

The error message was shown as well:

indel.bam' returned non-zero exit status 1 transIndel_RNA build starts running: 2020-12-09 21:49:11 Checking for 'samtools': found /data/anaconda3/envs/NeoAg/bin/samtools

Traceback (most recent call last): File "/data/tools/transIndel/transIndel_build_RNA.py", line 304, in main() File "/data/tools/transIndel/transIndel_build_RNA.py", line 296, in main softclipping_realignment(mapq_cutoff, max_del_len, input, output, ref_genome, gtf, splice_bin) File "/data/tools/transIndel/transIndel_build_RNA.py", line 170, in softclipping_realignment if read.mapq >= mapq_cutoff and not read.is_secondary and not read.has_tag('XA'): AttributeError: 'pysam.csamtools.AlignedRead' object has no attribute 'has_tag'

Just wondering about the version of Pysam package is v0.16.0.1. Could you please let me know what's going on and how to resolve it? Thank you very much, Paul

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[paulhtyang]

Hello Tingyou, Thanks for your kind reply. I did read this message before contacting you. However, the current version of Pysam package (v0.16.0.1) I'm using is updated. Do you have other idea? Paul

[dolittle007]

The "AlignedRead" type was replaced by "AlignedSegment" after pysam 0.8.1. So you indeed have pysam 0.16.0.1 (the latest one) installed, but Python is loading an old version. I am not sure how you run transIndel programs. if ./transIndels, you'd better change the #!/usr/bin/python to #!/usr/bin/env python elif python transIndels, you can check the pysam version by typing python -c 'import pysam;print(pysam.__version__)' Hope it helps.

[paulhtyang]

Thanks for your information that is really helpful. When I checked the version of pysam package, it showed 0.11.2.2 (see below). Looks like the Python 2.7 limited the conda environment only to this version rather than the most updated one. $ python -c 'import pysam;print(pysam.version)' 0.11.2.2

After changing the #!/usr/bin/python to #!/usr/bin/env python in the head of python script, the error message was gone and the job was completely done. Thanks again!