Some tasks failed when using v1.2.0 of Wtp

[quliping]

I'm so happy that the question which I mentioned before about virsorter2 was solved. By the way, previous quention about phigaro was also resovled by running singularity run /public/cachedir/multifractal-phigaro-0.5.2.img then phigaro-setup --no-updatedb. However, I got some other problems.

Here is my command:

conda activate wtp
cat list-all.txt|while read line
do
if [[ ! -d "A_vrius_wtp/${line}" ]]; then mkdir "A_vrius_wtp/${line}"; fi
if [[ ! -d "wtpwork_temp/${line}_workdir" ]]; then mkdir "wtpwork_temp/${line}_workdir"; fi
nextflow run /public/apps/What_the_Phage-v1.2.0/phage.nf --filter 1000 --cores 72 -profile local,singularity \
--databases /public/data/database/wtp_database --cachedir /public/cachedir --workdir wtpwork_temp/${line}_workdir \
--fasta 03_connected_assembly/${line}.fasta --output A_vrius_wtp/${line} --all_tools
done
conda deactivate

Here is the report: execution.zip

These tasks failed using v1.2.0 but successed using v1.1.0:

1. deepvirfinder_wf:deepvirfinder 36.zip

2. virnet_wf:virnet b7.zip

3. markdown_report_wf:summary 35.zip

4. phage_annotation_wf:chromomap b3.zip

Problem 4 also occurred using test data:

nextflow run /public/apps/What_the_Phage-v1.2.0/phage.nf --cores 16 -profile smalltest,local,singularity \
--cachedir /public/cachedir --databases /public/data/database/wtp_database

execution_test.zip b6.zip

Problem 1, 2, and 3 not occurred when using test data.

[mult1fractal]

Hey quliping

1 & 2 the difference from v1.1.0 to v1.2.0 is that I removed not benchmarked tools them from the default execution. So I did not touch any tool processes. It also seems more tensorflow related? But unfortunately I have no experience with tensorflow.

3. Yes this is a real problem... see here #169 again I need the files to solve this

4. I will run your command and check what happened

[quliping]

Thanks for your reply. You mean the files from work dir, right? I put associate files just above the picture from each problem. For problem-3, the zip file containing work dir was named as '35.zip'. You can also use this link to download: https://github.com/replikation/What_the_Phage/files/9680558/35.zip

[mult1fractal]

I used the following command: nextflow run phage.nf -profile local,docker,smalltest -work-dir /media/6tb_1/work/ --cores 20

and the workflow finished succesfully. could you delete and reload the singularity image? (nanozoo/r_fungi:0.1--097b1bb) idk why the docker?singularity image is not working now... it is locked to a specific version (I also didnt touched it in the new release)

I will also clean my docker cache and rerun the command

[mult1fractal]

so I removed all docker containers installd on my machine and run the command again nextflow run phage.nf -profile local,docker,smalltest -work-dir /media/6tb_1/work/ --cores 20

the workflow finished successfully and I can't reproduce this error. Also your files look fine (b6)