[2023-06-28 06:39:54,156] [INFO] DFAST_QC pipeline started.
[2023-06-28 06:39:54,159] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 06:39:54,159] [INFO] DQC Reference Directory: /var/lib/cwl/stg04830ac0-1ac3-4a71-a8b5-62c1f05c474c/dqc_reference
[2023-06-28 06:39:55,410] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 06:39:55,411] [INFO] Task started: Prodigal
[2023-06-28 06:39:55,411] [INFO] Running command: gunzip -c /var/lib/cwl/stg965e3273-de36-4d96-b1b5-95be5d20b010/GCA_913054305.1_SRR5268667_bin.44_MetaBAT_v2.12.1_MAG_genomic.fna.gz | prodigal -d GCA_913054305.1_SRR5268667_bin.44_MetaBAT_v2.12.1_MAG_genomic.fna/cds.fna -a GCA_913054305.1_SRR5268667_bin.44_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 06:40:03,454] [INFO] Task succeeded: Prodigal
[2023-06-28 06:40:03,455] [INFO] Task started: HMMsearch
[2023-06-28 06:40:03,455] [INFO] Running command: hmmsearch --tblout GCA_913054305.1_SRR5268667_bin.44_MetaBAT_v2.12.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg04830ac0-1ac3-4a71-a8b5-62c1f05c474c/dqc_reference/reference_markers.hmm GCA_913054305.1_SRR5268667_bin.44_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-28 06:40:03,705] [INFO] Task succeeded: HMMsearch
[2023-06-28 06:40:03,707] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg965e3273-de36-4d96-b1b5-95be5d20b010/GCA_913054305.1_SRR5268667_bin.44_MetaBAT_v2.12.1_MAG_genomic.fna.gz]
[2023-06-28 06:40:03,736] [INFO] Query marker FASTA was written to GCA_913054305.1_SRR5268667_bin.44_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta
[2023-06-28 06:40:03,737] [INFO] Task started: Blastn
[2023-06-28 06:40:03,737] [INFO] Running command: blastn -query GCA_913054305.1_SRR5268667_bin.44_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg04830ac0-1ac3-4a71-a8b5-62c1f05c474c/dqc_reference/reference_markers.fasta -out GCA_913054305.1_SRR5268667_bin.44_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 06:40:04,323] [INFO] Task succeeded: Blastn
[2023-06-28 06:40:04,327] [INFO] Selected 25 target genomes.
[2023-06-28 06:40:04,327] [INFO] Target genome list was writen to GCA_913054305.1_SRR5268667_bin.44_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt
[2023-06-28 06:40:04,328] [INFO] Task started: fastANI
[2023-06-28 06:40:04,328] [INFO] Running command: fastANI --query /var/lib/cwl/stg965e3273-de36-4d96-b1b5-95be5d20b010/GCA_913054305.1_SRR5268667_bin.44_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913054305.1_SRR5268667_bin.44_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt --output GCA_913054305.1_SRR5268667_bin.44_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 06:40:21,828] [INFO] Task succeeded: fastANI
[2023-06-28 06:40:21,829] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg04830ac0-1ac3-4a71-a8b5-62c1f05c474c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 06:40:21,829] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg04830ac0-1ac3-4a71-a8b5-62c1f05c474c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 06:40:21,849] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 06:40:21,849] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 06:40:21,849] [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
Olleya aquimaris	strain=DSM 24464	GCA_003259525.1	639310	639310	type	True	76.9757	97	731	95	below_threshold
Winogradskyella wandonensis	strain=CECT 8445	GCA_004346845.1	1442586	1442586	type	True	76.8582	75	731	95	below_threshold
Bizionia algoritergicola	strain=APA-1	GCA_008086165.1	291187	291187	type	True	76.8099	100	731	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	76.7361	106	731	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	76.7082	94	731	95	below_threshold
Oceanihabitans sediminis	strain=S9-10	GCA_003337215.1	1812012	1812012	type	True	76.6731	96	731	95	below_threshold
Confluentibacter sediminis	strain=DSL-48	GCA_003258355.1	2219045	2219045	type	True	76.6597	92	731	95	below_threshold
Algibacter mikhailovii	strain=KCTC 12710	GCA_014651495.1	425498	425498	type	True	76.6269	104	731	95	below_threshold
Winogradskyella jejuensis	strain=DSM 25330	GCA_900129745.1	1089305	1089305	type	True	76.6161	89	731	95	below_threshold
Hyunsoonleella pacifica	strain=SW033	GCA_004310335.1	1080224	1080224	type	True	76.6161	100	731	95	below_threshold
Mangrovimonas spongiae	strain=HN-E26	GCA_003944795.1	2494697	2494697	type	True	76.6005	86	731	95	below_threshold
Winogradskyella marina	strain=F6397	GCA_015645385.1	2785530	2785530	type	True	76.5998	88	731	95	below_threshold
Winogradskyella helgolandensis	strain=Z963	GCA_013404085.1	2697010	2697010	type	True	76.5886	93	731	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	76.5398	105	731	95	below_threshold
Bizionia echini	strain=DSM 23925	GCA_900115185.1	649333	649333	type	True	76.5233	103	731	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	76.5201	119	731	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	76.5103	95	731	95	below_threshold
Bizionia myxarmorum	strain=ADA-4	GCA_008086205.1	291186	291186	type	True	76.5094	84	731	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	76.5077	84	731	95	below_threshold
Yeosuana marina	strain=JLT21	GCA_011762485.1	1565536	1565536	type	True	76.4439	130	731	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	76.423	112	731	95	below_threshold
Mesoflavibacter profundi	strain=YC1039	GCA_014764305.1	2708110	2708110	type	True	76.4125	113	731	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	76.4109	114	731	95	below_threshold
