andrewjpage
commented
6 years ago Hi, I've extend the automated tests to check more samtools versions (1.3, 1.3.1, 1.4, 1.4.1, 1.5, 1.6). As you can see the tests all pass for all samtools versions which would indicate theres a different problem with your setup. It might be that you need to update PySam or your environment is picking up 0.1.18. https://travis-ci.org/andrewjpage/iva/builds/286571341 Regards, Andrew
$ iva --test --trimmomatic /data/Trimmomatic-0.36/trimmomatic-0.36.jar /home/user123/ivatest/ Running iva in test mode... Copied input test files into here: /home/user123/ivatest Current working directory: /data/home/user123/ivatest Running iva on the test data with the command: /opt/python3.6/bin/iva --threads 1 --trimmomatic /data/Trimmomatic-0.36/trimmomatic-0.36.jar --pcr_primers hiv_pcr_primers.fa -f reads_1.fq.gz -r reads_2.fq.gz iva.out The following command failed with exit code 1 /opt/python3.6/bin/iva --threads 1 --trimmomatic /data/Trimmomatic-0.36/trimmomatic-0.36.jar --pcr_primers hiv_pcr_primers.fa -f reads_1.fq.gz -r reads_2.fq.gz iva.out
The output was:
Traceback (most recent call last): File "/opt/python3.6/bin/iva", line 129, in
iva.external_progs.get_all_versions(iva.external_progs.assembly_progs)
File "/opt/python3.6/lib/python3.6/site-packages/iva/external_progs.py", line 103, in get_all_versions
raise Error('Found version ' + version + ' of ' + prog + ' but must be at least ' + minimum_versions[prog] + '. Cannot continue')
iva.external_progs.Error: Found version 0.1.18 of samtools but must be at least 0.1.19. Cannot continue