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jtamames / SqueezeMeta

A complete pipeline for metagenomic analysis
GNU General Public License v3.0
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Issues at step-10 #603

Closed RPIASRI closed 1 year ago

RPIASRI commented 1 year ago

I am trying to run squeezemeta over my dataset but is getting stuck at step 10 again and again. Also tried restart but is getting the same error which is provide below:

[12 hours, 24 minutes, 36 seconds]: STEP10 -> MAPPING READS: 10.mapsamples.pl Reading mapping file from /cabinfs/home/ratna/WHEAT20_12/data/00.WHEAT20_12.samples Metagenomes found: 1 Mapping with Bowtie2 (Langmead and Salzberg 2012, Nat Methods 9(4), 357-9) Creating reference from contigs ImportError: No module named site Working with sample 1: Wheat Getting raw reads Aligning to reference with bowtie (ERR): "/cabinfs/home/ratna/WHEAT20_12/data/WHEAT20_12.bowtie" does not exist or is not a Bowtie 2 index Exiting now ... (ERR): "/cabinfs/home/ratna/WHEAT20_12/data/WHEAT20_12.bowtie" does not exist or is not a Bowtie 2 index Exiting now ... An error occurred during mapping! at /cabinfs/opt/applications/SqueezeMeta/scripts/10.mapsamples.pl line 179. Stopping in STEP10 -> 10.mapsamples.pl. Program finished abnormally sh: tree: command not found

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 /cabinfs/home/ratna/WHEAT20_12/syslog file (zip it first) Died at /opt/software/applications/SqueezeMeta/scripts/SqueezeMeta.pl line 1367.

jtamames commented 1 year ago

Hello What does test_install.pl says? Best, J

RPIASRI commented 1 year ago

Checking that SqueezeMeta is properly configured... checking database in /cabinfs/opt/applications/SqueezeMeta/database/db nr.db OK CheckM manifest OK LCA_tax DB OK

WARNING: Some SqueezeMeta dependencies could not be found in your environment!

jtamames commented 1 year ago

How did you install the software? Did you use conda?

RPIASRI commented 1 year ago

Yes sir, it was installed by conda.

fpusan commented 1 year ago

Then are you properly activating the environment? Several dependencies are missing, those should be present if you installed things with conda. Can you reinstall in a fresh miniconda3 installation?

RPIASRI commented 1 year ago

ok Sir, I will try for fresh installation and then will let you know.

fpusan commented 1 year ago

Closing due to lack of activity, feel free to reopen