Error during "creating z y v clusters from the final set of bins" avamb workflow

[eperezv]

Hello,

I'm running avamb snakemake workflow on my dataset and everything worked perfect when I specified "min_comp": "0.9" and "max_cont": "0.05" on the config file. However, I repeated the process to specify "min_comp": "0.7" and "max_cont": "0.1" (from the scratch as I couldn't find a way to run the workflow after just changing that) and I am getting the following error.

I have found the same error with two different datasets:

creating z y v clusters from the final set of bins
/home/eduardo/tools/avamb/vamb/workflow_avamb/src/write_clusters_from_dereplicated_and_ripped_bins.sh: 22: [[: not found
/home/eduardo/tools/avamb/vamb/workflow_avamb/src/write_clusters_from_dereplicated_and_ripped_bins.sh: 22: [[: not found
/home/eduardo/tools/avamb/vamb/workflow_avamb/src/write_clusters_from_dereplicated_and_ripped_bins.sh: 22: [[: not found
/home/eduardo/tools/avamb/vamb/workflow_avamb/src/write_clusters_from_dereplicated_and_ripped_bins.sh: 22: [[: not found
/home/eduardo/tools/avamb/vamb/workflow_avamb/src/write_clusters_from_dereplicated_and_ripped_bins.sh: 22: [[: not found
/home/eduardo/tools/avamb/vamb/workflow_avamb/src/write_clusters_from_dereplicated_and_ripped_bins.sh: 22: [[: not found
/home/eduardo/tools/avamb/vamb/workflow_avamb/src/write_clusters_from_dereplicated_and_ripped_bins.sh: 22: [[: not found
/home/eduardo/tools/avamb/vamb/workflow_avamb/src/write_clusters_from_dereplicated_and_ripped_bins.sh: 22: [[: not found
Waiting at most 5 seconds for missing files.
MissingOutputException in rule write_clusters_from_nc_folders in file /home/eduardo/tools/avamb/vamb/workflow_avamb/avamb.snake.conda.smk, line 677:
Job 175  completed successfully, but some output files are missing. Missing files after 5 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
avamb_outdir_megahit_gpu_re/avamb/avamb_manual_drep_disjoint_clusters.tsv
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2024-03-09T154306.573274.snakemake.log

[jakobnissen]

It is possible that this command was not run with the shell Bash, but with another kind of shell. @eperezv Do you know for sure that Snakemake executed using the Bash shell?

CC @Paupiera - perhaps this can be rewritten in Python? Since we know that the user certainly has a functioning Python install, but we do not necessarily know which shell they are using.

[eperezv]

Hi, thanks for your answer. Yes, it is Bash for sure (from the snakemake output):

Using shell:/usr/bin/bash

[Paupiera]

Hello,

I am sorry that you are experiencing problems. For a better interpretation of the error, could you share a tarball with the tmp/snakemake_tmp and the log folders?

[eperezv]

Here are the files. I tried to re-run it one time, not sure if that altered something log.tar.gz tmp/snakemake_tmp is too heavy for this, I uploaded to onedrive: https://1drv.ms/u/s!AhO14pDwo9Qjq5lJSgYN_iRSzBhzCQ?e=4Okf5y

[Paupiera]

Hi,

Everything looks normal regarding the workflow from the log and tmp. Could you try executing the command outside the snakemake workflow? This is the command that should be executed:

/home/eduardo/tools/avamb/vamb/workflow_avamb/src/write_clusters_from_dereplicated_and_ripped_bins.sh  -d avamb_outdir_megahit_gpu_re/Final_bins -o avamb_outdir_megahit_gpu_re/

Please let me know the error you get in case it does not run.

[eperezv]

Hi, thanks for checking it in detail. It does not give any error message.

[Paupiera]

Great. The script executed should have created the final clusters avamb_outdir_megahit_gpu_re/avamb/avamb_manual_drep_disjoint_clusters.tsv, which should match the bins contained in the avamb_outdir_megahit_gpu_re/Final_bins folder.

[eperezv]

I'm not sure. I have checked and I have a avamb_manual_drep_disjoint_clusters.tsv file under tmp, not under avamb folder. According to the file modification, the file was created before, not now...

[Paupiera]

That should not happen, since the:

/home/eduardo/tools/avamb/vamb/workflow_avamb/src/write_clusters_from_dereplicated_and_ripped_bins.sh  -d avamb_outdir_megahit_gpu_re/Final_bins -o avamb_outdir_megahit_gpu_re/

command should create the avamb_outdir_megahit_gpu_re/avamb/avamb_manual_drep_disjoint_clusters.tsv. Could you confirm that the content of avamb_manual_drep_disjoint_clusters.tsv matches the Final_bins fasta files? As start, I would check that all bins from Final_bins/ are present in the clusters file, and that the same number of contigs appear in both.

[kellynntan]

Hi,

Everything looks normal regarding the workflow from the log and tmp. Could you try executing the command outside the snakemake workflow? This is the command that should be executed:

/home/eduardo/tools/avamb/vamb/workflow_avamb/src/write_clusters_from_dereplicated_and_ripped_bins.sh  -d avamb_outdir_megahit_gpu_re/Final_bins -o avamb_outdir_megahit_gpu_re/

Please let me know the error you get in case it does not run.

Hi, I am having the same issue. I tried to run the above but was given the error

vamb/workflow_avamb/src/write_clusters_from_dereplicated_and_ripped_bins.sh: line 29: avamb_outdir/: Is a directory

Is there a possible solve?