[2024-01-24 12:07:18,919] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:07:18,922] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:07:18,922] [INFO] DQC Reference Directory: /var/lib/cwl/stgbe860d3c-e095-4eaf-8a44-db1655e7bff8/dqc_reference
[2024-01-24 12:07:20,174] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:07:20,175] [INFO] Task started: Prodigal
[2024-01-24 12:07:20,175] [INFO] Running command: gunzip -c /var/lib/cwl/stg90ec0da8-14cc-4afc-9017-01643a5f6cd1/GCF_002849605.1_ASM284960v1_genomic.fna.gz | prodigal -d GCF_002849605.1_ASM284960v1_genomic.fna/cds.fna -a GCF_002849605.1_ASM284960v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:07:29,111] [INFO] Task succeeded: Prodigal
[2024-01-24 12:07:29,112] [INFO] Task started: HMMsearch
[2024-01-24 12:07:29,112] [INFO] Running command: hmmsearch --tblout GCF_002849605.1_ASM284960v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbe860d3c-e095-4eaf-8a44-db1655e7bff8/dqc_reference/reference_markers.hmm GCF_002849605.1_ASM284960v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:07:29,403] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:07:29,405] [INFO] Found 6/6 markers.
[2024-01-24 12:07:29,444] [INFO] Query marker FASTA was written to GCF_002849605.1_ASM284960v1_genomic.fna/markers.fasta
[2024-01-24 12:07:29,445] [INFO] Task started: Blastn
[2024-01-24 12:07:29,445] [INFO] Running command: blastn -query GCF_002849605.1_ASM284960v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe860d3c-e095-4eaf-8a44-db1655e7bff8/dqc_reference/reference_markers.fasta -out GCF_002849605.1_ASM284960v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:30,187] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:30,191] [INFO] Selected 12 target genomes.
[2024-01-24 12:07:30,192] [INFO] Target genome list was writen to GCF_002849605.1_ASM284960v1_genomic.fna/target_genomes.txt
[2024-01-24 12:07:30,200] [INFO] Task started: fastANI
[2024-01-24 12:07:30,200] [INFO] Running command: fastANI --query /var/lib/cwl/stg90ec0da8-14cc-4afc-9017-01643a5f6cd1/GCF_002849605.1_ASM284960v1_genomic.fna.gz --refList GCF_002849605.1_ASM284960v1_genomic.fna/target_genomes.txt --output GCF_002849605.1_ASM284960v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:41,785] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:41,786] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbe860d3c-e095-4eaf-8a44-db1655e7bff8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:41,787] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbe860d3c-e095-4eaf-8a44-db1655e7bff8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:41,804] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:07:41,804] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:07:41,804] [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
Photobacterium carnosum	strain=TMW 2.2021	GCA_002849605.1	2023717	2023717	type	True	100.0	1474	1479	95	conclusive
Photobacterium iliopiscarium	strain=ATCC 51760	GCA_003026395.1	56192	56192	type	True	92.8965	1157	1479	95	below_threshold
Photobacterium iliopiscarium	strain=ATCC 51760	GCA_000950265.1	56192	56192	type	True	92.8359	1150	1479	95	below_threshold
Photobacterium piscicola	strain=type strain: NCCB 100098	GCA_900166965.1	1378299	1378299	type	True	89.1122	1152	1479	95	below_threshold
Photobacterium toruni	strain=CECT 9189	GCA_900166975.1	1935446	1935446	type	True	88.0057	1100	1479	95	below_threshold
Photobacterium toruni	strain=CECT 9189	GCA_024529955.1	1935446	1935446	type	True	87.9137	1132	1479	95	below_threshold
Photobacterium phosphoreum	strain=JCM 21184	GCA_002954725.1	659	659	type	True	87.3287	1107	1479	95	below_threshold
Photobacterium phosphoreum	strain=ATCC 11040	GCA_003026275.1	659	659	type	True	87.3233	1080	1479	95	below_threshold
Photobacterium phosphoreum	strain=ATCC 11040	GCA_000949955.1	659	659	type	True	87.1899	1079	1479	95	below_threshold
Photobacterium sanguinicancri	strain=CECT 7579	GCA_024346675.1	875932	875932	type	True	78.9516	352	1479	95	below_threshold
