samtools in draw_circos_for_mitogenome_auto_depth.pl line 138

[xiekunwhy]

samtools in draw_circos_for_mitogenome_auto_depth.pl line 138

[linzhi2013]

Hi Kun,

thanks for the message!

You are right, samtools should be $samtools.

but luckily, whenever we are in the mitozEnv environment, both samtools and $samtools will work.

[xiekunwhy]

Yeah, but samtools print help massage and pipeline stopped somtimes, and every thing goes well when I change samtools to $samtools

Usage: samtools view [options] <in.bam>|<in.sam> [region1 [...]]

Options: -b output BAM
-h print header for the SAM output
-H print header only (no alignments)
-S input is SAM
-u uncompressed BAM output (force -b)
-1 fast compression (force -b)
-x output FLAG in HEX (samtools-C specific)
-X output FLAG in string (samtools-C specific)
-c print only the count of matching records
-B collapse the backward CIGAR operation
-@ INT number of BAM compression threads [0]
-L FILE output alignments overlapping the input BED FILE [null]
-t FILE list of reference names and lengths (force -S) [null]
-T FILE reference sequence file (force -S) [null]
-o FILE output file name [stdout]
-R FILE list of read groups to be outputted [null]
-f INT required flag, 0 for unset [0]
-F INT filtering flag, 0 for unset [0]
-q INT minimum mapping quality [0]
-l STR only output reads in library STR [null]
-r STR only output reads in read group STR [null]
-s FLOAT fraction of templates to subsample; integer part as seed [-1]
-? longer help

[linzhi2013]

Hi Kun,

Agree, $samtools will always work.

Could you please indicate when samtools alone doesn't work? Like when submitting the job to an SGE cluster to run? I am just curious about it, I will change the code to $samtools in later releases. Maybe in some situations when executing the above commands the current environmental variables (i.e., $PATH) were not inherited.

[linzhi2013]

See https://github.com/linzhi2013/MitoZ/releases/tag/3.5