[2024-01-24 12:45:18,810] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:45:18,813] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:45:18,813] [INFO] DQC Reference Directory: /var/lib/cwl/stg4b74ca50-b822-4852-b8a9-70fc318c383a/dqc_reference
[2024-01-24 12:45:20,027] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:45:20,028] [INFO] Task started: Prodigal
[2024-01-24 12:45:20,028] [INFO] Running command: gunzip -c /var/lib/cwl/stg3e884bb9-e066-4309-be6d-5b053a60a41d/GCF_007954355.1_ASM795435v1_genomic.fna.gz | prodigal -d GCF_007954355.1_ASM795435v1_genomic.fna/cds.fna -a GCF_007954355.1_ASM795435v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:28,104] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:28,104] [INFO] Task started: HMMsearch
[2024-01-24 12:45:28,105] [INFO] Running command: hmmsearch --tblout GCF_007954355.1_ASM795435v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4b74ca50-b822-4852-b8a9-70fc318c383a/dqc_reference/reference_markers.hmm GCF_007954355.1_ASM795435v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:28,374] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:28,376] [INFO] Found 6/6 markers.
[2024-01-24 12:45:28,417] [INFO] Query marker FASTA was written to GCF_007954355.1_ASM795435v1_genomic.fna/markers.fasta
[2024-01-24 12:45:28,418] [INFO] Task started: Blastn
[2024-01-24 12:45:28,418] [INFO] Running command: blastn -query GCF_007954355.1_ASM795435v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b74ca50-b822-4852-b8a9-70fc318c383a/dqc_reference/reference_markers.fasta -out GCF_007954355.1_ASM795435v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:29,138] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:29,141] [INFO] Selected 21 target genomes.
[2024-01-24 12:45:29,142] [INFO] Target genome list was writen to GCF_007954355.1_ASM795435v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:29,189] [INFO] Task started: fastANI
[2024-01-24 12:45:29,189] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e884bb9-e066-4309-be6d-5b053a60a41d/GCF_007954355.1_ASM795435v1_genomic.fna.gz --refList GCF_007954355.1_ASM795435v1_genomic.fna/target_genomes.txt --output GCF_007954355.1_ASM795435v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:43,883] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:43,884] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4b74ca50-b822-4852-b8a9-70fc318c383a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:43,884] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4b74ca50-b822-4852-b8a9-70fc318c383a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:43,897] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:45:43,897] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:43,898] [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
Colwellia hornerae	strain=ACAM 607	GCA_007954355.1	89402	89402	type	True	100.0	1415	1421	95	conclusive
Colwellia ponticola	strain=OISW-25	GCA_005885605.1	2304625	2304625	type	True	78.3997	285	1421	95	below_threshold
Colwellia demingiae	strain=ACAM 459	GCA_007954275.1	89401	89401	type	True	78.3471	315	1421	95	below_threshold
Cognaticolwellia mytili	strain=KCTC 52417	GCA_002104475.1	1888913	1888913	type	True	78.3059	327	1421	95	below_threshold
Colwellia piezophila	strain=ATCC BAA-637	GCA_000378625.1	211668	211668	type	True	78.1793	261	1421	95	below_threshold
Colwellia echini	strain=A3	GCA_002843355.2	1982103	1982103	type	True	78.1395	249	1421	95	below_threshold
Litorilituus lipolyticus	strain=RZ04	GCA_006439335.1	2491017	2491017	type	True	78.0571	210	1421	95	below_threshold
Pseudocolwellia agarivorans	strain=QM50	GCA_002000085.1	1911682	1911682	type	True	78.0351	266	1421	95	below_threshold
Litorilituus sediminis	strain=JCM 17549	GCA_004295665.1	718192	718192	type	True	77.8883	225	1421	95	below_threshold
Colwellia chukchiensis	strain=CGMCC 1.9127	GCA_900109795.1	641665	641665	type	True	77.8648	231	1421	95	below_threshold
Colwellia chukchiensis	strain=CGMCC 1.9127	GCA_002104455.1	641665	641665	type	True	77.8333	239	1421	95	below_threshold
Thalassotalea profundi	strain=CGMCC 1.15922	GCA_014653195.1	2036687	2036687	type	True	77.8066	237	1421	95	below_threshold
Thalassomonas viridans	strain=XOM25	GCA_000948985.1	137584	137584	type	True	77.2986	107	1421	95	below_threshold
Thalassotalea algicola	strain=M1531	GCA_012932965.1	2716224	2716224	type	True	77.2304	159	1421	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:43,899] [INFO] DFAST Taxonomy check result was written to GCF_007954355.1_ASM795435v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:43,899] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:43,900] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:43,900] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4b74ca50-b822-4852-b8a9-70fc318c383a/dqc_reference/checkm_data
[2024-01-24 12:45:43,901] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:43,942] [INFO] Task started: CheckM
[2024-01-24 12:45:43,943] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007954355.1_ASM795435v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007954355.1_ASM795435v1_genomic.fna/checkm_input GCF_007954355.1_ASM795435v1_genomic.fna/checkm_result
[2024-01-24 12:46:13,933] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:13,935] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:13,953] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:13,953] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:13,953] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007954355.1_ASM795435v1_genomic.fna/markers.fasta)
[2024-01-24 12:46:13,954] [INFO] Task started: Blastn
[2024-01-24 12:46:13,954] [INFO] Running command: blastn -query GCF_007954355.1_ASM795435v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b74ca50-b822-4852-b8a9-70fc318c383a/dqc_reference/reference_markers_gtdb.fasta -out GCF_007954355.1_ASM795435v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:15,075] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:15,078] [INFO] Selected 8 target genomes.
[2024-01-24 12:46:15,079] [INFO] Target genome list was writen to GCF_007954355.1_ASM795435v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:15,091] [INFO] Task started: fastANI
[2024-01-24 12:46:15,091] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e884bb9-e066-4309-be6d-5b053a60a41d/GCF_007954355.1_ASM795435v1_genomic.fna.gz --refList GCF_007954355.1_ASM795435v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007954355.1_ASM795435v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:22,725] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:22,734] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:22,734] [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_007954355.1	s__Colwellia_A hornerae	100.0	1415	1421	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	100.00	100.00	0.99	0.99	3	conclusive
GCF_001767295.1	s__Colwellia_A sp001767295	90.4716	1187	1421	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	96.63	96.27	0.86	0.85	17	-
GCF_014076845.1	s__Colwellia_A sp014076845	84.1328	953	1421	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	99.15	95.49	0.95	0.86	8	-
GCA_013215295.1	s__Colwellia_A sp013215295	81.6441	812	1421	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215385.1	s__Colwellia_A sp013215385	80.6245	687	1421	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215655.1	s__Colwellia_A sp013215655	78.4923	335	1421	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014077505.1	s__Cognaticolwellia sp014077505	78.4357	380	1421	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002000025.1	s__Cognaticolwellia aestuarii	78.0696	325	1421	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:22,736] [INFO] GTDB search result was written to GCF_007954355.1_ASM795435v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:22,736] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:22,739] [INFO] DFAST_QC result json was written to GCF_007954355.1_ASM795435v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:22,739] [INFO] DFAST_QC completed!
[2024-01-24 12:46:22,739] [INFO] Total running time: 0h1m4s