failed: output.plasmer.length.unclass.fasta, Error: no input sequences to analyze

[tianrenmaogithub]

Thank you for developing the tool. I am having an issue running it. Below is the command I ran with docker.

docker run -d -v /media/Data_1/tianrm/projects/plasmid_identification/4/testing/plasmidome:/input -v /media/Data_1/tianrm/projects/plasmid_identification/4/testing/benchmarking/Plasmer:/output -v /media/Data_1/tianrm/databases/plasmer:/db nekokoe/plasmer:latest /bin/sh /scripts/Plasmer -g /input/plasmidome_1k-3k -d /db -t 8 -o /output/plasmidome_1k-3k

The input has 1000 contigs (1 - 3 Kbp).
Below is a list of files in the output directory. They are empty files.

-rw-r--r-- 1 root root 0 May 21 16:11 output.plasmer.predClass.tsv
-rw-r--r-- 1 root root 0 May 21 16:11 output.plasmer.predPlasmids.fa
-rw-r--r-- 1 root root 0 May 21 16:11 output.plasmer.predPlasmids.taxon
-rw-r--r-- 1 root root 0 May 21 16:09 output.plasmer.shorterM.fasta

Below is a list of the intermediate files.

-rw-r--r-- 1 root root 0 May 21 16:11 output.aa
-rw-r--r-- 1 root root 221 May 21 16:11 output_blastn.sh
-rw-r--r-- 1 root root 57 May 21 16:11 output.conjugation.domtblout.feature
-rw-r--r-- 1 root root 225 May 21 16:11 output_diamond.sh
-rw-r--r-- 1 root root 0 May 21 16:11 output.gff
-rw-r--r-- 1 root root 1.3K May 21 16:11 output_hmmscan.sh
-rw-r--r-- 1 root root 57 May 21 16:11 output.mobilization.domtblout.feature
-rw-r--r-- 1 root root 33 May 21 16:11 output.mps.rds.feature
-rw-r--r-- 1 root root 57 May 21 16:11 output.ncbifam-amr.domtblout.feature
-rw-r--r-- 1 root root 0 May 21 16:11 output.orit.blastn.out
-rw-r--r-- 1 root root 39 May 21 16:11 output.orit.feature
-rw-r--r-- 1 root root 97 May 21 16:10 output.p.common_table
-rw-r--r-- 1 root root 0 May 21 16:11 output.p.common_table.features
-rw-r--r-- 1 root root 0 May 21 16:09 output.plasmer.length.class
-rw-r--r-- 1 root root 0 May 21 16:09 output.plasmer.length.unclass.fasta
-rw-r--r-- 1 root root 0 May 21 16:11 output.plasmer.predPlasmids.k2.report
-rw-r--r-- 1 root root 0 May 21 16:09 output.plasmer.shorterM.class
-rw-r--r-- 1 root root 122 May 21 16:10 output.pmr.common_table
-rw-r--r-- 1 root root 0 May 21 16:11 output.pmr.common_table.features
-rw-r--r-- 1 root root 112 May 21 16:11 output.r.common_table
-rw-r--r-- 1 root root 0 May 21 16:11 output.r.common_table.features
-rw-r--r-- 1 root root 57 May 21 16:11 output.replication.domtblout.feature
-rw-r--r-- 1 root root 124 May 21 16:10 output.rmp.common_table
-rw-r--r-- 1 root root 0 May 21 16:11 output.rmp.common_table.features
-rw-r--r-- 1 root root 39 May 21 16:11 output.rRNA.feature
-rw-r--r-- 1 root root 74 May 21 16:09 output.sample.list
-rw-r--r-- 1 root root 93K May 21 16:09 output.seqkit

The output.seqkit showed the input sequences, like this:

