ViFi pipeline has warning messages and test dataset can't generate expected results

sara-javadzadeh / FastViFi

Detect viral infection and integration sites on NGS input. Manuscript is in preparation.

GNU General Public License v3.0

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ViFi pipeline has warning messages and test dataset can't generate expected results #2

Closed shengzhulst closed 2 years ago

shengzhulst commented 2 years ago

Hi Sara, I did meet another problem when I tested the ViFi pipeline, I used the most updated docker version of ViFi and run_ViFi.py script. The pipeline works well on the beginning steps and It seems like fail at the step run the merge_viral_reads.py. I check the reduced.csv and find it's empty. I am using the last line command in the setup_linux_mac.sh and set up everything well. Here I stick the error message here and can you help me check what's happening?

sara-jvz commented 2 years ago

Hi Shiting,

Thanks for bringing this up. In order to locate the problem, could you please provide the following?

The entire output. The screenshot seems to be be missing part of the output. Sharing the output in text format could be the easiest.
Did you set the environment variables $AA_DATA_REPO and $REFERENCE_REPO? If possible, could you please share the output of these? ls $AA_DATA_REPO and ls $REFERENCE_REPO

shengzhulst commented 2 years ago

Hi Sara, Sorry to reply a little late, I post the output.txt(stdoutput) and output.log(stderr) here. And the command I run is python $VIFI_DIR/scripts/run_vifi.py --cpus 2 --hmm_list /shiting/ViFi_reference/viral_data/${virus}/hmms/hmms.txt -f $VIFI_DIR/test/data/test_R1.fq.gz -r $VIFI_DIR/test/data/test_R2.fq.gz -o $VIFI_DIR/tmp/docker/ --docker --viral_reference_dir $REFERENCE_REPO --hg_data_dir $AA_DATA_REPO --vifi_dir $VIFI_DIR 2>&1 >output.log ViFi_output.log ViFi_output.txt

For the ls $AA_DATA_REPO, ls $REFERENCE_REPOI have a picture here.

sara-javadzadeh commented 2 years ago

Hi Shiting,

Thanks for providing the info. Looks like the file 'reference.txt' in 'data_repo' directory is missing. I updated the ViFi repository installation script and README to create the file as a step of the installation (https://github.com/sara-javadzadeh/ViFi/commit/26a6fb8c1f33eece25d64cd83e3cc9c7ecdac3fe) Please remove the 'data_repo' directory and repeat the installation steps.

For any other problems with ViFi, I would appreciate it if you could open an issue on the ViFi repository (https://github.com/sara-javadzadeh/ViFi). It would be much easier to link the issues and fix commits on the same repo. Also, others can follow the ViFi installation issues easier on the ViFi repository.

Thanks, Sara