ModuleNotFoundError: No module named 'fastpathz'

[JSSaini]

cp: ‘/home/users/s/saini7/scratch/MS3/Cenote-Taker2/dummy_template.sbt’ and ‘/home/users/s/saini7/scratch/MS3/Cenote-Taker2/dummy_template.sbt’ are the same file tail: cannot open ‘viruses_am_ct_9m25.tax_guide.blastx.tab’ for reading: No such file or directory Entrez Direct does not support positional arguments. Please remember to quote parameter values containing whitespace or shell metacharacters. tail: cannot open ‘viruses_am_ct_9m250.tax_guide.blastx.tab’ for reading: No such file or directory Entrez Direct does not support positional arguments. Please remember to quote parameter values containing whitespace or shell metacharacters. tail: cannot open ‘viruses_am_ct_9m510.tax_guide.blastx.tab’ for reading: No such file or directory Entrez Direct does not support positional arguments. Please remember to quote parameter values containing whitespace or shell metacharacters. tail: cannot open ‘viruses_am_ct_9m314.tax_guide.blastx.tab’ for reading: No such file or directory Entrez Direct does not support positional arguments. Please remember to quote parameter values containing whitespace or shell metacharacters. tail: cannot open ‘viruses_am_ct_9m1649.tax_guide.blastx.tab’ for reading: No such file or directory Entrez Direct does not support positional arguments. Please remember to quote parameter values containing whitespace or shell metacharacters. tail: cannot open ‘viruses_am_ct_9m153.tax_guide.blastx.tab’ for reading: No such file or directory Entrez Direct does not support positional arguments. Please remember to quote parameter values containing whitespace or shell metacharacters. tail: cannot open ‘viruses_am_ct_9m781.tax_guide.blastx.tab’ for reading: No such file or directory Entrez Direct does not support positional arguments. Please remember to quote parameter values containing whitespace or shell metacharacters. tail: cannot open ‘viruses_am_ct_9m167.tax_guide.blastx.tab’ for reading: No such file or directory Entrez Direct does not support positional arguments. Please remember to quote parameter values containing whitespace or shell metacharacters. Traceback (most recent call last): File "/home/users/s/saini7/scratch/MS3/Cenote-Taker2/PHANOTATE/phanotate.py", line 7, in import fastpathz as fz ModuleNotFoundError: No module named 'fastpathz' Traceback (most recent call last): File "/home/users/s/saini7/scratch/MS3/Cenote-Taker2/PHANOTATE/phanotate.py", line 7, in import fastpathz as fz ModuleNotFoundError: No module named 'fastpathz' Traceback (most recent call last): File "/home/users/s/saini7/scratch/MS3/Cenote-Taker2/PHANOTATE/phanotate.py", line 7, in import fastpathz as fz ModuleNotFoundError: No module named 'fastpathz' Traceback (most recent call last): File "/home/users/s/saini7/scratch/MS3/Cenote-Taker2/PHANOTATE/phanotate.py", line 7, in import fastpathz as fz ModuleNotFoundError: No module named 'fastpathz' Traceback (most recent call last): File "/home/users/s/saini7/scratch/MS3/Cenote-Taker2/PHANOTATE/phanotate.py", line 7, in import fastpathz as fz ModuleNotFoundError: No module named 'fastpathz' sed: can't read .phan.fasta: No such file or directory sed: can't read .trans.fasta: No such file or directory

[JSSaini]

Please suggest how to get around this error?

[mtisza1]

Hi JSSaini,

Thanks for raising this issue. I apologize for the long delay in responding. I was unable to respond to github issues for a several weeks.

Regarding fastpathz, there was a previous user who seemed to have a similar problem #3 , and they resolved it by directly installing fastpath

conda activate cenote-taker2_env
pip install fastpath

Let me know if this helps.

Your issues that appear to involve "blastx.tab" files and Entrez Direct are likely an issue caused by improper set up of the krona database, as in issue #22

To fix this, change to the main Cenote-Taker 2 directory and use these commands (This requires at least 4 CPUs for some reason and will take 20-40 minutes, so please have those resources available):

KRONA_DIR=$( which python | sed 's/bin\/python/opt\/krona/g' )
cd ${KRONA_DIR}
sh updateTaxonomy.sh
cd ${KRONA_DIR}
sh updateAccessions.sh

If you are able to complete this fixes, please test on a small dataset, such as the DNA test contigs provided with the script, and send me the log file and a zipped directory of the output.

Best,

Mike