816f8014-0726-4b8e-8848-f12a74caa1fa_utg000001l_pilon_pilon_pilon_pilon_pilon 2087 51.22 7.58
c7dbf8f4-58c3-427b-ae75-f61c4d2c3ff3_utg000001l_pilon_pilon_pilon_pilon_pilon 2596 55.86 2.21
86d53998-8e37-496e-849a-47b39de7025c_utg000001c_pilon_pilon_pilon_pilon_pilon 1440 40.42 -3.09
73dc658b-2172-433b-873a-e2fc7fcf876b_utg000001l_pilon_pilon_pilon_pilon_pilon 1845 60.11 1.71
d8261810-2e07-4546-8cb0-722d9b2f53bf_utg000001c_pilon_pilon_pilon_pilon_pilon 1064 68.61 3.84
5c3d0fe6-b48a-4f62-962b-a32b40e6aef2_utg000001c_pilon_pilon_pilon_pilon_pilon 1643 36.82 4.79
8d402ee4-324e-4bcd-8f10-2ce69d621885_utg000001c_pilon_pilon_pilon_pilon_pilon 1501 42.04 4.60

but the output.plasmer.length.unclass.fasta and many other files are empty.
I also installed with conda to run it and got the same outputs.
Below is the screen output.

Usage: Plasmer -h|--help -g|--genome -v|--version -p|--prefix -d|--db -t|--threads -m|minimum_length -l|--length -o|--outpath
Checking sequence length...
Generating k-mer features...
Kmer-db version 1.11.1 (07.03.2023)
S. Deorowicz, A. Gudys, M. Dlugosz, M. Kokot, and A. Danek (c) 2018

Analysis started at Wed May 22 05:09:59 2024

Set of new samples (from fasta genomes) versus entire database comparison
Loading k-mer database /db/plsdb_minus_ncbi_representative.k25.kmer-db...
Loading k-mer hashtables (raw)...
(plasmer) [tianrm@Sabalan 4]$ docker logs -f 94f7e21894141e3c66524f6f903f91c08f484c68d9008e89cd0bbf3f9a512257
Usage: Plasmer -h|--help -g|--genome -v|--version -p|--prefix -d|--db -t|--threads -m|minimum_length -l|--length -o|--outpath
Checking sequence length...
Generating k-mer features...
Kmer-db version 1.11.1 (07.03.2023)
S. Deorowicz, A. Gudys, M. Dlugosz, M. Kokot, and A. Danek (c) 2018

Analysis started at Wed May 22 05:09:59 2024

Set of new samples (from fasta genomes) versus entire database comparison
Loading k-mer database /db/plsdb_minus_ncbi_representative.k25.kmer-db...
Loading k-mer hashtables (raw)...
262144/262144 hashtables loaded in 20.4286 s
Loading patterns...
2/2 patterns loaded in 1.105e-05 s
OK (21.1952 seconds)
Number of samples: 1
Number of patterns: 2 (0 B)
Number of k-mers: 967,521,022
K-mer length: 25
Minhash fraction: 1
Workers count: 8

Processing queries...
failed:/output/plasmidome_1k-3k/intermediate/output.plasmer.length.unclass.fasta

EXECUTION TIMES
Total: 0.00104653

Analysis finished at Wed May 22 05:10:22 2024

Kmer-db version 1.11.1 (07.03.2023)
S. Deorowicz, A. Gudys, M. Dlugosz, M. Kokot, and A. Danek (c) 2018

Analysis started at Wed May 22 05:10:23 2024

Set of new samples (from fasta genomes) versus entire database comparison
Loading k-mer database /db/plsdb.k25.kmer-db...
Loading k-mer hashtables (raw)...
262144/262144 hashtables loaded in 21.8257 s
Loading patterns...
2/2 patterns loaded in 3.69e-06 s
OK (22.6056 seconds)
Number of samples: 1
Number of patterns: 2 (0 B)
Number of k-mers: 1,033,690,553
K-mer length: 25
Minhash fraction: 1
Workers count: 8

Processing queries...
failed:/output/plasmidome_1k-3k/intermediate/output.plasmer.length.unclass.fasta

EXECUTION TIMES
Total: 0.00139297

Analysis finished at Wed May 22 05:10:47 2024

Kmer-db version 1.11.1 (07.03.2023)
S. Deorowicz, A. Gudys, M. Dlugosz, M. Kokot, and A. Danek (c) 2018

Analysis started at Wed May 22 05:10:48 2024

Set of new samples (from fasta genomes) versus entire database comparison
Loading k-mer database /db/ncbi_representative_minus_plsdb.k18.f0.1.kmer-db...
Loading k-mer hashtables (raw)...
256/256 hashtables loaded in 9.69607 s
Loading patterns...
2/2 patterns loaded in 5.93e-06 s
OK (10.4482 seconds)
Number of samples: 1
Number of patterns: 2 (0 B)
Number of k-mers: 615,903,503
K-mer length: 18
Minhash fraction: 0.1
Workers count: 8

