[2024-01-24 14:11:50,847] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:11:50,855] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:11:50,856] [INFO] DQC Reference Directory: /var/lib/cwl/stgd5ada1b1-a191-43a6-9a8f-8828c2db4f70/dqc_reference
[2024-01-24 14:11:52,374] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:11:52,375] [INFO] Task started: Prodigal
[2024-01-24 14:11:52,375] [INFO] Running command: gunzip -c /var/lib/cwl/stg73773258-5fe5-4e52-9e3c-8e86b647bc22/GCF_002218045.2_ASM221804v2_genomic.fna.gz | prodigal -d GCF_002218045.2_ASM221804v2_genomic.fna/cds.fna -a GCF_002218045.2_ASM221804v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:02,771] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:02,772] [INFO] Task started: HMMsearch
[2024-01-24 14:12:02,772] [INFO] Running command: hmmsearch --tblout GCF_002218045.2_ASM221804v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd5ada1b1-a191-43a6-9a8f-8828c2db4f70/dqc_reference/reference_markers.hmm GCF_002218045.2_ASM221804v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:03,180] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:03,185] [INFO] Found 6/6 markers.
[2024-01-24 14:12:03,223] [INFO] Query marker FASTA was written to GCF_002218045.2_ASM221804v2_genomic.fna/markers.fasta
[2024-01-24 14:12:03,224] [INFO] Task started: Blastn
[2024-01-24 14:12:03,224] [INFO] Running command: blastn -query GCF_002218045.2_ASM221804v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgd5ada1b1-a191-43a6-9a8f-8828c2db4f70/dqc_reference/reference_markers.fasta -out GCF_002218045.2_ASM221804v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:05,092] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:05,099] [INFO] Selected 11 target genomes.
[2024-01-24 14:12:05,099] [INFO] Target genome list was writen to GCF_002218045.2_ASM221804v2_genomic.fna/target_genomes.txt
[2024-01-24 14:12:05,107] [INFO] Task started: fastANI
[2024-01-24 14:12:05,108] [INFO] Running command: fastANI --query /var/lib/cwl/stg73773258-5fe5-4e52-9e3c-8e86b647bc22/GCF_002218045.2_ASM221804v2_genomic.fna.gz --refList GCF_002218045.2_ASM221804v2_genomic.fna/target_genomes.txt --output GCF_002218045.2_ASM221804v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:12:16,236] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:16,236] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd5ada1b1-a191-43a6-9a8f-8828c2db4f70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:12:16,237] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd5ada1b1-a191-43a6-9a8f-8828c2db4f70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:12:16,248] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:12:16,248] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:12:16,248] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Vibrio rumoiensis	strain=FERM P-14531	GCA_002218045.2	76258	76258	type	True	100.0	1399	1400	95	conclusive
Vibrio litoralis	strain=DSM 17657	GCA_000426765.1	335972	335972	type	True	85.348	971	1400	95	below_threshold
Vibrio algivorus	strain=SA2	GCA_002218005.2	1667024	1667024	type	True	84.4214	899	1400	95	below_threshold
Vibrio casei	strain=DSM 22364	GCA_002218025.2	673372	673372	type	True	81.8304	655	1400	95	below_threshold
Vibrio gangliei	strain=SZDIS-1	GCA_002934045.1	2077090	2077090	type	True	81.1299	659	1400	95	below_threshold
Vibrio aphrogenes	strain=CA-1004	GCA_002157735.2	1891186	1891186	type	True	80.9482	609	1400	95	below_threshold
Vibrio algicola	strain=SM1977	GCA_009601765.2	2662262	2662262	type	True	79.9631	481	1400	95	below_threshold
Vibrio chagasii	strain=LMG 21353	GCA_024347355.1	170679	170679	suspected-type	True	79.8329	208	1400	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	79.6768	195	1400	95	below_threshold
Vibrio gallaecicus	strain=CECT 7244	GCA_024347495.1	552386	552386	type	True	79.438	227	1400	95	below_threshold
Vibrio panuliri	strain=LBS 2	GCA_008830195.1	1381081	1381081	type	True	79.0432	191	1400	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:12:16,251] [INFO] DFAST Taxonomy check result was written to GCF_002218045.2_ASM221804v2_genomic.fna/tc_result.tsv
[2024-01-24 14:12:16,252] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:12:16,252] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:12:16,252] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd5ada1b1-a191-43a6-9a8f-8828c2db4f70/dqc_reference/checkm_data
[2024-01-24 14:12:16,253] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:12:16,305] [INFO] Task started: CheckM
[2024-01-24 14:12:16,306] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002218045.2_ASM221804v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002218045.2_ASM221804v2_genomic.fna/checkm_input GCF_002218045.2_ASM221804v2_genomic.fna/checkm_result
[2024-01-24 14:12:54,448] [INFO] Task succeeded: CheckM
[2024-01-24 14:12:54,450] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:12:54,478] [INFO] ===== Completeness check finished =====
[2024-01-24 14:12:54,478] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:12:54,478] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002218045.2_ASM221804v2_genomic.fna/markers.fasta)
[2024-01-24 14:12:54,479] [INFO] Task started: Blastn
[2024-01-24 14:12:54,479] [INFO] Running command: blastn -query GCF_002218045.2_ASM221804v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgd5ada1b1-a191-43a6-9a8f-8828c2db4f70/dqc_reference/reference_markers_gtdb.fasta -out GCF_002218045.2_ASM221804v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:55,721] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:55,724] [INFO] Selected 8 target genomes.
[2024-01-24 14:12:55,725] [INFO] Target genome list was writen to GCF_002218045.2_ASM221804v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:12:55,732] [INFO] Task started: fastANI
[2024-01-24 14:12:55,733] [INFO] Running command: fastANI --query /var/lib/cwl/stg73773258-5fe5-4e52-9e3c-8e86b647bc22/GCF_002218045.2_ASM221804v2_genomic.fna.gz --refList GCF_002218045.2_ASM221804v2_genomic.fna/target_genomes_gtdb.txt --output GCF_002218045.2_ASM221804v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:13:03,760] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:03,773] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:13:03,773] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_002218045.2	s__Vibrio rumoiensis	100.0	1399	1400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000426765.1	s__Vibrio litoralis	85.3436	972	1400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.36	97.06	0.89	0.86	3	-
GCF_002218005.2	s__Vibrio algivorus	84.4138	900	1400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.65	98.65	0.88	0.88	2	-
GCF_002218025.2	s__Vibrio casei	81.8192	658	1400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.63	99.33	0.95	0.89	5	-
GCF_002934045.1	s__Vibrio gangliei	81.1223	659	1400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002157735.2	s__Vibrio aphrogenes	80.9218	611	1400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000286955.2	s__Vibrio rumoiensis_A	80.6282	557	1400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014694375.1	s__Vibrio sp014694375	79.5256	433	1400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:13:03,775] [INFO] GTDB search result was written to GCF_002218045.2_ASM221804v2_genomic.fna/result_gtdb.tsv
[2024-01-24 14:13:03,775] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:13:03,779] [INFO] DFAST_QC result json was written to GCF_002218045.2_ASM221804v2_genomic.fna/dqc_result.json
[2024-01-24 14:13:03,779] [INFO] DFAST_QC completed!
[2024-01-24 14:13:03,779] [INFO] Total running time: 0h1m13s