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Occured when writing output.
Expected output files were written, except for files core_gene_alignment.aln and core_gene_alignment_filtered.aln according to the manual
Output:
pre-processing gff3 files...
100%|██████████████████████████████████████████████████████████████████████████████████████████████████| 5/5 [00:02<00:00, 1.92it/s]
running cmd: cd-hit -T 1 -i test0/combined_protein_CDS.fasta -o test0/combined_protein_cdhit_out.txt -c 0.98 -s 0.98 -aL 0.0 -AL 99999999 -aS 0.0 -AS 99999999 -M 0 -d 999 -g 1 -n 2
================================================================
Program: CD-HIT, V4.8.1 (+OpenMP), May 15 2023, 22:49:31
Command: cd-hit -T 1 -i test0/combined_protein_CDS.fasta -o
test0/combined_protein_cdhit_out.txt -c 0.98 -s 0.98
-aL 0.0 -AL 99999999 -aS 0.0 -AS 99999999 -M 0 -d 999
-g 1 -n 2
Started: Thu Oct 12 19:35:34 2023
================================================================
Output
----------------------------------------------------------------
Your word length is 2, using 5 may be faster!
total seq: 8474
longest and shortest : 1932 and 25
Total letters: 2580143
Sequences have been sorted
Approximated minimal memory consumption:
Sequence : 3M
Buffer : 1 X 16M = 16M
Table : 1 X 0M = 0M
Miscellaneous : 0M
Total : 20M
Table limit with the given memory limit:
Max number of representatives: 4000000
Max number of word counting entries: 240466000
comparing sequences from 0 to 8474
........
8474 finished 1745 clusters
Approximated maximum memory consumption: 22M
writing new database
writing clustering information
program completed !
Total CPU time 1.62
generating initial network...
Processing paralogs...
100%|█████████████████████████████████████████████████████████████████████████████████████████████████| 1/1 [00:00<00:00, 852.15it/s]
collapse mistranslations...
Processing depth: 1
Iteration: 1
100%|█████████████████████████████████████████████████████████████████████████████████████████| 1746/1746 [00:00<00:00, 66675.66it/s]
Iteration: 2
100%|██████████████████████████████████████████████████████████████████████████████████████████████| 17/17 [00:00<00:00, 3871.17it/s]
Iteration: 3
100%|███████████████████████████████████████████████████████████████████████████████████████████████| 3/3 [00:00<00:00, 65196.44it/s]
Processing depth: 2
Iteration: 1
100%|████████████████████████████████████████████████████████████████████████████████████████| 1719/1719 [00:00<00:00, 421169.96it/s]
Processing depth: 3
Iteration: 1
100%|████████████████████████████████████████████████████████████████████████████████████████| 1719/1719 [00:00<00:00, 403176.68it/s]
collapse gene families...
Processing depth: 1
Iteration: 1
100%|████████████████████████████████████████████████████████████████████████████████████████| 1719/1719 [00:00<00:00, 295383.20it/s]
Iteration: 2
100%|███████████████████████████████████████████████████████████████████████████████████████████████| 1/1 [00:00<00:00, 27594.11it/s]
Processing depth: 2
Iteration: 1
100%|████████████████████████████████████████████████████████████████████████████████████████| 1717/1717 [00:00<00:00, 650259.14it/s]
Processing depth: 3
Iteration: 1
100%|████████████████████████████████████████████████████████████████████████████████████████| 1717/1717 [00:00<00:00, 618058.70it/s]
trimming contig ends...
refinding genes...
Number of searches to perform: 18
Searching...
5it [00:06, 1.26s/it]
translating hits...
removing by consensus...
Updating output...
Number of refound genes: 4
collapse gene families with refound genes...
