[2024-01-25 19:03:20,636] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:03:20,638] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:03:20,638] [INFO] DQC Reference Directory: /var/lib/cwl/stga9b9141c-42b7-47ad-99e6-d8d98c485232/dqc_reference
[2024-01-25 19:03:21,780] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:03:21,781] [INFO] Task started: Prodigal
[2024-01-25 19:03:21,781] [INFO] Running command: gunzip -c /var/lib/cwl/stg9171c119-9eed-489e-9efd-65a56a3be5d6/GCF_020042285.1_ASM2004228v1_genomic.fna.gz | prodigal -d GCF_020042285.1_ASM2004228v1_genomic.fna/cds.fna -a GCF_020042285.1_ASM2004228v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:03:34,238] [INFO] Task succeeded: Prodigal
[2024-01-25 19:03:34,239] [INFO] Task started: HMMsearch
[2024-01-25 19:03:34,239] [INFO] Running command: hmmsearch --tblout GCF_020042285.1_ASM2004228v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga9b9141c-42b7-47ad-99e6-d8d98c485232/dqc_reference/reference_markers.hmm GCF_020042285.1_ASM2004228v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:03:34,519] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:03:34,520] [INFO] Found 6/6 markers.
[2024-01-25 19:03:34,553] [INFO] Query marker FASTA was written to GCF_020042285.1_ASM2004228v1_genomic.fna/markers.fasta
[2024-01-25 19:03:34,553] [INFO] Task started: Blastn
[2024-01-25 19:03:34,553] [INFO] Running command: blastn -query GCF_020042285.1_ASM2004228v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga9b9141c-42b7-47ad-99e6-d8d98c485232/dqc_reference/reference_markers.fasta -out GCF_020042285.1_ASM2004228v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:03:35,129] [INFO] Task succeeded: Blastn
[2024-01-25 19:03:35,132] [INFO] Selected 19 target genomes.
[2024-01-25 19:03:35,132] [INFO] Target genome list was writen to GCF_020042285.1_ASM2004228v1_genomic.fna/target_genomes.txt
[2024-01-25 19:03:35,163] [INFO] Task started: fastANI
[2024-01-25 19:03:35,163] [INFO] Running command: fastANI --query /var/lib/cwl/stg9171c119-9eed-489e-9efd-65a56a3be5d6/GCF_020042285.1_ASM2004228v1_genomic.fna.gz --refList GCF_020042285.1_ASM2004228v1_genomic.fna/target_genomes.txt --output GCF_020042285.1_ASM2004228v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:03:52,595] [INFO] Task succeeded: fastANI
[2024-01-25 19:03:52,595] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga9b9141c-42b7-47ad-99e6-d8d98c485232/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:03:52,596] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga9b9141c-42b7-47ad-99e6-d8d98c485232/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:03:52,604] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:03:52,605] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:03:52,605] [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	100.0	1253	1253	95	conclusive
Lacibacter cauensis	strain=CGMCC 1.7271	GCA_007830055.1	510947	510947	type	True	76.8677	94	1253	95	below_threshold
Pinibacter aurantiacus	strain=MAH-26	GCA_019130065.1	2851599	2851599	type	True	76.7758	75	1253	95	below_threshold
Niabella ginsengisoli	strain=GR10-1	GCA_022513635.1	522298	522298	type	True	76.6761	71	1253	95	below_threshold
Ginsengibacter hankyongi	strain=BR5-29	GCA_008710285.1	2607284	2607284	type	True	76.5288	96	1253	95	below_threshold
Hydrotalea sandarakina	strain=DSM 23241	GCA_003254115.1	1004304	1004304	type	True	76.446	56	1253	95	below_threshold
Lacibacter luteus	strain=TTM-7	GCA_004118265.1	2508719	2508719	type	True	76.3558	109	1253	95	below_threshold
Hanamia caeni	strain=BO-59	GCA_003721595.1	2294116	2294116	type	True	76.25	65	1253	95	below_threshold
Panacibacter microcysteis	strain=DH6	GCA_015831355.1	2793269	2793269	type	True	76.2019	64	1253	95	below_threshold
Niastella yeongjuensis	strain=DSM 17621	GCA_900110245.1	354355	354355	type	True	75.6285	61	1253	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:03:52,606] [INFO] DFAST Taxonomy check result was written to GCF_020042285.1_ASM2004228v1_genomic.fna/tc_result.tsv
[2024-01-25 19:03:52,607] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:03:52,607] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:03:52,608] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga9b9141c-42b7-47ad-99e6-d8d98c485232/dqc_reference/checkm_data
[2024-01-25 19:03:52,608] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:03:52,647] [INFO] Task started: CheckM
[2024-01-25 19:03:52,647] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020042285.1_ASM2004228v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020042285.1_ASM2004228v1_genomic.fna/checkm_input GCF_020042285.1_ASM2004228v1_genomic.fna/checkm_result
[2024-01-25 19:04:30,122] [INFO] Task succeeded: CheckM
[2024-01-25 19:04:30,123] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:04:30,137] [INFO] ===== Completeness check finished =====
[2024-01-25 19:04:30,138] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:04:30,139] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020042285.1_ASM2004228v1_genomic.fna/markers.fasta)
[2024-01-25 19:04:30,139] [INFO] Task started: Blastn
[2024-01-25 19:04:30,139] [INFO] Running command: blastn -query GCF_020042285.1_ASM2004228v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga9b9141c-42b7-47ad-99e6-d8d98c485232/dqc_reference/reference_markers_gtdb.fasta -out GCF_020042285.1_ASM2004228v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:04:30,932] [INFO] Task succeeded: Blastn
[2024-01-25 19:04:30,934] [INFO] Selected 26 target genomes.
