mitoVGP crashes on start

[cement-head]

Crashes on start:

$ ./mitoVGP -a pacbio -s Rana_sylvatica -i aRanSyl -r NC_027236.1.fasta -t 124 

++++                        mitoVGP v2.0                         ++++
++++ The Vertebrate Genomes Project Mitogenome Assembly Pipeline ++++
++++     Credit: Giulio Formenti gformenti@rockefeller.edu       ++++

Started at at: 2021-02-16 08-27-23

With command:

./mitoVGP

Using 'NC_027236.1.fasta' as reference

Genome size not provided, using reference genome size: 17592 bp

Command: sh -e scripts/mtDNApipe -s Rana_sylvatica -i aRanSyl -r NC_027236.1.fasta -g 17592 -t 124 -a pacbio 2>&1 | tee Rana_sylvatica/aRanSyl/assembly_MT_rockefeller/intermediates/log/aRanSyl_mtDNApipe_20210216-082724.out
scripts/mtDNApipe: 3: set: Illegal option -o pipefail
scripts/blastMT: 3: set: Illegal option -o pipefail

[gf777]

Hi @cement-head ,

this looks like an issue with the linux version (what OS are you using?). Your system most likely does not support the (safer) -o pipefail option (https://vaneyckt.io/posts/safer_bash_scripts_with_set_euxo_pipefail/). You are probably good removing it from all the scripts where it is present.

[cement-head]

Ubuntu 18.04.5 LTS; okay, so that would mean to delete the -o option at the beginning of each script?

Example:

Change this ORIGINAL:

#!/bin/bash

set -e -o pipefail

#++++                  This script is part of:                    ++++
#++++                        mitoVGP v2.2                         ++++
#++++ The Vertebrate Genomes Project Mitogenome Assembly Pipeline ++++
#++++     Credit: Giulio Formenti gformenti@rockefeller.edu       ++++

TO this?

#!/bin/bash

set -e pipefail

#++++                  This script is part of:                    ++++
#++++                        mitoVGP v2.2                         ++++
#++++ The Vertebrate Genomes Project Mitogenome Assembly Pipeline ++++
#++++     Credit: Giulio Formenti gformenti@rockefeller.edu       ++++

Also, I'm a little unclear as to how to specify the input reads file (list). Would using the -1 option and giving the script the fastq filename be appropriate?

Example:

$ ./mitoVGP -a pacbio -s Rana_sylvatica -i aRanSyl -r NC_027236.1.fasta -t 124 -1 wfpbs2-abcd.fastq

[cement-head]

Okay, dash in Ubuntu (not bash) doesn't recognise pipefail: https://askubuntu.com/questions/886537/set-e-o-pipefail-not-working-on-bash-script-on-ubuntu-16

[gf777]

Thanks for checking this. It then seems more like a symlink issue in your environment, since the shebang line requests bash (#!/bin/bash). If you confirm we can close I think. Thanks!

[cement-head]

Yes; switching to bash prompt doesn't help. I'm using a very vanilla 18.04.5 LTS install; just for bioinformatics. Looks as though starting from bash bounces it back to dash. Current workaround is to comment out

#set -e -o pipefail

[gf777]

Thanks, good for other users who may encounter the same issue to know..closing!

[cement-head]

What DISTRO was this script coded on? CentOS? Other RedHat derivative? We're running into other problems; looks as if this (these) scripts are DISTRO specific.

[gf777]

Currently working fine on Red Hat Enterprise Linux Server 7.5. Tested a while ago on CentOS also worked fine. Maybe open a new thread with the specific issues?