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YuSugihara / QTL-seq

QTL-seq pipeline to identify causative mutations responsible for a phenotype
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samtools error #11

Closed Deeptirao closed 3 years ago

Deeptirao commented 3 years ago

I have used your package earlier without any issues. But, I am getting this error even if I used the files I had used to successfully generate plots earlier. Please help soon.

[QTL-seq:2020-11-24 03:42:56] start to run QTL-seq.[QTL-seq:2020-11-24 03:42:56] maximum number of threads which you can use is up to 8. [QTL-seq:2020-11-24 03:42:56] start to index reference fasta. [QTL-seq:2020-11-24 03:49:38] indexing of reference successfully finished. [QTL-seq:2020-11-24 03:49:38] start to filter reads. [QTL-seq:2020-11-24 04:10:35] !!ERROR!! samtools view -b -f 147 -o new_qtlseq_yusugihara_output_F6vsF4/20_bam/bulk2.1000.f147.bam new_qtlseq_yusugihara_output_F6vsF4/20_bam/bulk2.1000.bam >> new_qtlseq_yusugihara_output_F6vsF4/log/samtools.bulk2.1000.f147.log 2>&1 [QTL-seq:2020-11-24 04:10:35] !!ERROR!! samtools view -b -f 83 -o new_qtlseq_yusugihara_output_F6vsF4/20_bam/bulk2.1000.f83.bam new_qtlseq_yusugihara_output_F6vsF4/20_bam/bulk2.1000.bam >> new_qtlseq_yusugihara_output_F6vsF4/log/samtools.bulk2.1000.f83.log 2>&1

YuSugihara commented 3 years ago

Sorry for my late response.

In some environments, SAMtools cannot be installed properly. This is not the error of QTL-seq but the error of SAMtools in bioconda.

Probably, you can solve that problem by installing SAMtools independently from Github. Also, please check if the version of QLT-seq is the retest version.