run_tapis.py error

[luping]

Hello: I got a error when run the run_tapis.py

Warning: trimmed ends info not available, recommend running alignPacBio.py first! Warning: trimmed ends info not available, recommend running alignPacBio.py first! Warning: trimmed ends info not available, recommend running alignPacBio.py first! Traceback (most recent call last): File "/disk/luping/tools/comp_bio-tapis-44cc05ebc78c/TAPIS/bin/run_tapis.py", line 945, in <module> clusterReads(args.bamfile, cluster_treesP, cluster_treesN, readDict) File "/disk/luping/tools/comp_bio-tapis-44cc05ebc78c/TAPIS/bin/run_tapis.py", line 223, in clusterReads chrom = bamfile.getrname(read.tid) File "calignmentfile.pyx", line 529, in pysam.calignmentfile.AlignmentFile.getrname (pysam/calignmentfile.c:7337) ValueError: reference_id -1 out of range 0<=tid<6

I don't konw how to fix it

[XIAOYUZHAN]

Same as yours

[maria angela diroma]

Hi! Did someone solve this issue?

[Anthony Bayega]

Which version of GMAP are you running?

[maria angela diroma]

Hi

GMAP version 2016-11-07

Il giorno mar 21 ago 2018 alle ore 19:59 Anthony Bayega <

[Anthony Bayega]

Try the latest GMAP version

[maria angela diroma]

Hi,

using an updated version of GMAP, I fixed the issue. Thanks. However, I faced another problem, involving SAMtools.

Sorting BAM file [bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files Usage: samtools sort [options...] [in.bam]

Could you please tell me which version of SAMtools is required? I am using version 1.3.1. Moreover, I would like to be sure it is correct using TAPIS with PacBio CCS sequence, rather than subreads.

Thanks for your help

Maria Angela