Error File "cmd_line_sctcrseq.py", line 111

[benjaminviart]

Hi,

I'm trying to run scTCRseq and it sends the following error =>

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~/bin/scTCRseq/scTCRseq$ python cmd_line_sctcrseq.py --fastq1 ./XXXR1.fastq.gz --fastq2 ./XXXR2.fastq.gz --species human --outdir ./OUT --label test
running on PE FQ files ./XXXR1.fastq.gz and ./XXXR2.fastq.gz
species=human
BLAST eval=1e-10
MIN COVERAGE=5
INSERT SIZE=300
outdir=./OUT
label=test
Killed
Killed
Traceback (most recent call last):
File "cmd_line_sctcrseq.py", line 111, in
medianLengths=sctcrfuncs.return_fastq_median_read_lengths(myFastq1,outName+".medianreadlength.txt",lengthScript)
File "/home/benjamin/bin/scTCRseq/scTCRseq/sctcrfuncs.py", line 96, in return_fastq_median_read_lengths
return(int(os.popen(cmd).read()))
ValueError: invalid literal for int() with base 10: ''

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