Test Data Failure

[NLZT]

Hello,

I have been trying to install and use SqueezeMeta, however I can't even seem to get the test data to run to confirm it is working properly.

I am using an Ubuntu VM, and it fails at step 10.

[18 hours, 29 minutes, 21 seconds]: STEP10 -> MAPPING READS: 10.mapsamples.pl
  Reading samples from /opt/apps/data/test/Hadza/data/00.Hadza.samples
  Metagenomes found: 2
  Mapping with Bowtie2 (Langmead and Salzberg 2012, Nat Methods 9(4), 357-9)
  Creating reference from contigs
  Working with sample 1: SRR1927149
  Getting raw reads
  Aligning to reference with bowtie
[bam_sort_core] merging from 0 files and 12 in-memory blocks...
  Calculating contig coverage
  Reading contig length from /opt/apps/data/test/Hadza/intermediate/01.Hadza.lon
Illegal division by zero at /opt/apps/SqueezeMeta/scripts/10.mapsamples.pl line 445.
Stopping in STEP10 -> 10.mapsamples.pl. Program finished abnormally
  If you don't know what went wrong or want further advice, please look for similar issues in https://github.com/jtamames/SqueezeMeta/issues
  Feel free to open a new issue if you don't find the answer there. Please add a brief description of the problem and upload the /opt/apps/data/test/Hadza/syslog file (zip it first)
Died at /opt/apps/SqueezeMeta/scripts/SqueezeMeta.pl line 941.

syslog.txt

I've tried rerunning the last command before it exits and I get this

nturner4@squeeze:/opt/apps/data/test$ sudo /opt/apps/SqueezeMeta/bin/bowtie2/bowtie2 -x /opt/apps/data/test/Hadza/data/Hadza.bowtie -1 /opt/apps/data/test/Hadza/temp/Hadza.SRR1927149.current_1.gz -2 /opt/apps/data/test/Hadza/temp/Hadza.SRR1927149.current_2.gz --quiet -p 32 -S /opt/apps/data/test/Hadza/data/bam/Hadza.SRR1927149.sam --very-sensitive-local
Error: Encountered internal Bowtie 2 exception (#1)
Command: /opt/apps/SqueezeMeta/bin/bowtie2/bowtie2-align-s --wrapper basic-0 -x /opt/apps/data/test/Hadza/data/Hadza.bowtie --quiet -p 32 -S /opt/apps/data/test/Hadza/data/bam/Hadza.SRR1927149.sam --very-sensitive-local -1 /opt/apps/data/test/Hadza/temp/Hadza.SRR1927149.current_1.gz -2 /opt/apps/data/test/Hadza/temp/Hadza.SRR1927149.current_2.gz
(ERR): bowtie2-align exited with value 1

I'm trying to read more into bowtie as to what might cause the issue, but I haven't found anything yet. Any help would be greatly appreciated.

[fpusan]

Does the error persist if you run the command as a normal user rather than using sudo? Can you try installing SqueezeMeta from conda instead of manually? We have a dev version (to be released oficially this week) that helps with binary compatibility issue You can install it with mamba create -n SqueezeMeta -c conda-forge -c bioconda -c anaconda -c fpusan squeezemeta-dev=1.6.3.beta2 --no-channel-priority

[NLZT]

I get the same error without sudo.

I have not tried the conda installation, but I can give it a shot. I'll let you know how it goes.

[jtamames]

Also, if Bowtie keeps crashing, you can try a different mapper, for instance minimap2 or bwa. Specify it using the -map flag in the command line.

Best, J

[NLZT]

I've been trying to go the conda route and the installation runs without any errors, but now it is unable to download the databases, or at least clear the checks for them.

WARNING: Some SqueezeMeta dependencies could not be found in your environment or failed to execute!
        - ERROR: Error running kmer-db -h
        The LCA_tax/taxid.db database is not present in /home/nturner4/data/db, it is malformed, or there is other problem with your SQLite configuration

I suppose I could try a manual install, get the db, delete, install through conda, but that seems a bit round about, and might not even be the issue.

Thanks, I'll try using a different mapper if the conda installation doesn't end up working for me.

[fpusan]

How have you installed things with conda exactly? Have you re-linked the databases using configure_nodb.pl? See the section about upgrading SqueezeMeta in the readme

[fpusan]

Closing due to lack of activity, feel free to reopen