smoove requires bash to be default SHELL. should just use bash instead of assuming.

[hepcat72]

I just got smoove installed today and tried running it for the first time. I downloaded some bam files and a reference from a galaxy history where I'd already analyzed SVs. Here's what I see when I run smoove...

>smoove call --name testcb15 --removepr --duphold --fasta CB15_reference.fasta -p 1 --genotype --support 1 --noextrafilters Caulobacter_crescentus_strain_CB15.bam Caulobacter_spp.bam NA1000.bam
[smoove] 2019/06/03 17:16:31 starting with version 0.2.3
[smoove]: ([E]lumpy-filter) 2019/06/03 17:16:31 set: Variable name must begin with a letter.
[smoove]:2019/06/03 17:16:31 finished process: lumpy-filter (set -eu; lumpy_filter -f CB15_reference.fasta Caulobacter_crescentus_strain_CB15.bam .//Caulobacter_) in user-time:57.991ms system-time:52.991ms
[smoove]:2019/06/03 17:16:31 error running command: set -eu; lumpy_filter -f CB15_reference.fasta Caulobacter_crescentus_strain_CB15.bam .//Caulobacter_crescentus_strain_CB15_Demultiplexed-fastq-fileset-sample-20161014_GM3PlasmidPool-from-flowcell-000000000-ANC0P-on-2017-03-29_Read_passed_filter.split.bam.tmp.bam .//Caulobacter_crescentus_strain_CB15_Demultiplexed-fastq-fileset-sample-20161014_GM3PlasmidPool-from-flowcell-000000000-ANC0P-on-2017-03-29_Read_passed_filter.disc.bam.tmp.bam 2 && mv .//Caulobacter_crescentus_strain_CB15_Demultiplexed-fastq-fileset-sample-20161014_GM3PlasmidPool-from-flowcell-000000000-ANC0P-on-2017-03-29_Read_passed_filter.split.bam.tmp.bam .//Caulobacter_crescentus_strain_CB15_Demultiplexed-fastq-fileset-sample-20161014_GM3PlasmidPool-from-flowcell-000000000-ANC0P-on-2017-03-29_Read_passed_filter.split.bam && mv .//Caulobacter_crescentus_strain_CB15_Demultiplexed-fastq-fileset-sample-20161014_GM3PlasmidPool-from-flowcell-000000000-ANC0P-on-2017-03-29_Read_passed_filter.disc.bam.tmp.bam .//Caulobacter_crescentus_strain_CB15_Demultiplexed-fastq-fileset-sample-20161014_GM3PlasmidPool-from-flowcell-000000000-ANC0P-on-2017-03-29_Read_passed_filter.disc.bam && cp .//Caulobacter_crescentus_strain_CB15_Demultiplexed-fastq-fileset-sample-20161014_GM3PlasmidPool-from-flowcell-000000000-ANC0P-on-2017-03-29_Read_passed_filter.split.bam .//Caulobacter_crescentus_strain_CB15_Demultiplexed-fastq-fileset-sample-20161014_GM3PlasmidPool-from-flowcell-000000000-ANC0P-on-2017-03-29_Read_passed_filter.split.bam.orig.bam && cp .//Caulobacter_crescentus_strain_CB15_Demultiplexed-fastq-fileset-sample-20161014_GM3PlasmidPool-from-flowcell-000000000-ANC0P-on-2017-03-29_Read_passed_filter.disc.bam .//Caulobacter_crescentus_strain_CB15_Demultiplexed-fastq-fileset-sample-20161014_GM3PlasmidPool-from-flowcell-000000000-ANC0P-on-2017-03-29_Read_passed_filter.disc.bam.orig.bam -> exit status 1
[smoove]:([E]lumpy-filter) 2019/06/03 17:16:31 set: Variable name must begin with a letter.
[smoove]:2019/06/03 17:16:31 finished process: lumpy-filter (set -eu; lumpy_filter -f CB15_reference.fasta Caulobacter_spp.bam .//Caulobacter_spp_Demultiplexed-f) in user-time:62.99ms system-time:41.993ms
