[2024-01-24 14:46:50,920] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:50,922] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:50,922] [INFO] DQC Reference Directory: /var/lib/cwl/stgb0a4266c-59c2-4c82-8b80-01dd0036d7a6/dqc_reference
[2024-01-24 14:46:55,365] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:55,366] [INFO] Task started: Prodigal
[2024-01-24 14:46:55,367] [INFO] Running command: gunzip -c /var/lib/cwl/stg306fc7e9-5ec4-4e85-b859-a60ab911703a/GCF_009910675.1_ASM991067v1_genomic.fna.gz | prodigal -d GCF_009910675.1_ASM991067v1_genomic.fna/cds.fna -a GCF_009910675.1_ASM991067v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:12,435] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:12,435] [INFO] Task started: HMMsearch
[2024-01-24 14:47:12,435] [INFO] Running command: hmmsearch --tblout GCF_009910675.1_ASM991067v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb0a4266c-59c2-4c82-8b80-01dd0036d7a6/dqc_reference/reference_markers.hmm GCF_009910675.1_ASM991067v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:12,941] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:12,943] [INFO] Found 6/6 markers.
[2024-01-24 14:47:13,015] [INFO] Query marker FASTA was written to GCF_009910675.1_ASM991067v1_genomic.fna/markers.fasta
[2024-01-24 14:47:13,016] [INFO] Task started: Blastn
[2024-01-24 14:47:13,016] [INFO] Running command: blastn -query GCF_009910675.1_ASM991067v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0a4266c-59c2-4c82-8b80-01dd0036d7a6/dqc_reference/reference_markers.fasta -out GCF_009910675.1_ASM991067v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:13,966] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:13,970] [INFO] Selected 17 target genomes.
[2024-01-24 14:47:13,970] [INFO] Target genome list was writen to GCF_009910675.1_ASM991067v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:13,981] [INFO] Task started: fastANI
[2024-01-24 14:47:13,982] [INFO] Running command: fastANI --query /var/lib/cwl/stg306fc7e9-5ec4-4e85-b859-a60ab911703a/GCF_009910675.1_ASM991067v1_genomic.fna.gz --refList GCF_009910675.1_ASM991067v1_genomic.fna/target_genomes.txt --output GCF_009910675.1_ASM991067v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:33,368] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:33,368] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb0a4266c-59c2-4c82-8b80-01dd0036d7a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:33,369] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb0a4266c-59c2-4c82-8b80-01dd0036d7a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:33,387] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:47:33,388] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:33,388] [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 alginatilyticum	strain=P03D4	GCA_009910675.1	1775171	1775171	type	True	100.0	2051	2059	95	conclusive
Photobacterium proteolyticum	strain=13-12	GCA_001939735.1	1903952	1903952	type	True	93.7322	1772	2059	95	below_threshold
Photobacterium chitinilyticum	strain=BEI247	GCA_004104355.1	2485123	2485123	type	True	83.6897	1370	2059	95	below_threshold
Photobacterium marinum	strain=AK15	GCA_000331515.1	1056511	1056511	type	True	80.6421	774	2059	95	below_threshold
Photobacterium sanctipauli	strain=A-394	GCA_000730475.1	1342794	1342794	type	True	80.6277	430	2059	95	below_threshold
Photobacterium sanctipauli	strain=DSM 100436	GCA_003026495.1	1342794	1342794	type	True	80.278	602	2059	95	below_threshold
Photobacterium rosenbergii	strain=DSM 19138	GCA_003026455.1	294936	294936	type	True	79.962	618	2059	95	below_threshold
Photobacterium ganghwense	strain=JCM 12487	GCA_003025595.1	320778	320778	type	True	79.7052	522	2059	95	below_threshold
Photobacterium sanguinicancri	strain=CECT 7579	GCA_024346675.1	875932	875932	type	True	79.6644	418	2059	95	below_threshold
Photobacterium ganghwense	strain=DSM 22954	GCA_001029455.1	320778	320778	type	True	79.5272	524	2059	95	below_threshold
Photobacterium jeanii	strain=DSM 100339	GCA_003025495.1	858640	858640	type	True	79.4465	446	2059	95	below_threshold
Photobacterium aquae	strain=CGMCC 1.12159	GCA_001029445.1	1195763	1195763	type	True	79.4282	515	2059	95	below_threshold
Photobacterium jeanii	strain=R-40508	GCA_001650345.1	858640	858640	type	True	79.3443	451	2059	95	below_threshold
Photobacterium swingsii	strain=CECT 7576	GCA_024346715.1	680026	680026	type	True	79.3115	444	2059	95	below_threshold
Photobacterium galatheae	strain=DSM 100496	GCA_023653475.1	1654360	1654360	type	True	78.5638	330	2059	95	below_threshold
