[2024-01-25 19:36:20,516] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:36:20,517] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:36:20,517] [INFO] DQC Reference Directory: /var/lib/cwl/stg6c2d7368-3926-4aca-9c3d-fe31d48c508b/dqc_reference
[2024-01-25 19:36:21,700] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:36:21,701] [INFO] Task started: Prodigal
[2024-01-25 19:36:21,701] [INFO] Running command: gunzip -c /var/lib/cwl/stg1320c61a-d447-4d3a-b573-fe432afe2ca9/GCF_030409685.1_ASM3040968v1_genomic.fna.gz | prodigal -d GCF_030409685.1_ASM3040968v1_genomic.fna/cds.fna -a GCF_030409685.1_ASM3040968v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:36:48,938] [INFO] Task succeeded: Prodigal
[2024-01-25 19:36:48,939] [INFO] Task started: HMMsearch
[2024-01-25 19:36:48,939] [INFO] Running command: hmmsearch --tblout GCF_030409685.1_ASM3040968v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6c2d7368-3926-4aca-9c3d-fe31d48c508b/dqc_reference/reference_markers.hmm GCF_030409685.1_ASM3040968v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:36:49,367] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:36:49,369] [INFO] Found 6/6 markers.
[2024-01-25 19:36:49,427] [INFO] Query marker FASTA was written to GCF_030409685.1_ASM3040968v1_genomic.fna/markers.fasta
[2024-01-25 19:36:49,427] [INFO] Task started: Blastn
[2024-01-25 19:36:49,427] [INFO] Running command: blastn -query GCF_030409685.1_ASM3040968v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c2d7368-3926-4aca-9c3d-fe31d48c508b/dqc_reference/reference_markers.fasta -out GCF_030409685.1_ASM3040968v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:36:50,018] [INFO] Task succeeded: Blastn
[2024-01-25 19:36:50,021] [INFO] Selected 25 target genomes.
[2024-01-25 19:36:50,022] [INFO] Target genome list was writen to GCF_030409685.1_ASM3040968v1_genomic.fna/target_genomes.txt
[2024-01-25 19:36:50,048] [INFO] Task started: fastANI
[2024-01-25 19:36:50,048] [INFO] Running command: fastANI --query /var/lib/cwl/stg1320c61a-d447-4d3a-b573-fe432afe2ca9/GCF_030409685.1_ASM3040968v1_genomic.fna.gz --refList GCF_030409685.1_ASM3040968v1_genomic.fna/target_genomes.txt --output GCF_030409685.1_ASM3040968v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:37:12,177] [INFO] Task succeeded: fastANI
[2024-01-25 19:37:12,177] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6c2d7368-3926-4aca-9c3d-fe31d48c508b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:37:12,177] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6c2d7368-3926-4aca-9c3d-fe31d48c508b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:37:12,188] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:37:12,188] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:37:12,188] [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
Ferruginibacter albus	strain=KIS38-8	GCA_020042285.1	2875540	2875540	type	True	76.6542	139	2292	95	below_threshold
Panacibacter ginsenosidivorans	strain=Gsoil1550	GCA_007971225.1	1813871	1813871	type	True	76.1337	121	2292	95	below_threshold
Lacibacter luteus	strain=TTM-7	GCA_004118265.1	2508719	2508719	type	True	75.9941	119	2292	95	below_threshold
Phnomibacter ginsenosidimutans	strain=SB-02	GCA_009740285.1	2676868	2676868	type	True	75.9437	68	2292	95	below_threshold
Flavisolibacter ginsengisoli	strain=DSM 18119	GCA_900129295.1	462367	462367	type	True	75.9281	63	2292	95	below_threshold
Flavihumibacter cheonanensis	strain=WS16	GCA_022352215.1	1442385	1442385	type	True	75.8625	65	2292	95	below_threshold
Sediminibacterium salmoneum	strain=NBRC 103935	GCA_000511175.1	426421	426421	type	True	75.8151	68	2292	95	below_threshold
Segetibacter koreensis	strain=DSM 18137	GCA_000374045.1	398037	398037	type	True	75.6764	91	2292	95	below_threshold
Hydrotalea lipotrueae	strain=TMF_100	GCA_019249625.1	2803817	2803817	type	True	75.6722	80	2292	95	below_threshold
Agriterribacter humi	strain=YJ03	GCA_009192765.1	1104781	1104781	type	True	75.6558	90	2292	95	below_threshold
Foetidibacter luteolus	strain=YG09	GCA_009650435.1	2608880	2608880	type	True	75.65	113	2292	95	below_threshold
Chitinophaga niastensis	strain=DSM 24859	GCA_003014755.1	536980	536980	type	True	75.6493	63	2292	95	below_threshold
Hydrotalea flava	strain=CCUG 51397	GCA_001623405.1	714549	714549	suspected-type	True	75.5863	89	2292	95	below_threshold
Deminuibacter soli	strain=K23C18032701	GCA_003412455.1	2291815	2291815	type	True	75.5512	98	2292	95	below_threshold
Niastella caeni	strain=HX-16-21	GCA_004834005.1	2569763	2569763	type	True	75.3195	79	2292	95	below_threshold
Mucilaginibacter gotjawali	strain=CECT 8628	GCA_014191635.1	1550579	1550579	type	True	75.1372	50	2292	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:37:12,190] [INFO] DFAST Taxonomy check result was written to GCF_030409685.1_ASM3040968v1_genomic.fna/tc_result.tsv
