[2023-06-29 19:25:01,741] [INFO] DFAST_QC pipeline started.
[2023-06-29 19:25:01,743] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 19:25:01,743] [INFO] DQC Reference Directory: /var/lib/cwl/stgdd10e979-f6d1-4096-80cb-3a4840b7e7ac/dqc_reference
[2023-06-29 19:25:04,254] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 19:25:04,257] [INFO] Task started: Prodigal
[2023-06-29 19:25:04,258] [INFO] Running command: gunzip -c /var/lib/cwl/stge642caf3-424a-42d5-b207-2e59136d1a44/GCA_937967255.1_SRR6231210_bin.11_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937967255.1_SRR6231210_bin.11_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937967255.1_SRR6231210_bin.11_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 19:25:16,981] [INFO] Task succeeded: Prodigal
[2023-06-29 19:25:16,981] [INFO] Task started: HMMsearch
[2023-06-29 19:25:16,981] [INFO] Running command: hmmsearch --tblout GCA_937967255.1_SRR6231210_bin.11_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdd10e979-f6d1-4096-80cb-3a4840b7e7ac/dqc_reference/reference_markers.hmm GCA_937967255.1_SRR6231210_bin.11_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 19:25:17,304] [INFO] Task succeeded: HMMsearch
[2023-06-29 19:25:17,305] [INFO] Found 6/6 markers.
[2023-06-29 19:25:17,341] [INFO] Query marker FASTA was written to GCA_937967255.1_SRR6231210_bin.11_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-29 19:25:17,342] [INFO] Task started: Blastn
[2023-06-29 19:25:17,342] [INFO] Running command: blastn -query GCA_937967255.1_SRR6231210_bin.11_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd10e979-f6d1-4096-80cb-3a4840b7e7ac/dqc_reference/reference_markers.fasta -out GCA_937967255.1_SRR6231210_bin.11_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:25:18,017] [INFO] Task succeeded: Blastn
[2023-06-29 19:25:18,022] [INFO] Selected 29 target genomes.
[2023-06-29 19:25:18,022] [INFO] Target genome list was writen to GCA_937967255.1_SRR6231210_bin.11_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-29 19:25:18,023] [INFO] Task started: fastANI
[2023-06-29 19:25:18,023] [INFO] Running command: fastANI --query /var/lib/cwl/stge642caf3-424a-42d5-b207-2e59136d1a44/GCA_937967255.1_SRR6231210_bin.11_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937967255.1_SRR6231210_bin.11_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937967255.1_SRR6231210_bin.11_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 19:25:41,643] [INFO] Task succeeded: fastANI
[2023-06-29 19:25:41,643] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdd10e979-f6d1-4096-80cb-3a4840b7e7ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 19:25:41,644] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdd10e979-f6d1-4096-80cb-3a4840b7e7ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 19:25:41,652] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 19:25:41,652] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 19:25:41,652] [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
Sediminibacterium salmoneum	strain=NBRC 103935	GCA_000511175.1	426421	426421	type	True	79.7379	484	904	95	below_threshold
Sediminibacterium goheungense	strain=DSM 28323	GCA_004361915.1	1086393	1086393	type	True	76.8479	122	904	95	below_threshold
Sediminibacterium ginsengisoli	strain=DSM 22335	GCA_900167075.1	413434	413434	type	True	76.5882	59	904	95	below_threshold
Limnovirga soli	strain=KCS-6	GCA_013106755.1	2656915	2656915	type	True	76.5106	71	904	95	below_threshold
Hydrotalea flava	strain=CCUG 51397	GCA_001623405.1	714549	714549	suspected-type	True	76.2917	77	904	95	below_threshold
Hydrotalea sandarakina	strain=DSM 23241	GCA_003254115.1	1004304	1004304	type	True	76.1294	85	904	95	below_threshold
Hydrotalea lipotrueae	strain=TMF_100	GCA_019249625.1	2803817	2803817	type	True	76.0637	80	904	95	below_threshold
Lacibacter cauensis	strain=CGMCC 1.7271	GCA_007830055.1	510947	510947	type	True	75.9226	51	904	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 19:25:41,655] [INFO] DFAST Taxonomy check result was written to GCA_937967255.1_SRR6231210_bin.11_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-29 19:25:41,655] [INFO] ===== Taxonomy check completed =====