Processing queries...
failed:/output/plasmidome_1k-3k/intermediate/output.plasmer.length.unclass.fasta

EXECUTION TIMES
Total: 0.00145148

Analysis finished at Wed May 22 05:11:00 2024

Kmer-db version 1.11.1 (07.03.2023)
S. Deorowicz, A. Gudys, M. Dlugosz, M. Kokot, and A. Danek (c) 2018

Analysis started at Wed May 22 05:11:00 2024

Set of new samples (from fasta genomes) versus entire database comparison
Loading k-mer database /db/ncbi_representative.k18.f0.1.kmer-db...
Loading k-mer hashtables (raw)...
256/256 hashtables loaded in 10.3467 s
Loading patterns...
2/2 patterns loaded in 7.24e-06 s
OK (11.0935 seconds)
Number of samples: 1
Number of patterns: 2 (0 B)
Number of k-mers: 660,014,131
K-mer length: 18
Minhash fraction: 0.1
Workers count: 8

Processing queries...
failed:/output/plasmidome_1k-3k/intermediate/output.plasmer.length.unclass.fasta

EXECUTION TIMES
Total: 0.00122173

Analysis finished at Wed May 22 05:11:12 2024

Predicting gene with Prodigal...

PRODIGAL v2.6.3 [February, 2016]
Univ of Tenn / Oak Ridge National Lab
Doug Hyatt, Loren Hauser, et al.

Request: Metagenomic, Phase: Training
Initializing training files...done!

Request: Metagenomic, Phase: Gene Finding

Error: no input sequences to analyze.

Searching with BLASTN...
Warning: [blastn] Examining 5 or more matches is recommended
Warning: [blastn] Query is Empty!
Searching with DIAMOND...
diamond v2.0.8.146 (C) Max Planck Society for the Advancement of Science
Documentation, support and updates available at http://www.diamondsearch.org

#CPU threads: 8
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)
Temporary directory: /output/plasmidome_1k-3k/intermediate
#Target sequences to report alignments for: 1
Opening the database... [0.11s]
Database: /db/platon_db/mps.dmnd (type: Diamond database, sequences: 4847438, letters: 1549533412)
Block size = 2000000000
Opening the input file... [0s]
Error: Error detecting input file format. First line seems to be blank.
Searching with hmmsearch...

Error: Sequence file /output/plasmidome_1k-3k/intermediate/output.aa is empty or misformatted

Error: Sequence file /output/plasmidome_1k-3k/intermediate/output.aa is empty or misformatted

Error: Sequence file /output/plasmidome_1k-3k/intermediate/output.aa is empty or misformatted

Error: Sequence file /output/plasmidome_1k-3k/intermediate/output.aa is empty or misformatted

Error: Sequence file /output/plasmidome_1k-3k/intermediate/output.plasmer.length.unclass.fasta is empty or misformatted

Generating genomic features...
Merging features...
Error in read.table(chromosomek18, sep = "\t") :
no lines available in input
Execution halted
Predicting...
randomForest 4.7-1.1
Type rfNews() to see new features/changes/bug fixes.
Error in file(file, "rt") : cannot open the connection
Calls: read.table -> file
In addition: Warning message:
In file(file, "rt") :
cannot open file '/output/plasmidome_1k-3k/intermediate/output.allFeatures': No such file or directory
Execution halted
cat: /output/plasmidome_1k-3k/intermediate/output.allFeatures.plasmer.predClass.tsv: No such file or directory
mv: cannot stat '/output/plasmidome_1k-3k/intermediate/output.allFeatures.plasmer.predProb.tsv': No such file or directory
Predicting finished!
See your result in /output/plasmidome_1k-3k/results/
Classifying taxonomy...
Loading database information... done.
0 sequences (0.00 Mbp) processed in 0.002s (0.0 Kseq/m, 0.00 Mbp/m).
0 sequences classified (-nan%)
0 sequences unclassified (-nan%)
cut: /output/plasmidome_1k-3k/intermediate/output.plasmer.predPlasmids.k2.out: No such file or directory
Plasmid taxonomy finished!
See your result in /output/plasmidome_1k-3k/results/

[tianrenmaogithub]

We are using Fedora OS and AMD EPYC 7551 32-Core Processor.