[smoove]:2019/06/03 17:16:31 error running command: set -eu; lumpy_filter -f CB15_reference.fasta Caulobacter_spp.bam .//Caulobacter_spp_Demultiplexed-fastq-fileset-sample-20161014_GM3PlasmidPool-from-flowcell-000000000-ANC0P-on-2017-03-29_Read_passed_filter.split.bam.tmp.bam .//Caulobacter_spp_Demultiplexed-fastq-fileset-sample-20161014_GM3PlasmidPool-from-flowcell-000000000-ANC0P-on-2017-03-29_Read_passed_filter.disc.bam.tmp.bam 2 && mv .//Caulobacter_spp_Demultiplexed-fastq-fileset-sample-20161014_GM3PlasmidPool-from-flowcell-000000000-ANC0P-on-2017-03-29_Read_passed_filter.split.bam.tmp.bam .//Caulobacter_spp_Demultiplexed-fastq-fileset-sample-20161014_GM3PlasmidPool-from-flowcell-000000000-ANC0P-on-2017-03-29_Read_passed_filter.split.bam && mv .//Caulobacter_spp_Demultiplexed-fastq-fileset-sample-20161014_GM3PlasmidPool-from-flowcell-000000000-ANC0P-on-2017-03-29_Read_passed_filter.disc.bam.tmp.bam .//Caulobacter_spp_Demultiplexed-fastq-fileset-sample-20161014_GM3PlasmidPool-from-flowcell-000000000-ANC0P-on-2017-03-29_Read_passed_filter.disc.bam && cp .//Caulobacter_spp_Demultiplexed-fastq-fileset-sample-20161014_GM3PlasmidPool-from-flowcell-000000000-ANC0P-on-2017-03-29_Read_passed_filter.split.bam .//Caulobacter_spp_Demultiplexed-fastq-fileset-sample-20161014_GM3PlasmidPool-from-flowcell-000000000-ANC0P-on-2017-03-29_Read_passed_filter.split.bam.orig.bam && cp .//Caulobacter_spp_Demultiplexed-fastq-fileset-sample-20161014_GM3PlasmidPool-from-flowcell-000000000-ANC0P-on-2017-03-29_Read_passed_filter.disc.bam .//Caulobacter_spp_Demultiplexed-fastq-fileset-sample-20161014_GM3PlasmidPool-from-flowcell-000000000-ANC0P-on-2017-03-29_Read_passed_filter.disc.bam.orig.bam -> exit status 1
[smoove] 2019/06/03 17:16:31 calculating bam stats for 3 bams
[smoove]:([E]lumpy-filter) 2019/06/03 17:16:31 set: Variable name must begin with a letter.
[smoove]:2019/06/03 17:16:31 finished process: lumpy-filter (set -eu; lumpy_filter -f CB15_reference.fasta NA1000.bam .//NA1000_Demultiplexed-fastq-fileset-sampl) in user-time:60.99ms system-time:43.993ms
[smoove]:2019/06/03 17:16:31 error running command: set -eu; lumpy_filter -f CB15_reference.fasta NA1000.bam .//NA1000_Demultiplexed-fastq-fileset-sample-20161014_GM3PlasmidPool-from-flowcell-000000000-ANC0P-on-2017-03-29_Read_passed_filter.split.bam.tmp.bam .//NA1000_Demultiplexed-fastq-fileset-sample-20161014_GM3PlasmidPool-from-flowcell-000000000-ANC0P-on-2017-03-29_Read_passed_filter.disc.bam.tmp.bam 2 && mv .//NA1000_Demultiplexed-fastq-fileset-sample-20161014_GM3PlasmidPool-from-flowcell-000000000-ANC0P-on-2017-03-29_Read_passed_filter.split.bam.tmp.bam .//NA1000_Demultiplexed-fastq-fileset-sample-20161014_GM3PlasmidPool-from-flowcell-000000000-ANC0P-on-2017-03-29_Read_passed_filter.split.bam && mv .//NA1000_Demultiplexed-fastq-fileset-sample-20161014_GM3PlasmidPool-from-flowcell-000000000-ANC0P-on-2017-03-29_Read_passed_filter.disc.bam.tmp.bam .//NA1000_Demultiplexed-fastq-fileset-sample-20161014_GM3PlasmidPool-from-flowcell-000000000-ANC0P-on-2017-03-29_Read_passed_filter.disc.bam && cp .//NA1000_Demultiplexed-fastq-fileset-sample-20161014_GM3PlasmidPool-from-flowcell-000000000-ANC0P-on-2017-03-29_Read_passed_filter.split.bam .//NA1000_Demultiplexed-fastq-fileset-sample-20161014_GM3PlasmidPool-from-flowcell-000000000-ANC0P-on-2017-03-29_Read_passed_filter.split.bam.orig.bam && cp .//NA1000_Demultiplexed-fastq-fileset-sample-20161014_GM3PlasmidPool-from-flowcell-000000000-ANC0P-on-2017-03-29_Read_passed_filter.disc.bam .//NA1000_Demultiplexed-fastq-fileset-sample-20161014_GM3PlasmidPool-from-flowcell-000000000-ANC0P-on-2017-03-29_Read_passed_filter.disc.bam.orig.bam -> exit status 1

[brentp]

before you run smoove, can you do:

export SHELL=/bin/bash

in the same script and see if this resolves the issue?