Vibrio neonatus	strain=JCM 21521	GCA_024346975.1	278860	278860	type	True	78.0235	152	1479	95	below_threshold
Vibrio algicola	strain=SM1977	GCA_009601765.2	2662262	2662262	type	True	77.9463	165	1479	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:41,806] [INFO] DFAST Taxonomy check result was written to GCF_002849605.1_ASM284960v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:41,806] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:41,807] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:41,807] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbe860d3c-e095-4eaf-8a44-db1655e7bff8/dqc_reference/checkm_data
[2024-01-24 12:07:41,808] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:41,853] [INFO] Task started: CheckM
[2024-01-24 12:07:41,854] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002849605.1_ASM284960v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002849605.1_ASM284960v1_genomic.fna/checkm_input GCF_002849605.1_ASM284960v1_genomic.fna/checkm_result
[2024-01-24 12:08:13,472] [INFO] Task succeeded: CheckM
[2024-01-24 12:08:13,474] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:08:13,500] [INFO] ===== Completeness check finished =====
[2024-01-24 12:08:13,500] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:08:13,501] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002849605.1_ASM284960v1_genomic.fna/markers.fasta)
[2024-01-24 12:08:13,501] [INFO] Task started: Blastn
[2024-01-24 12:08:13,501] [INFO] Running command: blastn -query GCF_002849605.1_ASM284960v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe860d3c-e095-4eaf-8a44-db1655e7bff8/dqc_reference/reference_markers_gtdb.fasta -out GCF_002849605.1_ASM284960v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:08:14,450] [INFO] Task succeeded: Blastn
[2024-01-24 12:08:14,454] [INFO] Selected 7 target genomes.
[2024-01-24 12:08:14,454] [INFO] Target genome list was writen to GCF_002849605.1_ASM284960v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:08:14,459] [INFO] Task started: fastANI
[2024-01-24 12:08:14,459] [INFO] Running command: fastANI --query /var/lib/cwl/stg90ec0da8-14cc-4afc-9017-01643a5f6cd1/GCF_002849605.1_ASM284960v1_genomic.fna.gz --refList GCF_002849605.1_ASM284960v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002849605.1_ASM284960v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:23,185] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:23,195] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:08:23,195] [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_002849605.1	s__Photobacterium carnosum	100.0	1474	1479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	98.77	98.77	0.93	0.93	2	conclusive
GCF_003026395.1	s__Photobacterium iliopiscarium	92.9125	1156	1479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	99.31	98.95	0.95	0.91	7	-
GCF_900166965.1	s__Photobacterium piscicola	89.1117	1152	1479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	98.92	98.92	0.94	0.94	2	-
GCF_900166975.1	s__Photobacterium toruni	87.9938	1101	1479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954725.1	s__Photobacterium phosphoreum	87.3279	1107	1479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	98.41	96.65	0.93	0.88	23	-
GCF_002954455.1	s__Photobacterium aquimaris	85.6038	1063	1479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	98.51	95.34	0.95	0.87	6	-
GCF_003026355.1	s__Photobacterium kishitanii	85.4796	1052	1479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	98.67	97.61	0.95	0.91	24	-
--------------------------------------------------------------------------------
[2024-01-24 12:08:23,197] [INFO] GTDB search result was written to GCF_002849605.1_ASM284960v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:23,198] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:23,201] [INFO] DFAST_QC result json was written to GCF_002849605.1_ASM284960v1_genomic.fna/dqc_result.json
[2024-01-24 12:08:23,201] [INFO] DFAST_QC completed!
[2024-01-24 12:08:23,201] [INFO] Total running time: 0h1m4s