[2024-01-25 19:04:30,934] [INFO] Target genome list was writen to GCF_020042285.1_ASM2004228v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:04:30,975] [INFO] Task started: fastANI
[2024-01-25 19:04:30,976] [INFO] Running command: fastANI --query /var/lib/cwl/stg9171c119-9eed-489e-9efd-65a56a3be5d6/GCF_020042285.1_ASM2004228v1_genomic.fna.gz --refList GCF_020042285.1_ASM2004228v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020042285.1_ASM2004228v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:04:47,882] [INFO] Task succeeded: fastANI
[2024-01-25 19:04:47,896] [INFO] Found 25 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:04:47,896] [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_017983695.1	s__Ferruginibacter sp017983695	76.9592	176	1253	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	76.9524	163	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	98.79	98.54	0.91	0.89	5	-
GCA_016722465.1	s__Ferruginibacter sp016722465	76.931	156	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013141115.1	s__Ferruginibacter sp013141115	76.8373	176	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019130065.1	s__Parasegetibacter sp019130065	76.7758	75	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Parasegetibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016703625.1	s__Ferruginibacter sp016703625	76.6728	111	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	97.77	96.12	0.94	0.91	5	-
GCA_002352045.1	s__Ferruginibacter sp002352045	76.5648	116	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	99.67	99.67	0.93	0.93	2	-
GCA_016713965.1	s__Ferruginibacter sp016713965	76.557	108	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016710165.1	s__Ferruginibacter sp016710165	76.5493	92	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	99.37	99.37	0.98	0.98	3	-
GCF_008710285.1	s__Ginsengibacter hankyongi	76.5288	96	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ginsengibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016710935.1	s__Ferruginibacter sp016710935	76.446	154	1253	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	76.4249	72	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268085.1	s__Ferruginibacter sp018268085	76.404	120	1253	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	76.4039	150	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002337145.1	s__UBA1930 sp002337145	76.356	63	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__UBA1930	95.0	99.95	99.95	0.99	0.99	2	-
GCF_004118265.1	s__Lacibacter luteus	76.3558	109	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Lacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268135.1	s__Ferruginibacter sp018268135	76.3014	112	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	99.79	99.79	0.93	0.93	2	-
GCA_004028795.1	s__CW01 sp004028795	76.2325	109	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__CW01	95.0	99.97	99.97	0.97	0.97	2	-
GCA_002400415.1	s__JJ008 sp002400415	76.1785	64	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002127295.1	s__JJ008 sp002127295	76.1172	71	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903841915.1	s__CAILAF01 sp903841915	75.9992	55	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__CAILAF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002050465.1	s__Ginsengibacter sp002050465	75.9786	60	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ginsengibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903832075.1	s__CAILAF01 sp903832075	75.9268	72	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__CAILAF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826165.1	s__JJ008 sp902826165	75.8182	70	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902168225.1	s__Sediminibacterium sp902168225	75.6272	61	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:04:47,898] [INFO] GTDB search result was written to GCF_020042285.1_ASM2004228v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:04:47,899] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:04:47,902] [INFO] DFAST_QC result json was written to GCF_020042285.1_ASM2004228v1_genomic.fna/dqc_result.json
[2024-01-25 19:04:47,902] [INFO] DFAST_QC completed!
[2024-01-25 19:04:47,902] [INFO] Total running time: 0h1m27s