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YuSugihara / QTL-seq

QTL-seq pipeline to identify causative mutations responsible for a phenotype
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getting error while generating vcf #24

Open shanmugavadivelps opened 3 years ago

shanmugavadivelps commented 3 years ago

I am using version 2.2.2 installed manually and encountering error during vcf generation after successful completion of bam file generation.

the error as follows

File "/home/iipruser/yes/bin/qtlseq", line 33, in sys.exit(load_entry_point('qtlseq', 'console_scripts', 'qtlseq')()) File "/home/iipruser/QTL-seq/qtlseq/qtlseq.py", line 171, in main QTLseq(args).run() File "/home/iipruser/QTL-seq/qtlseq/qtlseq.py", line 166, in run self.mpileup() File "/home/iipruser/QTL-seq/qtlseq/qtlseq.py", line 122, in mpileup mp.run() File "/home/iipruser/QTL-seq/qtlseq/mpileup.py", line 231, in run self.concat() File "/home/iipruser/QTL-seq/qtlseq/mpileup.py", line 182, in concat sbp.run(cmd1, stdout=sbp.DEVNULL, stderr=sbp.DEVNULL, shell=True, check=True) File "/home/iipruser/yes/lib/python3.8/subprocess.py", line 512, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command 'cat /media/iipruser/Drive_2/FW_qtlseq_icrisat2/log/bcftools.*.log > /media/iipruser/Drive_2/FW_qtlseq_icrisat2/log/bcftools.log' returned non-zero exit status 2.

pls help me to solve

YuSugihara commented 2 years ago

This error seems to fail the concatenation of log files. Please check the files in /media/iipruser/Drive_2/FW_qtlseq_icrisat2/log/. If you could find the log file related to bcftools, you may find why bcftools 'mpileup' failed.

shanmugavadivelps commented 2 years ago

kindly mention the organism. If the genome assembly consist of many scaffold or contigs (>15), this could be a reason the QTL-seq throws an error. IN that case, extract maximum10-15 scaffold/contig's variants at a time to generate the graph of QTL-seq.

On Wed, Jul 6, 2022 at 9:14 AM anusinghrao @.***> wrote:

I am using version 2.2.2 installed manually and encountering error during vcf generation after successful completion of bam file generation.

the error as follows

File "/home/iipruser/yes/bin/qtlseq", line 33, in sys.exit(load_entry_point('qtlseq', 'console_scripts', 'qtlseq')()) File "/home/iipruser/QTL-seq/qtlseq/qtlseq.py", line 171, in main QTLseq(args).run() File "/home/iipruser/QTL-seq/qtlseq/qtlseq.py", line 166, in run self.mpileup() File "/home/iipruser/QTL-seq/qtlseq/qtlseq.py", line 122, in mpileup mp.run() File "/home/iipruser/QTL-seq/qtlseq/mpileup.py", line 231, in run self.concat() File "/home/iipruser/QTL-seq/qtlseq/mpileup.py", line 182, in concat sbp.run(cmd1, stdout=sbp.DEVNULL, stderr=sbp.DEVNULL, shell=True, check=True) File "/home/iipruser/yes/lib/python3.8/subprocess.py", line 512, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command 'cat /media/iipruser/Drive_2/FW_qtlseq_icrisat2/log/bcftools.*.log > /media/iipruser/Drive_2/FW_qtlseq_icrisat2/log/bcftools.log' returned non-zero exit status 2.

pls help me to solve

Hello! I am getting the same error. Please share how did you resolve this issue?

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