Closed hzaumsq closed 5 years ago
/public/msq/WHF4-1/script/PreprocessSAMs.pl MI.sam ../Mi_Wuhan.fasta
Thu Nov 1 08:56:13 2018: PreprocessSAMs.pl: /public/msq/WHF4-1/script/make_bed_around_RE_site.pl ../Mi_Wuhan.fasta GATC 500 Can't exec "/public/msq/WHF4-1/script/make_bed_around_RE_site.pl": Permission denied at /public/msq/WHF4-1/script/PreprocessSAMs.pl line 75. Thu Nov 1 08:56:13 2018: PreprocessSAMs.pl: /usr/local/bin/bedtools intersect -abam MI.bam -b ../Mi_Wuhan.fasta.near_GATC.500.bed > MI.REduced.bam Error: Unable to open file ../Mi_Wuhan.fasta.near_GATC.500.bed. Exiting. Thu Nov 1 08:56:13 2018: PreprocessSAMs.pl: /public/msq/miniconda2/bin/samtools view -F12 MI.REduced.bam -b -o MI.REduced.paired_only.bam Thu Nov 1 08:56:13 2018: PreprocessSAMs.pl: /public/msq/miniconda2/bin/samtools flagstat MI.REduced.paired_only.bam > MI.REduced.paired_only.flagstat
/public/msq/WHF4-1/script/PreprocessSAMs.pl MI.sam ../Mi_Wuhan.fasta
Thu Nov 1 08:56:13 2018: PreprocessSAMs.pl: /public/msq/WHF4-1/script/make_bed_around_RE_site.pl ../Mi_Wuhan.fasta GATC 500 Can't exec "/public/msq/WHF4-1/script/make_bed_around_RE_site.pl": Permission denied at /public/msq/WHF4-1/script/PreprocessSAMs.pl line 75. Thu Nov 1 08:56:13 2018: PreprocessSAMs.pl: /usr/local/bin/bedtools intersect -abam MI.bam -b ../Mi_Wuhan.fasta.near_GATC.500.bed > MI.REduced.bam Error: Unable to open file ../Mi_Wuhan.fasta.near_GATC.500.bed. Exiting. Thu Nov 1 08:56:13 2018: PreprocessSAMs.pl: /public/msq/miniconda2/bin/samtools view -F12 MI.REduced.bam -b -o MI.REduced.paired_only.bam Thu Nov 1 08:56:13 2018: PreprocessSAMs.pl: /public/msq/miniconda2/bin/samtools flagstat MI.REduced.paired_only.bam > MI.REduced.paired_only.flagstat