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oschwengers / platon

Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.
https://doi.org/10.1099/mgen.0.000398
GNU General Public License v3.0
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Marker protein search failed! and ERROR - MAIN - diamond execution failed! diamond-error-code=-11 #45

Closed bayraktar1 closed 7 months ago

bayraktar1 commented 7 months ago

I get the same error that was reported here: #12

Command and error message:

(platon) bayraktar@archlinux:~/Downloads$ platon --db db/ --output results/ --verbose --threads 8 E_coli_test.fasta 
Platon v1.7
Options and arguments:
        input: /home/bayraktar/Downloads/E_coli_test.fasta
        db: /home/bayraktar/Downloads/db
        output: /home/bayraktar/Downloads/results
        prefix: E_coli_test
        mode: accuracy
        characterize: False
        tmp path: /tmp/tmp1l0x7gk_
        # threads: 8
parse draft genome...
        exclude contig 'SRR6985737_202105251828_1_length_878894_cov_36.967575', too long (878894)
        exclude contig 'SRR6985737_202105251828_2_length_588050_cov_36.850970', too long (588050)
        parsed 80 raw contigs
        excluded 2 contigs by size filter
        analyze 78 contigs
predict ORFs...
        found 3655 ORFs
search marker protein sequences (MPS)...
Marker protein search failed!

Log file:

2024-03-06 12:50:59,800 - INFO - CONFIG - metagenome=False
2024-03-06 12:50:59,803 - INFO - UTILS - dependency check: tool=prodigal, version=v2.6.3
2024-03-06 12:50:59,805 - INFO - UTILS - dependency check: tool=diamond, version=v2.1.9
2024-03-06 12:50:59,856 - INFO - UTILS - dependency check: tool=blastn, version=v2.15.0
2024-03-06 12:50:59,857 - INFO - UTILS - dependency check: tool=hmmsearch, version=v3.4.0
2024-03-06 12:50:59,858 - INFO - UTILS - dependency check: tool=nucmer, version=v4.0.0
2024-03-06 12:50:59,861 - INFO - UTILS - dependency check: tool=cmscan, version=v1.1.5
2024-03-06 12:50:59,866 - INFO - MAIN - exclude contig: too long: id=SRR6985737_202105251828_1_length_878894_cov_36.967575, length=878894
2024-03-06 12:50:59,867 - INFO - MAIN - exclude contig: too long: id=SRR6985737_202105251828_2_length_588050_cov_36.850970, length=588050
2024-03-06 12:50:59,871 - INFO - MAIN - length contig filter: # input=80, # discarded=2, # remaining=78
2024-03-06 12:51:04,412 - INFO - MAIN - ORF detection: # ORFs=3655
2024-03-06 12:51:04,412 - INFO - MAIN - ORF contig filter disabled! # passed contigs=78
2024-03-06 12:51:21,723 - ERROR - MAIN - diamond execution failed! diamond-error-code=-11
2024-03-06 12:51:21,723 - DEBUG - MAIN - diamond execution: cmd=['diamond', 'blastp', '--db', '/home/bayraktar/Downloads/db/mps.dmnd', '--query', '/tmp/tmp1l0x7gk_/proteins.faa', '--out', '/tmp/tmp1l0x7gk_/diamond.tsv', '--max-target-seqs', '1', '--id', '90', '--query-cover', '80', '--subject-cover', '80', '--threads', '8', '--tmpdir', '/tmp/tmp1l0x7gk_'], stdout='', stderr='diamond v2.1.9.163 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen
Documentation, support and updates available at http://www.diamondsearch.org
Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021)

#CPU threads: 8
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)
Temporary directory: /tmp/tmp1l0x7gk_
#Target sequences to report alignments for: 1
Opening the database...  [0.02s]
Database: /home/bayraktar/Downloads/db/mps.dmnd (type: Diamond database, sequences: 4847438, letters: 1549533412)
Block size = 2000000000
Opening the input file...  [0s]
Opening the output file...  [0s]
Loading query sequences...  [0.003s]
Length sorting queries...  [0.001s]
Masking queries...  [0.008s]
Building query seed set...  [0.07s]
Algorithm: Query-indexed
Building query histograms...  [0.006s]
Seeking in database...  [0s]
Loading reference sequences...  [0.855s]
Length sorting reference...  [0.667s]
Initializing temporary storage...  [0.002s]
Building reference histograms...  [2.18s]
Allocating buffers...  [0s]
Processing query block 1, reference block 1/1, shape 1/2.
Building reference seed array...  [1.33s]
Building query seed array...  [0.006s]
Computing hash join...  [0.276s]
Searching alignments...  [0.423s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 2/2.
Building reference seed array...  [1.118s]
Building query seed array...  [0.005s]
Computing hash join...  [0.25s]
Searching alignments...  [0.423s]
Deallocating memory...  [0s]
Deallocating buffers...  [0.014s]
Clearing query masking...  [0s]
Computing alignments... Loading trace points...  [0.063s]
Sorting trace points...  [0.02s]
Computing alignments... '
bayraktar1 commented 7 months ago

I installed the dependencies listed on the main page manually into my conda env, and it fixed the error

oschwengers commented 7 months ago

Hi @bayraktar1 , glad to hear that it's working. Just in case: available memory is also a regular cause of such errors.

jpaganini commented 5 months ago

As @oschwengers, I got the exact same error due to lack of memory (I was requesting 8GBs). Requesting 20G fixed it.