Flavobacterium oreochromis	strain=Costa Rica 04-02-TN	GCA_019565455.1	2906078	2906078	type	True	75.7325	51	731	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 06:40:21,852] [INFO] DFAST Taxonomy check result was written to GCA_913054305.1_SRR5268667_bin.44_MetaBAT_v2.12.1_MAG_genomic.fna/tc_result.tsv
[2023-06-28 06:40:21,852] [INFO] ===== Taxonomy check completed =====
[2023-06-28 06:40:21,852] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 06:40:21,853] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg04830ac0-1ac3-4a71-a8b5-62c1f05c474c/dqc_reference/checkm_data
[2023-06-28 06:40:21,854] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 06:40:21,890] [INFO] Task started: CheckM
[2023-06-28 06:40:21,890] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_913054305.1_SRR5268667_bin.44_MetaBAT_v2.12.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_913054305.1_SRR5268667_bin.44_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_input GCA_913054305.1_SRR5268667_bin.44_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_result
[2023-06-28 06:40:51,565] [INFO] Task succeeded: CheckM
[2023-06-28 06:40:51,567] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-06-28 06:40:51,593] [INFO] ===== Completeness check finished =====
[2023-06-28 06:40:51,593] [INFO] ===== Start GTDB Search =====
[2023-06-28 06:40:51,593] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_913054305.1_SRR5268667_bin.44_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta)
[2023-06-28 06:40:51,594] [INFO] Task started: Blastn
[2023-06-28 06:40:51,594] [INFO] Running command: blastn -query GCA_913054305.1_SRR5268667_bin.44_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg04830ac0-1ac3-4a71-a8b5-62c1f05c474c/dqc_reference/reference_markers_gtdb.fasta -out GCA_913054305.1_SRR5268667_bin.44_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 06:40:52,344] [INFO] Task succeeded: Blastn
[2023-06-28 06:40:52,349] [INFO] Selected 20 target genomes.
[2023-06-28 06:40:52,349] [INFO] Target genome list was writen to GCA_913054305.1_SRR5268667_bin.44_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 06:40:52,351] [INFO] Task started: fastANI
[2023-06-28 06:40:52,351] [INFO] Running command: fastANI --query /var/lib/cwl/stg965e3273-de36-4d96-b1b5-95be5d20b010/GCA_913054305.1_SRR5268667_bin.44_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913054305.1_SRR5268667_bin.44_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_913054305.1_SRR5268667_bin.44_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 06:41:03,304] [INFO] Task succeeded: fastANI
[2023-06-28 06:41:03,332] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 06:41:03,332] [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
GCA_905479065.1	s__CAJQLB01 sp905479065	99.1664	685	731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__CAJQLB01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011777505.1	s__CAU-1491 sp011777505	77.2452	168	731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__CAU-1491	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013151975.1	s__PRS1 sp013151975	77.1406	111	731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__PRS1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259525.1	s__Olleya aquimaris	76.9757	97	731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003144015.1	s__Xanthomarina sp003144015	76.9631	114	731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004346845.1	s__Winogradskyella wandonensis	76.8582	75	731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008084905.1	s__Xanthomarina maritima	76.8283	111	731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014526325.1	s__Psychroserpens algicola	76.8007	102	731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001747085.1	s__Algibacter_C aquaticus	76.7859	115	731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610635.1	s__Ichthyenterobacterium magnum	76.7498	140	731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ichthyenterobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003258355.1	s__Confluentibacter sp003258355	76.6597	92	731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Confluentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129745.1	s__Winogradskyella jejuensis	76.6161	89	731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013404085.1	s__Winogradskyella helgolandensis	76.5886	93	731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	98.14	98.14	0.94	0.94	2	-
GCF_003944795.1	s__Mangrovimonas spongiae	76.5778	87	731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mangrovimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002162765.1	s__MAAR01 sp002162765	76.5762	109	731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAAR01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860565.1	s__Winogradskyella psychrotolerans_B	76.5586	106	731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014638915.1	s__Xanthomarina arctica	76.5218	117	731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003387355.1	s__Winogradskyella sediminis	76.5077	84	731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	98.63	98.63	0.93	0.93	2	-
GCA_002682935.1	s__Winogradskyella sp002682935	75.8618	77	731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 06:41:03,335] [INFO] GTDB search result was written to GCA_913054305.1_SRR5268667_bin.44_MetaBAT_v2.12.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-28 06:41:03,335] [INFO] ===== GTDB Search completed =====
[2023-06-28 06:41:03,341] [INFO] DFAST_QC result json was written to GCA_913054305.1_SRR5268667_bin.44_MetaBAT_v2.12.1_MAG_genomic.fna/dqc_result.json
[2023-06-28 06:41:03,341] [INFO] DFAST_QC completed!
[2023-06-28 06:41:03,341] [INFO] Total running time: 0h1m9s