[2023-06-29 19:25:41,655] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 19:25:41,657] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdd10e979-f6d1-4096-80cb-3a4840b7e7ac/dqc_reference/checkm_data
[2023-06-29 19:25:41,658] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 19:25:41,691] [INFO] Task started: CheckM
[2023-06-29 19:25:41,691] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937967255.1_SRR6231210_bin.11_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937967255.1_SRR6231210_bin.11_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937967255.1_SRR6231210_bin.11_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-29 19:26:21,430] [INFO] Task succeeded: CheckM
[2023-06-29 19:26:21,431] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 6.25%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-29 19:26:21,459] [INFO] ===== Completeness check finished =====
[2023-06-29 19:26:21,460] [INFO] ===== Start GTDB Search =====
[2023-06-29 19:26:21,460] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937967255.1_SRR6231210_bin.11_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-29 19:26:21,460] [INFO] Task started: Blastn
[2023-06-29 19:26:21,461] [INFO] Running command: blastn -query GCA_937967255.1_SRR6231210_bin.11_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd10e979-f6d1-4096-80cb-3a4840b7e7ac/dqc_reference/reference_markers_gtdb.fasta -out GCA_937967255.1_SRR6231210_bin.11_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:26:22,226] [INFO] Task succeeded: Blastn
[2023-06-29 19:26:22,232] [INFO] Selected 11 target genomes.
[2023-06-29 19:26:22,232] [INFO] Target genome list was writen to GCA_937967255.1_SRR6231210_bin.11_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 19:26:22,233] [INFO] Task started: fastANI
[2023-06-29 19:26:22,234] [INFO] Running command: fastANI --query /var/lib/cwl/stge642caf3-424a-42d5-b207-2e59136d1a44/GCA_937967255.1_SRR6231210_bin.11_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937967255.1_SRR6231210_bin.11_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937967255.1_SRR6231210_bin.11_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 19:26:29,055] [INFO] Task succeeded: fastANI
[2023-06-29 19:26:29,070] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 19:26:29,070] [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_017996795.1	s__Sediminibacterium sp017996795	98.2554	525	904	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001829005.1	s__Sediminibacterium sp001829005	89.9574	786	904	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	98.07	96.16	0.93	0.87	3	-
GCA_002281875.1	s__Sediminibacterium sp002281875	89.6939	744	904	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	99.93	99.91	0.97	0.97	3	-
GCA_002281575.1	s__Sediminibacterium sp002281575	86.3439	733	904	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002786355.1	s__Sediminibacterium sp002786355	84.1378	703	904	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	98.29	98.29	0.87	0.87	2	-
GCF_000508085.1	s__Sediminibacterium sp000508085	79.8627	479	904	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000511175.1	s__Sediminibacterium salmoneum	79.727	485	904	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018335935.1	s__CAIVPM01 sp018335935	78.4606	96	904	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__CAIVPM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018061385.1	s__UBA1930 sp018061385	76.8654	69	904	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__UBA1930	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903927185.1	s__Sediminibacterium sp903927185	76.384	135	904	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	99.80	99.71	0.93	0.90	3	-
GCA_018267705.1	s__CW01 sp018267705	76.289	118	904	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__CW01	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-06-29 19:26:29,072] [INFO] GTDB search result was written to GCA_937967255.1_SRR6231210_bin.11_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 19:26:29,073] [INFO] ===== GTDB Search completed =====
[2023-06-29 19:26:29,076] [INFO] DFAST_QC result json was written to GCA_937967255.1_SRR6231210_bin.11_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-29 19:26:29,076] [INFO] DFAST_QC completed!
[2023-06-29 19:26:29,076] [INFO] Total running time: 0h1m27s