[2024-01-25 18:06:20,639] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:06:20,640] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:06:20,640] [INFO] DQC Reference Directory: /var/lib/cwl/stg20d3fe73-0a18-4f62-ad30-0eec33360bff/dqc_reference
[2024-01-25 18:06:21,758] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:06:21,759] [INFO] Task started: Prodigal
[2024-01-25 18:06:21,759] [INFO] Running command: gunzip -c /var/lib/cwl/stg3d8a06cf-d843-4bae-be3f-72df8501f674/GCF_003413745.1_ASM341374v1_genomic.fna.gz | prodigal -d GCF_003413745.1_ASM341374v1_genomic.fna/cds.fna -a GCF_003413745.1_ASM341374v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:06:31,921] [INFO] Task succeeded: Prodigal
[2024-01-25 18:06:31,921] [INFO] Task started: HMMsearch
[2024-01-25 18:06:31,922] [INFO] Running command: hmmsearch --tblout GCF_003413745.1_ASM341374v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg20d3fe73-0a18-4f62-ad30-0eec33360bff/dqc_reference/reference_markers.hmm GCF_003413745.1_ASM341374v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:06:32,155] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:06:32,156] [INFO] Found 6/6 markers.
[2024-01-25 18:06:32,186] [INFO] Query marker FASTA was written to GCF_003413745.1_ASM341374v1_genomic.fna/markers.fasta
[2024-01-25 18:06:32,186] [INFO] Task started: Blastn
[2024-01-25 18:06:32,186] [INFO] Running command: blastn -query GCF_003413745.1_ASM341374v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg20d3fe73-0a18-4f62-ad30-0eec33360bff/dqc_reference/reference_markers.fasta -out GCF_003413745.1_ASM341374v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:06:32,789] [INFO] Task succeeded: Blastn
[2024-01-25 18:06:32,792] [INFO] Selected 22 target genomes.
[2024-01-25 18:06:32,793] [INFO] Target genome list was writen to GCF_003413745.1_ASM341374v1_genomic.fna/target_genomes.txt
[2024-01-25 18:06:32,816] [INFO] Task started: fastANI
[2024-01-25 18:06:32,816] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d8a06cf-d843-4bae-be3f-72df8501f674/GCF_003413745.1_ASM341374v1_genomic.fna.gz --refList GCF_003413745.1_ASM341374v1_genomic.fna/target_genomes.txt --output GCF_003413745.1_ASM341374v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:06:47,275] [INFO] Task succeeded: fastANI
[2024-01-25 18:06:47,275] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg20d3fe73-0a18-4f62-ad30-0eec33360bff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:06:47,275] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg20d3fe73-0a18-4f62-ad30-0eec33360bff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:06:47,288] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:06:47,288] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:06:47,288] [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
Marixanthomonas ophiurae	strain=KMM 3046	GCA_003413745.1	387659	387659	type	True	100.0	1098	1098	95	conclusive
Marixanthomonas spongiae	strain=HN-E44	GCA_003095375.1	2174845	2174845	type	True	80.2756	632	1098	95	below_threshold
Altibacter lentus	strain=JLT2010	GCA_000746845.1	1223410	1223410	type	True	77.7754	140	1098	95	below_threshold
Luteirhabdus pelagi	strain=A3-108	GCA_016827595.1	2792783	2792783	type	True	77.7601	169	1098	95	below_threshold
Marinirhabdus gelatinilytica	strain=DSM 101478	GCA_003353425.1	1703343	1703343	type	True	77.4125	172	1098	95	below_threshold
Aequorivita capsosiphonis	strain=DSM 23843	GCA_000429125.1	487317	487317	type	True	77.4085	194	1098	95	below_threshold
Constantimarinum furrinae	strain=ALE3EI	GCA_014295415.1	2562285	2562285	type	True	77.3031	117	1098	95	below_threshold
Cochleicola gelatinilyticus	strain=LPB0005	GCA_001637325.1	1763537	1763537	type	True	77.2471	212	1098	95	below_threshold
Aequorivita sinensis	strain=S1-10	GCA_006346335.1	1382458	1382458	type	True	77.2355	179	1098	95	below_threshold
Ulvibacter litoralis	strain=DSM 16195	GCA_900102055.1	227084	227084	type	True	77.2088	244	1098	95	below_threshold
Ulvibacter litoralis	strain=KCTC 12104	GCA_014651275.1	227084	227084	type	True	77.1931	239	1098	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	77.1669	90	1098	95	below_threshold
Aequorivita soesokkakensis	strain=RSSK-12	GCA_001641085.1	1385699	1385699	type	True	76.7919	196	1098	95	below_threshold
Zobellia barbeyronii	strain=KMM 6746	GCA_018603515.1	2748009	2748009	type	True	76.7064	68	1098	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	76.5931	93	1098	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.5577	106	1098	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	76.4117	98	1098	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	76.404	81	1098	95	below_threshold
Kordia antarctica	strain=IMCC3317	GCA_009901525.1	1218801	1218801	type	True	76.4019	95	1098	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	76.186	93	1098	95	below_threshold
Aquimarina muelleri	strain=DSM 19832	GCA_000430665.1	279356	279356	type	True	76.0923	99	1098	95	below_threshold
Flavobacterium cyclinae	strain=KSM-R2A25	GCA_021172145.1	2895947	2895947	type	True	75.9771	67	1098	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:06:47,290] [INFO] DFAST Taxonomy check result was written to GCF_003413745.1_ASM341374v1_genomic.fna/tc_result.tsv
[2024-01-25 18:06:47,290] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:06:47,290] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:06:47,291] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg20d3fe73-0a18-4f62-ad30-0eec33360bff/dqc_reference/checkm_data
[2024-01-25 18:06:47,291] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:06:47,326] [INFO] Task started: CheckM
[2024-01-25 18:06:47,326] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003413745.1_ASM341374v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003413745.1_ASM341374v1_genomic.fna/checkm_input GCF_003413745.1_ASM341374v1_genomic.fna/checkm_result
[2024-01-25 18:07:20,071] [INFO] Task succeeded: CheckM
[2024-01-25 18:07:20,072] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:07:20,108] [INFO] ===== Completeness check finished =====
[2024-01-25 18:07:20,108] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:07:20,108] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003413745.1_ASM341374v1_genomic.fna/markers.fasta)
[2024-01-25 18:07:20,109] [INFO] Task started: Blastn
[2024-01-25 18:07:20,109] [INFO] Running command: blastn -query GCF_003413745.1_ASM341374v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg20d3fe73-0a18-4f62-ad30-0eec33360bff/dqc_reference/reference_markers_gtdb.fasta -out GCF_003413745.1_ASM341374v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:07:21,025] [INFO] Task succeeded: Blastn
[2024-01-25 18:07:21,028] [INFO] Selected 9 target genomes.
[2024-01-25 18:07:21,028] [INFO] Target genome list was writen to GCF_003413745.1_ASM341374v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:07:21,054] [INFO] Task started: fastANI
[2024-01-25 18:07:21,055] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d8a06cf-d843-4bae-be3f-72df8501f674/GCF_003413745.1_ASM341374v1_genomic.fna.gz --refList GCF_003413745.1_ASM341374v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003413745.1_ASM341374v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:07:26,969] [INFO] Task succeeded: fastANI
[2024-01-25 18:07:26,976] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:07:26,976] [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_003413745.1	s__Marixanthomonas ophiurae	100.0	1098	1098	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002364245.1	s__Marixanthomonas sp002364245	85.1535	502	1098	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002631855.1	s__Marixanthomonas sp002631855	84.8869	806	1098	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002360635.1	s__Marixanthomonas sp002360635	84.3281	790	1098	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	98.57	97.61	0.95	0.92	4	-
GCF_003095375.1	s__Marixanthomonas sp003095375	80.2769	633	1098	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002337605.1	s__Marinirhabdus sp002337605	78.1661	200	1098	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	98.69	98.69	0.95	0.95	2	-
GCF_001637325.1	s__Cochleicola gelatinilyticus	77.245	213	1098	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cochleicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733185.1	s__GCA-002733185 sp002733185	76.6461	139	1098	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014526325.1	s__Psychroserpens algicola	76.4548	110	1098	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:07:26,979] [INFO] GTDB search result was written to GCF_003413745.1_ASM341374v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:07:26,979] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:07:26,982] [INFO] DFAST_QC result json was written to GCF_003413745.1_ASM341374v1_genomic.fna/dqc_result.json
[2024-01-25 18:07:26,982] [INFO] DFAST_QC completed!
[2024-01-25 18:07:26,982] [INFO] Total running time: 0h1m6s