ISEScan Stuck in a Non-responsive State After Running for 30 Hours

[wanghang7410]

Title: ISEScan Stuck in a Non-responsive State After Running for 30 Hours

Body: I've been running the following command in ISEScan for about 30 hours, but the program seems to have entered a non-responsive state without producing any output or making further progress. The last output I received is as follows:

no significant hit with E-value <= 1e-10 found for k97_999147
no significant hit with E-value <= 1e-10 found for k97_999170
no significant hit with E-value <= 1e-10 found for k97_999210
no significant hit with E-value <= 1e-10 found for k97_999261
no significant hit with E-value <= 1e-10 found for k97_999285
no significant hit with E-value <= 1e-10 found for k97_999368
no significant hit with E-value <= 1e-10 found for k97_999392
no significant hit with E-value <= 1e-10 found for k97_999417
no significant hit with E-value <= 1e-10 found for k97_999418
no significant hit with E-value <= 1e-10 found for k97_999433
no significant hit with E-value <= 1e-10 found for k97_999527
no significant hit with E-value <= 1e-10 found for k97_999559
no significant hit with E-value <= 1e-10 found for k97_999564
no significant hit with E-value <= 1e-10 found for k97_99968
no significant hit with E-value <= 1e-10 found for k97_999689
no significant hit with E-value <= 1e-10 found for k97_999751
no significant hit with E-value <= 1e-10 found for k97_999785
no significant hit with E-value <= 1e-10 found for k97_999806
no significant hit with E-value <= 1e-10 found for k97_999835
no significant hit with E-value <= 1e-10 found for k97_999839
no significant hit with E-value <= 1e-10 found for k97_999844
no significant hit with E-value <= 1e-10 found for k97_999849
no significant hit with E-value <= 1e-10 found for k97_999904
no significant hit with E-value <= 1e-10 found for k97_999924

The command I ran is:

isescan.py --seqfile /io/fasta/xx.fasta --output /io/isescan/xxx --nthread 8

I would like to understand why the program is not responding and how to resolve this issue. Any insights or suggestions would be greatly appreciated.

[xiezhq]

If ISEScan keeps printing the message on your screen for different sequences in your xx.fasta (e.g. k97_999849, k97_999904, ...), it indicates the ISEScan is still running. It may take long time for ISEScan to process all sequences in your input file, xx.fasta, if there are lots of sequences in your xx.fasta. If you like to finish ISEScan running earlier for each input file, you can split your xx.fasta (e.g. 1000 sequences included in xx.fasta) into 10 or 100 *.fasta and then run ISEScan against each smaller .fasta file.

[wanghang7410]

Thank you for your reply. The last output occurred after 30 hours of execution, and the subsequent program continued running for another 30 hours without any output, with the CPU remaining idle.

[flowhub-team]

It seems that the logic in the BLAST section has frozen.

[xiezhq]

Could you try:

1. Place only two sequences, k97_999924 and the next sequence (k97_xxx) in your xx.fasta, into your input file, test.fasta.
2. Run ISEScan on the new input file, test.fasta.
3. Let me know the result when ISEScan running completes.

[wanghang7410]

I ran the test according to the method you provided, and the original command is stuck

I extracted several sequences before and after k97 999990 and re-ran them isescan.py --seqfile ./test.fasta --output ./test_out/ --nthread 128 ISEScan starts at Sat Mar 30 01:54:34 2024 predict and translate genes from genome sequence into protein database using FragGeneScan program

Begin to translate genome into proteome. /FragGeneScan1.31/FragGeneScan -s ./test.fasta -o ./test_out/proteome/./test.fasta -w 0 -t illumina_5 -p 128 Using 128 threads. no. of seqs: 10 Clock time used (by 128 threads) = 0.01 mins prepare gff file.. Time elapsed: 0 hours 0 minutes and 1 seconds. Translating genome into proteome for ./test.fasta , return 0

Finish translating genome into proteome. Sat Mar 30 01:54:35 2024

Begin to phmmer search against proteome database. Sat Mar 30 01:54:35 2024 Finish phmmer searching /ISEScan/pHMMs/clusters.single.faa against ./test_out/proteome/./test.fasta.faa , output ./test_out/hmm/./clusters.single.faa.test.fasta.faa

Finish phmmer searching against proteome database. Sat Mar 30 01:54:50 2024

Begin to profile HMM search against proteome database. Sat Mar 30 01:54:50 2024 Finish Profile HMM searching /ISEScan/pHMMs/clusters.faa.hmm against ./test_out/proteome/./test.fasta.faa , output ./test_out/hmm/./clusters.faa.hmm.test.fasta.faa

Finish profile HMM searching against proteome database. Sat Mar 30 01:54:57 2024 pred begins at Sat Mar 30 01:54:57 2024 Warning: no significant hit with E-value <= 1e-10 found for k97_999982 Warning: no significant hit with E-value <= 1e-10 found for k97_999983 Warning: no significant hit with E-value <= 1e-10 found for k97_999984 Warning: no significant hit with E-value <= 1e-10 found for k97_999985 Warning: no significant hit with E-value <= 1e-10 found for k97_999986 Warning: no significant hit with E-value <= 1e-10 found for k97_999990 Warning: no significant hit with E-value <= 1e-10 found for k97_999991 Warning: no significant hit with E-value <= 1e-10 found for k97_999992 Warning: no significant hit with E-value <= 1e-10 found for k97_999993 Warning: no significant hit with E-value <= 1e-10 found for k97_999994 Warning: no significant hit with E-value <= 1e-10 found for k97_999982,k97_999983,k97_999984,k97_999985,k97_999986,k97_999990,k97_999991,k97_999992,k97_999993,k97_999994 End in pred Sat Mar 30 01:54:57 2024 Both complete and partial IS elements are reported. ISEScan ends at Sat Mar 30 01:54:57 2024

Run is complete

[flowhub-team]

It seems that the BLASTN process is stuck from my perspective.