Processing depth: 1
Iteration: 1
100%|████████████████████████████████████████████████████████████████████████████████████████| 1711/1711 [00:00<00:00, 519205.19it/s]
Processing depth: 2
Iteration: 1
100%|████████████████████████████████████████████████████████████████████████████████████████| 1711/1711 [00:00<00:00, 634186.47it/s]
Processing depth: 3
Iteration: 1
100%|████████████████████████████████████████████████████████████████████████████████████████| 1711/1711 [00:00<00:00, 592997.37it/s]
writing output...
*** Error in `/home/davidtong28/.conda/envs/panaroo_1.3.4/bin/python3.9': double free or corruption (!prev): 0x000055f18142deb0 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x7d1fd)[0x7f2fbafe41fd]
/home/davidtong28/.conda/envs/panaroo_1.3.4/bin/python3.9(PyObject_GC_Del+0x1c7)[0x55f180b93c57]
/home/davidtong28/.conda/envs/panaroo_1.3.4/bin/python3.9(+0x1449ec)[0x55f180bb39ec]
/home/davidtong28/.conda/envs/panaroo_1.3.4/bin/python3.9(+0x13e533)[0x55f180bad533]
/home/davidtong28/.conda/envs/panaroo_1.3.4/bin/python3.9(+0x121a07)[0x55f180b90a07]
/home/davidtong28/.conda/envs/panaroo_1.3.4/bin/python3.9(_PyModule_ClearDict+0xfc)[0x55f180c1300c]
/home/davidtong28/.conda/envs/panaroo_1.3.4/bin/python3.9(+0x209715)[0x55f180c78715]
/home/davidtong28/.conda/envs/panaroo_1.3.4/bin/python3.9(Py_FinalizeEx+0x182)[0x55f180c77602]
/home/davidtong28/.conda/envs/panaroo_1.3.4/bin/python3.9(Py_Exit+0x8)[0x55f180c78318]
/home/davidtong28/.conda/envs/panaroo_1.3.4/bin/python3.9(+0x2067eb)[0x55f180c757eb]
/home/davidtong28/.conda/envs/panaroo_1.3.4/bin/python3.9(PyErr_PrintEx+0x11)[0x55f180c754e1]
/home/davidtong28/.conda/envs/panaroo_1.3.4/bin/python3.9(+0x981eb)[0x55f180b071eb]
/home/davidtong28/.conda/envs/panaroo_1.3.4/bin/python3.9(Py_RunMain+0x38d)[0x55f180c6b3bd]
/home/davidtong28/.conda/envs/panaroo_1.3.4/bin/python3.9(Py_BytesMain+0x37)[0x55f180c3ef07]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x7f2fbaf88af5]
/home/davidtong28/.conda/envs/panaroo_1.3.4/bin/python3.9(+0x1cfe01)[0x55f180c3ee01]
======= Memory map: ========
55f180a6f000-55f180acb000 r--p 00000000 00:2a 65289962 /home/davidtong28/.conda/envs/panaroo_1.3.4/bin/python3.9
...(omitting hundreds of lines)...
7f2fb1cf5000-7f2fb1cf8000 r--p 00016000 00:2a 73981416 /home/davidtong28/.conda/envs/panaroo_1.3.4/lib/libgcc_s.so.1Aborted (core dumped)
This error would also appear when the input files are incorrect.
The text was updated successfully, but these errors were encountered:
This looks a bit odd and like it might be a memory issue. Have you been able to run it successfully on another set of files or have you tried running it on a small subset of these files?
If not, it might be an issue with the installation which will be harder to debug remotely.
No, the error would constantly appear in any given data, and even invalid data.
So I would also consider it to be an installation issue. I'll try using it on another cluster.
Luckily I'm not using the alignment files for now and all the other output files look usable.
Version
Installed using Conda as described
Command
panaroo -i ~/wgs_campy/total/bakta1.7/R1S5-[1-9][ABC]/*.gff3 --clean-mode strict --merge_paralogs -o test0
Error
Occured when writing output.
Expected output files were written, except for files
core_gene_alignment.aln
andcore_gene_alignment_filtered.aln
according to the manualOutput:
This error would also appear when the input files are incorrect.
The text was updated successfully, but these errors were encountered: