[2024-01-24 13:31:33,449] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:33,451] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:33,452] [INFO] DQC Reference Directory: /var/lib/cwl/stgf0e7fcfd-9f04-4275-b169-76baeeb0a469/dqc_reference
[2024-01-24 13:31:34,847] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:34,848] [INFO] Task started: Prodigal
[2024-01-24 13:31:34,848] [INFO] Running command: gunzip -c /var/lib/cwl/stga8f2ba19-7ab6-482d-9013-3f6c38515866/GCF_003254115.1_ASM325411v1_genomic.fna.gz | prodigal -d GCF_003254115.1_ASM325411v1_genomic.fna/cds.fna -a GCF_003254115.1_ASM325411v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:48,281] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:48,282] [INFO] Task started: HMMsearch
[2024-01-24 13:31:48,282] [INFO] Running command: hmmsearch --tblout GCF_003254115.1_ASM325411v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf0e7fcfd-9f04-4275-b169-76baeeb0a469/dqc_reference/reference_markers.hmm GCF_003254115.1_ASM325411v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:48,570] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:48,572] [INFO] Found 6/6 markers.
[2024-01-24 13:31:48,608] [INFO] Query marker FASTA was written to GCF_003254115.1_ASM325411v1_genomic.fna/markers.fasta
[2024-01-24 13:31:48,609] [INFO] Task started: Blastn
[2024-01-24 13:31:48,609] [INFO] Running command: blastn -query GCF_003254115.1_ASM325411v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0e7fcfd-9f04-4275-b169-76baeeb0a469/dqc_reference/reference_markers.fasta -out GCF_003254115.1_ASM325411v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:49,231] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:49,235] [INFO] Selected 17 target genomes.
[2024-01-24 13:31:49,235] [INFO] Target genome list was writen to GCF_003254115.1_ASM325411v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:49,243] [INFO] Task started: fastANI
[2024-01-24 13:31:49,243] [INFO] Running command: fastANI --query /var/lib/cwl/stga8f2ba19-7ab6-482d-9013-3f6c38515866/GCF_003254115.1_ASM325411v1_genomic.fna.gz --refList GCF_003254115.1_ASM325411v1_genomic.fna/target_genomes.txt --output GCF_003254115.1_ASM325411v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:02,710] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:02,711] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf0e7fcfd-9f04-4275-b169-76baeeb0a469/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:02,711] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf0e7fcfd-9f04-4275-b169-76baeeb0a469/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:02,722] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:02,722] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:02,722] [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
Hydrotalea sandarakina	strain=DSM 23241	GCA_003254115.1	1004304	1004304	type	True	100.0	1072	1075	95	conclusive
Hydrotalea lipotrueae	strain=TMF_100	GCA_019249625.1	2803817	2803817	type	True	79.5982	624	1075	95	below_threshold
Hydrotalea flava	strain=CCUG 51397	GCA_001623405.1	714549	714549	suspected-type	True	79.0885	621	1075	95	below_threshold
Segetibacter koreensis	strain=DSM 18137	GCA_000374045.1	398037	398037	type	True	76.4237	62	1075	95	below_threshold
Foetidibacter luteolus	strain=YG09	GCA_009650435.1	2608880	2608880	type	True	76.2556	68	1075	95	below_threshold
Ferruginibacter albus	strain=KIS38-8	GCA_020042285.1	2875540	2875540	type	True	76.2488	58	1075	95	below_threshold
Parafilimonas terrae	strain=DSM 28286	GCA_900115755.1	1465490	1465490	type	True	76.2362	73	1075	95	below_threshold
Lacibacter cauensis	strain=CGMCC 1.7271	GCA_007830055.1	510947	510947	type	True	76.062	59	1075	95	below_threshold
Sediminibacterium salmoneum	strain=NBRC 103935	GCA_000511175.1	426421	426421	type	True	76.0562	73	1075	95	below_threshold
Lacibacter luteus	strain=TTM-7	GCA_004118265.1	2508719	2508719	type	True	75.8812	64	1075	95	below_threshold
Limnovirga soli	strain=KCS-6	GCA_013106755.1	2656915	2656915	type	True	75.8809	104	1075	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:02,724] [INFO] DFAST Taxonomy check result was written to GCF_003254115.1_ASM325411v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:02,724] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:02,725] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:02,725] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf0e7fcfd-9f04-4275-b169-76baeeb0a469/dqc_reference/checkm_data
[2024-01-24 13:32:02,726] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:02,765] [INFO] Task started: CheckM
[2024-01-24 13:32:02,765] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003254115.1_ASM325411v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003254115.1_ASM325411v1_genomic.fna/checkm_input GCF_003254115.1_ASM325411v1_genomic.fna/checkm_result
[2024-01-24 13:32:45,061] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:45,062] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:45,080] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:45,080] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:45,080] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003254115.1_ASM325411v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:45,081] [INFO] Task started: Blastn
[2024-01-24 13:32:45,081] [INFO] Running command: blastn -query GCF_003254115.1_ASM325411v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0e7fcfd-9f04-4275-b169-76baeeb0a469/dqc_reference/reference_markers_gtdb.fasta -out GCF_003254115.1_ASM325411v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:45,937] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:45,940] [INFO] Selected 12 target genomes.
[2024-01-24 13:32:45,941] [INFO] Target genome list was writen to GCF_003254115.1_ASM325411v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:45,951] [INFO] Task started: fastANI
[2024-01-24 13:32:45,952] [INFO] Running command: fastANI --query /var/lib/cwl/stga8f2ba19-7ab6-482d-9013-3f6c38515866/GCF_003254115.1_ASM325411v1_genomic.fna.gz --refList GCF_003254115.1_ASM325411v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003254115.1_ASM325411v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:32:55,172] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:55,184] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:32:55,185] [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_003254115.1	s__Hydrotalea sandarakina	100.0	1072	1075	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Hydrotalea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_011362875.1	s__Hydrotalea flava_A	94.5204	922	1075	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Hydrotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001623405.1	s__Hydrotalea flava	79.1028	619	1075	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Hydrotalea	95.0	95.88	95.18	0.90	0.86	13	-
GCA_004028795.1	s__CW01 sp004028795	76.6425	166	1075	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__CW01	95.0	99.97	99.97	0.97	0.97	2	-
GCA_018267705.1	s__CW01 sp018267705	76.5084	188	1075	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__CW01	95.0	99.99	99.99	0.99	0.99	2	-
GCA_903870685.1	s__CAILAF01 sp903870685	76.4533	152	1075	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__CAILAF01	95.0	99.70	99.46	0.92	0.91	5	-
GCA_903881425.1	s__CAILAF01 sp903881425	76.4006	161	1075	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__CAILAF01	95.0	99.80	99.80	0.95	0.95	2	-
GCA_017304675.1	s__CW01 sp017304675	76.1921	126	1075	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__CW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018061385.1	s__UBA1930 sp018061385	75.9002	98	1075	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__UBA1930	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002337145.1	s__UBA1930 sp002337145	75.8753	66	1075	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__UBA1930	95.0	99.95	99.95	0.99	0.99	2	-
GCA_903832075.1	s__CAILAF01 sp903832075	75.794	137	1075	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__CAILAF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903927185.1	s__Sediminibacterium sp903927185	75.6846	74	1075	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	99.80	99.71	0.93	0.90	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:32:55,193] [INFO] GTDB search result was written to GCF_003254115.1_ASM325411v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:32:55,194] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:32:55,199] [INFO] DFAST_QC result json was written to GCF_003254115.1_ASM325411v1_genomic.fna/dqc_result.json
[2024-01-24 13:32:55,200] [INFO] DFAST_QC completed!
[2024-01-24 13:32:55,200] [INFO] Total running time: 0h1m22s