Error: Hangup

[dtx282000]

Hi, I faced an error as follows:

So, How I can solve it?

Best

Deng

[olivertam]

Hi,

Is the Hangup part of the error log, or are you indicating that it's taking a long time? Or was it from the cluster saying that it exceeded the allocated time limit? The Could not retrieve message is from pysam, and does not cause the software to fail. It might just be taking time reading through the alignments.

Thanks.

[dtx282000]

HI,

Also, I can't understand how to deal with it.

Thanks

[olivertam]

Hi,

Is the job still running, or did it end (with an error)? What is the command line you used? Are you using a cluster, such as SLURM, where you need to specify the time the program requires? As mentioned above, the pysam message does not cause any issue with TEtranscripts, except maybe slowing the run a bit. Have you tried re-running the program?

Thanks.

[dtx282000]

Hi,

This job has ended. My command line as follows:





In, addition, I have tried re-running the command line again. Also I faced the same error.

Thanks！

2024年8月4日 08:11，Oliver Tam @.***> 写道：

Hi,

Is the job still running, or did it end (with an error)? What is the command line you used? Are you using a cluster, such as SLURM, where you need to specify the time the program requires? As mentioned above, the pysam message does not cause any issue with TEtranscripts, except maybe slowing the run a bit. Have you tried re-running the program?

Thanks.

— Reply to this email directly, view it on GitHub https://github.com/mhammell-laboratory/TEtranscripts/issues/198#issuecomment-2267209546, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFZFH3E64IIHB4N453RHVALZPVWUVAVCNFSM6AAAAABLVLBIOSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENRXGIYDSNJUGY. You are receiving this because you authored the thread.

[olivertam]

Hi,

Could you re-post your command lines again? I cannot see them on Github. Also, how much memory are you allocating to TEtranscripts? We recommend at least 30Gb of memory for runs on human or mouse genomes, but this will depend on your organism's genome complexity.

Thanks.

[dtx282000]

HI, my command lines as follows:

Run TEtranscripts

Run samples in pairs

BAM_DIR="data/BAMs" gene_annot_gtf="data/NDDB_SH_1_genomic_chr.gtf" te_annot_gtf="data/Transposon_core_chr.gtf" TETRANS_OUT_DIR="data/TEtranscripts”

cat ./data/aa.txt | while read i;

do

singularity exec /pub/software/tetranscripts.sif TEcount \ --format BAM --mode multi \ -b $BAM_DIR/${i}.bam \ --GTF $gene_annot_gtf \ --TE $te_annot_gtf \ --project ${i} \ --outdir $TETRANS_OUT_DIR/reproductive done

2024年8月4日 11:43，Oliver Tam @.***> 写道：

Hi,

Could you re-post your command lines again? I cannot see them on Github.

Thanks.

— Reply to this email directly, view it on GitHub https://github.com/mhammell-laboratory/TEtranscripts/issues/198#issuecomment-2267281581, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFZFH3EE24TMACJW722M3RDZPWPNXAVCNFSM6AAAAABLVLBIOSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENRXGI4DCNJYGE. You are receiving this because you authored the thread.

[olivertam]

Hi,

Thank you for your command line. How much memory are you allocating (or have available) to run TEtranscripts?

Thanks.

[dtx282000]



2024年8月4日 12:03，Oliver Tam @.***> 写道：

Hi,

Thank you for your command line. How much memory are you allocating (or have available) to run TEtranscripts?

Thanks.

— Reply to this email directly, view it on GitHub https://github.com/mhammell-laboratory/TEtranscripts/issues/198#issuecomment-2267291084, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFZFH3GK524KX22LQREWPY3ZPWRX3AVCNFSM6AAAAABLVLBIOSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENRXGI4TCMBYGQ. You are receiving this because you authored the thread.

[olivertam]

Hi,

Sorry, again your response could not be seen on Github.

Thanks.

[dtx282000]

[olivertam]

Thank you for your screenshot. It looks like you have sufficient memory to run this, so I can't determine what the error is. Is the final line of the log file (when it crashes) Hangup as indicated in your initial post? Given that you're running a loop of TEcount, did every one of those runs fail (i.e. no output files generated)? Thanks

[dtx282000]

Hi，

Strangely, the other samples were analyzed normally, but only one of them was the case (error: Hangup)

Thanks

2024年8月4日 13:01，Oliver Tam @.***> 写道：

Thank you for your screenshot. It looks like you have sufficient memory to run this, so I can't determine what the error is. Is the final line of the log file (when it crashes) Hangup as indicated in your initial post? Given that you're running a loop of TEcount, did every one of those runs fail (i.e. no output files generated)? Thanks

— Reply to this email directly, view it on GitHub https://github.com/mhammell-laboratory/TEtranscripts/issues/198#issuecomment-2267335352, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFZFH3DWA7E5DOGKODCBVWLZPWYT7AVCNFSM6AAAAABLVLBIOSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENRXGMZTKMZVGI. You are receiving this because you authored the thread.

[olivertam]

Hi,

Do you notice anything unusual about the BAM file for the one that failed (e.g. size, samtools quickcheck) Might I suggest re-running the alignment for that particular sample? It sounds like it might be an issue with that particular input, as the other samples ran fine (which suggests it's not an issue with the GTF or the program itself).

Thanks.

[dtx282000]

Hi,

According to your suggestion, I run the alignment for the particular sample again. Also, I performed the sort for this sample bam file. The following code was used:

Looking forwards to your reply.

Thanks!

[olivertam]

Hi,

That is really strange. I have never encountered that error before (nor have I seen Hangup in the error message before). Could you confirm that in your other runs, you also got the following in your log file?

[E::idx_find_and_load] Could not retrieve index file for ....

Do you have a time-limit on your jobs? What system are you running this on (i.e. what OS or cluster manager)?

I also compared the current error log with the previous one, and noted that it stopped earlier (so not at the same step). Given that the --sortByPos takes more time, I'm really suspecting if you're hitting a time limit or something of that type. Again, I have not experienced this particular error message, but that's my best guess at this point.

Sorry if this has been not helpful.

Thanks

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