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RemiAllio / MitoFinder

MitoFinder: efficient automated large-scale extraction of mitogenomic data from high throughput sequencing data
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Installation problem related to megahit #59

Closed hector-romao closed 2 months ago

hector-romao commented 2 months ago

Hello I have installed MitoFinder through the singularity conatiner as recommended.

When i run the test data, the assembly step is not completed due MEGAHIT. The following command was used:

../../programas/mitofinder_v1.4.2.sif -j Aphaenogaster_megommata_SRR1303315 -1 Aphaenogaster_megommata_SRR1303315_R1_cleaned.fastq.gz -2 Aphaenogaster_megommata_SRR1303315_R2_cleaned.fastq.gz -r reference.gb -o 5 -p 5 -m 10

This give me the following message: ERROR: MEGAHIT didn't run well Please check log file : /media/lgbio-nas1/hectorromao/MitoFinder_container/test_case/Aphaenogaster_megommata_SRR1303315/megahit.log

With the log that contains the message:

2024-06-04 11:10:04 - MEGAHIT v1.2.7 2024-06-04 11:10:04 - Using megahit_core with POPCNT and BMI2 support Traceback (most recent call last): File "/opt/MitoFinder/megahit/megahit", line 1013, in main() File "/opt/MitoFinder/megahit/megahit", line 963, in main build_library() File "/opt/MitoFinder/megahit/megahit", line 258, in checked_or_call func(*args, **kwargs) File "/opt/MitoFinder/megahit/megahit", line 700, in build_library create_fifo('pe1', i, inpipe_cmd(opt.pe1[i])) File "/opt/MitoFinder/megahit/megahit", line 687, in create_fifo os.mkfifo(fifo_path)

I've already tried to use another installation executable of MEGAHIT bia the config file

../../programas/mitofinder_v1.4.2.sif -j Aphaenogaster_megommata_SRR1303315 -1 Aphaenogaster_megommata_SRR1303315_R1_cleaned.fastq.gz -2 Aphaenogaster_megommata_SRR1303315_R2_cleaned.fastq.gz -r reference.gb -o 5 -p 5 -m 10 -c Mitofinder.config  --override

But again an error message is given, this time describing:

/bin/sh: 1: /home/lgbio/programas/MitoFinder/megahit/build/megahit: not found

Which is strange, because the program is installed in this folder $ which megahit /home/lgbio/programas/MitoFinder/megahit/build/megahit

RemiAllio commented 2 months ago

Hi,

Thank you for your message and sorry for the inconvenience.

Can you try the following command: singularity run --bind /home/lgbio/programas/MitoFinder/megahit/build/ ../../programas/mitofinder_v1.4.2.sif -j Aphaenogaster_megommata_SRR1303315 -1 Aphaenogaster_megommata_SRR1303315_R1_cleaned.fastq.gz -2 Aphaenogaster_megommata_SRR1303315_R2_cleaned.fastq.gz -r reference.gb -o 5 -p 5 -m 10

hector-romao commented 2 months ago

Thanks for the quick reply I tried but got the same error. I assume the error is related to creating fifo files, which my server does not support.

Is there a way to set up a temporary dir to run the analysis?

RemiAllio commented 2 months ago

Okay so you got the error with the two megahit executables right?

If so, it may comes from write permissions indeed. It is not possible to set up a temporary directory but you can run the analyses from wherever you want (you don't need to be at the same place as your files). So if you have permissions in another directory, you may want to run the analysis from there. Is it something possible for you? Would it help?

hector-romao commented 2 months ago

Yes. This was a good workaround. Thanks for your attention.