flair quantify problem error

wdesaintjean commented 1 month ago

Hello,

Copy and paste the exact command you tried to run

cat $iso_fa >> flair_all_iso.fa
flair quantify -r $reads_manifest -i flair_all_iso.fa --sample_id_only 
cat $iso_bed >> flair_all_iso.bed
flair diffSplice -i flair_all_iso.bed -q flair.quantify.counts.tsv --out_dir results_diffsplice

How did you install Flair? I use the docker image in a nextflow pipeline: docker pull brookslab/flair:latest`

What happened?

I try to use flair in a nextflow pipeline, but the process fail at the step "flair quantify". Previously, I run flair collapse on each chromosome .bed, as recommended in the repository for big bed input. After that, I combine the output .fa with all isofroms to run flair quantify. But with 8 samples, the program seems to stop after running on 4 samples:

 Command error:
  Writing temporary files with prefixes similar to /tmp/tmp12j7ykc1
  Step 1/3. Aligning sample WT12_1, 1/8
  Step 1/3. Aligning sample WT9_2, 2/8
  Step 1/3. Aligning sample WT784_3, 3/8
  Step 1/3. Aligning sample WT13_4, 4/8
  Check /tmp/tmplfsvo041.sam.mm2_stderr.txt file

Curiously, flair works perfectly well on test data (4 samples with 1M reads), but return bug when running on the final dataset of 8 sample with 20M reads

Can you help me?

0317miaomiao commented 3 weeks ago

Hello,

Copy and paste the exact command you tried to run
cat $iso_fa >> flair_all_iso.fa
flair quantify -r $reads_manifest -i flair_all_iso.fa --sample_id_only 
cat $iso_bed >> flair_all_iso.bed
flair diffSplice -i flair_all_iso.bed -q flair.quantify.counts.tsv --out_dir results_diffsplice
How did you install Flair? I use the docker image in a nextflow pipeline: docker pull brookslab/flair:latest`

What happened?

I try to use flair in a nextflow pipeline, but the process fail at the step "flair quantify". Previously, I run flair collapse on each chromosome .bed, as recommended in the repository for big bed input. After that, I combine the output .fa with all isofroms to run flair quantify. But with 8 samples, the program seems to stop after running on 4 samples:
 Command error:
  Writing temporary files with prefixes similar to /tmp/tmp12j7ykc1
  Step 1/3. Aligning sample WT12_1, 1/8
  Step 1/3. Aligning sample WT9_2, 2/8
  Step 1/3. Aligning sample WT784_3, 3/8
  Step 1/3. Aligning sample WT13_4, 4/8
  Check /tmp/tmplfsvo041.sam.mm2_stderr.txt file
Curiously, flair works perfectly well on test data (4 samples with 1M reads), but return bug when running on the final dataset of 8 sample with 20M reads

Can you help me? I have the same error with you, and I try one way to solve it. I guess that this error may happen if you aren't set --temp_dir test.quant.temp, you can try to use it. Here are my command: $ flair quantify -r flair_long.tsv -i flair.collapse.isoforms.fa --temp_dir test.quant.temp --tpm -o test.quantify After using it, everything is ok. Hope this can solve your problem.

wdesaintjean commented 2 weeks ago

It's working with your command line! I had this problem for one month, I'm very happy to be able to run FLAIR on my datas

Thank you very much for your help.

0317miaomiao commented 2 weeks ago

It's working with your command line! I had this problem for one month, I'm very happy to be able to run FLAIR on my datas

Thank you very much for your help.

Good luck with the research！

BrooksLabUCSC / flair

flair quantify problem error #337