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DrosophilaGenomeEvolution / TrEMOLO

Transposable Elements MOvement detection using LOng reads
GNU General Public License v3.0
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LIFT_OFF Issue, no report #19

Open haoran-chn opened 7 months ago

haoran-chn commented 7 months ago

Hi, Thank you for providing TrEMOLO! I got an error when running test data via singularity. Check the error message below:

[SNK]--[Sun Apr 28 12:02:08 CEST 2024] LIFT_OFF •••

extracting features @SQ SN:Chr1 LN:30427671 @SQ SN:Chr2 LN:19698289 @SQ SN:Chr3 LN:23459830 @SQ SN:Chr4 LN:18585056 @SQ SN:Chr5 LN:26975502 @PG ID:minimap2 PN:minimap2 VN:2.24-r1122 CL:minimap2 -d TrEMOLO_OUTPUT/INPUT/TAIR10.fa.mmi -a --end-bonus 5 --eqx -N 50 -p 0.5 -t 80 TrEMOLO_OUTPUT/INPUT/TAIR10.fa aligning features lifting features AN ERROR OCCURRED!

[SNK INFO] ERROR PIPELINE; snakefile used : TrEMOLO_OUTPUT/SNAKE_USED/Snakefile_outsider.snk Check LOG : TrEMOLO_OUTPUT/log/Snakefile_outsider.log Check ERROR : TrEMOLO_OUTPUT/log/Snakefile_outsider.err

Removing temporary output file TrEMOLO_OUTPUT/rep_tmp_snk. [Sun Apr 28 12:03:04 2024] Finished job 0. 1 of 1 steps (100%) done

Complete log: snakemake/log/2024-04-28T114824.355614.snakemake.log CHECKING OF DB TE....

I attached the err.log also, however I could not see any error in the LEFT_OFF. Please let me if there is any solution and thanks in advance. LEFT_OFF.err.txt Snakefile_outsider.err.txt

Haoran

haoran-chn commented 7 months ago

/usr/bin/bash: line 68: DIFF_SIZE: unbound variable

M-D75 commented 7 months ago

Hello,

Thank you for your interest in the pipeline.

Thank you for reporting the issue. I can already see where the error is; it should be simple to correct. An update will be made soon, and I will notify you once it has been completed.

Thank you again, M-D

M-D75 commented 7 months ago

Hi, the update is available. M-D

haoran-chn commented 7 months ago

Hi,

Thanks so much, I am going to test it. Which means I need to recompile it, right?

H.R

M-D75 commented 7 months ago

Yeah, you just need to get the git update, either by performing a git pull in the TrEMOLO directory or by redoing a git clone https://github.com/DrosophilaGenomeEvolution/TrEMOLO. There is no need to rebuild the Singularity container.

I advise you to re-test the launch on the test dataset to ensure that no basic errors are present.

Best regards, M-D