[2024-01-25 19:37:12,190] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:37:12,190] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:37:12,191] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6c2d7368-3926-4aca-9c3d-fe31d48c508b/dqc_reference/checkm_data
[2024-01-25 19:37:12,191] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:37:12,270] [INFO] Task started: CheckM
[2024-01-25 19:37:12,270] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030409685.1_ASM3040968v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030409685.1_ASM3040968v1_genomic.fna/checkm_input GCF_030409685.1_ASM3040968v1_genomic.fna/checkm_result
[2024-01-25 19:38:24,878] [INFO] Task succeeded: CheckM
[2024-01-25 19:38:24,879] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:38:24,899] [INFO] ===== Completeness check finished =====
[2024-01-25 19:38:24,899] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:38:24,900] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030409685.1_ASM3040968v1_genomic.fna/markers.fasta)
[2024-01-25 19:38:24,900] [INFO] Task started: Blastn
[2024-01-25 19:38:24,900] [INFO] Running command: blastn -query GCF_030409685.1_ASM3040968v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c2d7368-3926-4aca-9c3d-fe31d48c508b/dqc_reference/reference_markers_gtdb.fasta -out GCF_030409685.1_ASM3040968v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:38:25,692] [INFO] Task succeeded: Blastn
[2024-01-25 19:38:25,695] [INFO] Selected 17 target genomes.
[2024-01-25 19:38:25,695] [INFO] Target genome list was writen to GCF_030409685.1_ASM3040968v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:38:25,706] [INFO] Task started: fastANI
[2024-01-25 19:38:25,706] [INFO] Running command: fastANI --query /var/lib/cwl/stg1320c61a-d447-4d3a-b573-fe432afe2ca9/GCF_030409685.1_ASM3040968v1_genomic.fna.gz --refList GCF_030409685.1_ASM3040968v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030409685.1_ASM3040968v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:38:38,597] [INFO] Task succeeded: fastANI
[2024-01-25 19:38:38,608] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:38:38,608] [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_014377975.1	s__Ferruginibacter sp014377975	79.485	723	2292	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016715365.1	s__Ferruginibacter sp016715365	77.3896	212	2292	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	98.79	98.54	0.91	0.89	5	-
GCA_013141115.1	s__Ferruginibacter sp013141115	76.9189	275	2292	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017983695.1	s__Ferruginibacter sp017983695	76.8903	246	2292	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016710935.1	s__Ferruginibacter sp016710935	76.8808	212	2292	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014379625.1	s__Ferruginibacter sp014379625	76.8521	283	2292	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016722465.1	s__Ferruginibacter sp016722465	76.7764	263	2292	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013288745.1	s__Ferruginibacter sp013288745	76.7115	87	2292	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016786725.1	s__Ferruginibacter sp016786725	76.7089	176	2292	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018266775.1	s__Ferruginibacter sp018266775	76.5735	211	2292	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014379905.1	s__Ferruginibacter sp014379905	76.5594	191	2292	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016721385.1	s__Ferruginibacter sp016721385	76.5215	122	2292	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016710745.1	s__Ferruginibacter sp016710745	76.4814	148	2292	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268155.1	s__Ferruginibacter sp018268155	76.3801	165	2292	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903837525.1	s__Ferruginibacter sp903837525	76.2845	81	2292	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016719015.1	s__JJ008 sp016719015	75.9982	80	2292	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	99.23	99.17	0.95	0.92	9	-
GCA_903881425.1	s__CAILAF01 sp903881425	75.4945	60	2292	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__CAILAF01	95.0	99.80	99.80	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:38:38,609] [INFO] GTDB search result was written to GCF_030409685.1_ASM3040968v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:38:38,610] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:38:38,614] [INFO] DFAST_QC result json was written to GCF_030409685.1_ASM3040968v1_genomic.fna/dqc_result.json
[2024-01-25 19:38:38,614] [INFO] DFAST_QC completed!
[2024-01-25 19:38:38,614] [INFO] Total running time: 0h2m18s