[hepcat72]

Hmmm...

I'm just trying on the command line. I usually run tcsh, so I switched to bash and tried it there. I still get the error:

bash-4.1$ export SHELL=/bin/bash
bash-4.1$ smoove call --name cb15 --removepr --duphold --fasta CB15_reference.fasta -p 1 --genotype --support 1 --noextrafilters Caulobacter_crescentus_strain_CB15.edit.bam Caulobacter_spp.edit.bam NA1000.edit.bam
[smoove] 2019/06/03 17:58:15 starting with version 0.2.3
[smoove] 2019/06/03 17:58:15 calculating bam stats for 3 bams
[smoove]: ([E]lumpy-filter) 2019/06/03 17:58:16 lumpy_filter: Unable to open BAM/SAM index.
[smoove]:2019/06/03 17:58:16 finished process: lumpy-filter (set -eu; lumpy_filter -f CB15_reference.fasta Caulobacter_crescentus_strain_CB15.edit.bam .//ccsCB15) in user-time:1.999ms system-time:14.997ms
[smoove]:2019/06/03 17:58:16 error running command: set -eu; lumpy_filter -f CB15_reference.fasta Caulobacter_crescentus_strain_CB15.edit.bam .//ccsCB15.split.bam.tmp.bam .//ccsCB15.disc.bam.tmp.bam 2 && mv .//ccsCB15.split.bam.tmp.bam .//ccsCB15.split.bam && mv .//ccsCB15.disc.bam.tmp.bam .//ccsCB15.disc.bam && cp .//ccsCB15.split.bam .//ccsCB15.split.bam.orig.bam && cp .//ccsCB15.disc.bam .//ccsCB15.disc.bam.orig.bam -> exit status 1
[smoove]:([E]lumpy-filter) 2019/06/03 17:58:16 lumpy_filter: Unable to open BAM/SAM index.
[smoove]:2019/06/03 17:58:16 finished process: lumpy-filter (set -eu; lumpy_filter -f CB15_reference.fasta Caulobacter_spp.edit.bam .//cs.split.bam.tmp.bam .//cs) in user-time:2.999ms system-time:6.998ms
[smoove]:2019/06/03 17:58:16 error running command: set -eu; lumpy_filter -f CB15_reference.fasta Caulobacter_spp.edit.bam .//cs.split.bam.tmp.bam .//cs.disc.bam.tmp.bam 2 && mv .//cs.split.bam.tmp.bam .//cs.split.bam && mv .//cs.disc.bam.tmp.bam .//cs.disc.bam && cp .//cs.split.bam .//cs.split.bam.orig.bam && cp .//cs.disc.bam .//cs.disc.bam.orig.bam -> exit status 1
[smoove]:([E]lumpy-filter) 2019/06/03 17:58:16 lumpy_filter: Unable to open BAM/SAM index.
[smoove]:2019/06/03 17:58:16 finished process: lumpy-filter (set -eu; lumpy_filter -f CB15_reference.fasta NA1000.edit.bam .//na1000.split.bam.tmp.bam .//na1000.) in user-time:999µs system-time:9.998ms
[smoove]:2019/06/03 17:58:16 error running command: set -eu; lumpy_filter -f CB15_reference.fasta NA1000.edit.bam .//na1000.split.bam.tmp.bam .//na1000.disc.bam.tmp.bam 2 && mv .//na1000.split.bam.tmp.bam .//na1000.split.bam && mv .//na1000.disc.bam.tmp.bam .//na1000.disc.bam && cp .//na1000.split.bam .//na1000.split.bam.orig.bam && cp .//na1000.disc.bam .//na1000.disc.bam.orig.bam -> exit status 1

[hepcat72]

Just FYI, I also just edited the bam files in between the previous attempt and this one to shorten the insanely long readgroup IDs. I saved them as "*.edit.bam".

[brentp]

so, no you have a different error. looks like you just need to index the bam files.

[hepcat72]

Doh! Let me try that.

[hepcat72]

It's been a long day. Thanks! It's working. Sorry to bother you.

[brentp]

no problem. I'll leave this open til I make it work under shells other than bash or have it print a message that is required.