About samtools invalid option in tigmint-make arcs mode

[ClarenceHsiang]

Dear Tigmint team:

I attached the Tigmint by using conda. When I run tigmint-make arcs by using 10X-linked reads, it showed the invalid option in samtools.

Could you give me some suggestions for solving the problem?

Thank you very much.

---

(Python3_6) [hsiang@pomology-serverIII 01_scaffolding_by_wgs]$ tigmint-make arcs draft=myassembly reads=myreads bwa mem -t8 -pC myassembly.fa myreads.fq.gz | samtools view -u -F4 | samtools sort -@8 -tBX -T$(mktemp -u -t myassembly.myreads.sortbx.bam.XXXXXX) -o myassembly.myreads.sortbx.bam sort: invalid option -- 't' sort: invalid option -- 'B' sort: invalid option -- 'X' sort: invalid option -- 'T' sort: invalid option -- '/' sort: invalid option -- 't'

Usage: samtools sort [options] Options: -n sort by read name -f use as full file name instead of prefix -o final output to stdout -l INT compression level, from 0 to 9 [-1] -@ INT number of sorting and compression threads [1] -m INT max memory per thread; suffix K/M/G recognized [768M]

Usage: samtools view [options] | [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

[M::bwa_idx_load_from_disk] read 0 ALT contigs make: *** [/home/hsiang/miniconda3/envs/Python3_6/bin/share/tigmint-1.2.4-0/bin/tigmint-make:191: myassembly.myreads.sortbx.bam] Error 1

---

[lcoombe]

HI @ClarenceHsiang,

Could you report the version of samtools that you are using? (With samtools --version) Also, could you double check that you are using your conda installat ion of samtools? (With which samtools) At first glance, it looks like you could be using an older version of samtools which is missing some of the options in newer versions.

Thank you for your interest in Tigmint! Lauren

[ClarenceHsiang]

Dear Tigmint Team: Good morning. Sorry for the late replay. The samtools version is Version: 0.1.19-44428cd by using conda.

Thank you very much

---

Program: samtools (Tools for alignments in the SAM format) Version: 0.1.19-44428cd

[lcoombe]

Hi @ClarenceHsiang,

Could you try updating your samtools to a later version? Ex. 1.15? Looking at the samtools release notes, the -t parameter was introduced in version 1.5 in 2017, so any version newer than that should work.

[github-actions[bot]]

This issue has been automatically marked as stale because it has not had any recent activity. It will be closed if no further activity occurs. Thank you for your interest in Tigmint!