Photobacterium salinisoli	strain=LAM9072	GCA_003614885.1	1616783	1616783	type	True	78.522	343	2059	95	below_threshold
Vibrio pelagius	strain=ATCC 25916	GCA_024347575.1	28169	28169	type	True	78.4794	167	2059	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:33,390] [INFO] DFAST Taxonomy check result was written to GCF_009910675.1_ASM991067v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:33,391] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:33,391] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:33,391] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb0a4266c-59c2-4c82-8b80-01dd0036d7a6/dqc_reference/checkm_data
[2024-01-24 14:47:33,393] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:33,483] [INFO] Task started: CheckM
[2024-01-24 14:47:33,483] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009910675.1_ASM991067v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009910675.1_ASM991067v1_genomic.fna/checkm_input GCF_009910675.1_ASM991067v1_genomic.fna/checkm_result
[2024-01-24 14:48:25,841] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:25,842] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 9.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:25,908] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:25,909] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:25,909] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009910675.1_ASM991067v1_genomic.fna/markers.fasta)
[2024-01-24 14:48:25,910] [INFO] Task started: Blastn
[2024-01-24 14:48:25,910] [INFO] Running command: blastn -query GCF_009910675.1_ASM991067v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0a4266c-59c2-4c82-8b80-01dd0036d7a6/dqc_reference/reference_markers_gtdb.fasta -out GCF_009910675.1_ASM991067v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:27,193] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:27,196] [INFO] Selected 11 target genomes.
[2024-01-24 14:48:27,197] [INFO] Target genome list was writen to GCF_009910675.1_ASM991067v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:27,207] [INFO] Task started: fastANI
[2024-01-24 14:48:27,208] [INFO] Running command: fastANI --query /var/lib/cwl/stg306fc7e9-5ec4-4e85-b859-a60ab911703a/GCF_009910675.1_ASM991067v1_genomic.fna.gz --refList GCF_009910675.1_ASM991067v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009910675.1_ASM991067v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:48:40,818] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:40,833] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:48:40,833] [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_009910675.1	s__Photobacterium alginatilyticum	100.0	2051	2059	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001939735.1	s__Photobacterium proteolyticum	93.7335	1772	2059	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004104355.1	s__Photobacterium chitinilyticum	83.685	1371	2059	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000331515.1	s__Photobacterium marinum	80.6338	777	2059	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	96.66	96.66	0.88	0.88	2	-
GCF_003026495.1	s__Photobacterium sanctipauli	80.2926	603	2059	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000940995.1	s__Photobacterium gaetbulicola	79.9763	648	2059	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	97.90	95.81	0.93	0.87	3	-
GCF_003026455.1	s__Photobacterium rosenbergii	79.9588	619	2059	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	95.32	95.32	0.83	0.83	2	-
GCF_003025595.1	s__Photobacterium ganghwense	79.6915	524	2059	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	99.50	98.82	0.97	0.96	4	-
GCF_001029445.1	s__Photobacterium aquae	79.4318	514	2059	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650345.1	s__Photobacterium jeanii	79.3519	453	2059	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001077885.1	s__Photobacterium swingsii	79.1785	439	2059	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	99.98	99.98	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:48:40,835] [INFO] GTDB search result was written to GCF_009910675.1_ASM991067v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:48:40,836] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:48:40,840] [INFO] DFAST_QC result json was written to GCF_009910675.1_ASM991067v1_genomic.fna/dqc_result.json
[2024-01-24 14:48:40,840] [INFO] DFAST_QC completed!
[2024-01-24 14:48:40,841] [INFO] Total running time: 0h1m50s