[2024-01-25 19:45:35,639] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:45:35,649] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:45:35,649] [INFO] DQC Reference Directory: /var/lib/cwl/stgf8c326c2-31db-44c0-abb5-136fd3f32048/dqc_reference
[2024-01-25 19:45:36,836] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:45:36,839] [INFO] Task started: Prodigal
[2024-01-25 19:45:36,839] [INFO] Running command: gunzip -c /var/lib/cwl/stgf1d4a90d-1363-45a4-a028-20eac23aac26/GCF_020076305.1_ASM2007630v1_genomic.fna.gz | prodigal -d GCF_020076305.1_ASM2007630v1_genomic.fna/cds.fna -a GCF_020076305.1_ASM2007630v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:45:56,347] [INFO] Task succeeded: Prodigal
[2024-01-25 19:45:56,347] [INFO] Task started: HMMsearch
[2024-01-25 19:45:56,347] [INFO] Running command: hmmsearch --tblout GCF_020076305.1_ASM2007630v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf8c326c2-31db-44c0-abb5-136fd3f32048/dqc_reference/reference_markers.hmm GCF_020076305.1_ASM2007630v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:45:56,608] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:45:56,609] [INFO] Found 6/6 markers.
[2024-01-25 19:45:56,649] [INFO] Query marker FASTA was written to GCF_020076305.1_ASM2007630v1_genomic.fna/markers.fasta
[2024-01-25 19:45:56,649] [INFO] Task started: Blastn
[2024-01-25 19:45:56,649] [INFO] Running command: blastn -query GCF_020076305.1_ASM2007630v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf8c326c2-31db-44c0-abb5-136fd3f32048/dqc_reference/reference_markers.fasta -out GCF_020076305.1_ASM2007630v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:45:57,200] [INFO] Task succeeded: Blastn
[2024-01-25 19:45:57,206] [INFO] Selected 22 target genomes.
[2024-01-25 19:45:57,207] [INFO] Target genome list was writen to GCF_020076305.1_ASM2007630v1_genomic.fna/target_genomes.txt
[2024-01-25 19:45:57,225] [INFO] Task started: fastANI
[2024-01-25 19:45:57,225] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1d4a90d-1363-45a4-a028-20eac23aac26/GCF_020076305.1_ASM2007630v1_genomic.fna.gz --refList GCF_020076305.1_ASM2007630v1_genomic.fna/target_genomes.txt --output GCF_020076305.1_ASM2007630v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:46:13,921] [INFO] Task succeeded: fastANI
[2024-01-25 19:46:13,922] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf8c326c2-31db-44c0-abb5-136fd3f32048/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:46:13,922] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf8c326c2-31db-44c0-abb5-136fd3f32048/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:46:13,930] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:46:13,930] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:46:13,931] [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
Flavihumibacter profundi	strain=KCTC 62290	GCA_020076305.1	2716883	2716883	type	True	100.0	1619	1620	95	conclusive
Flavihumibacter fluminis	strain=IMCC34837	GCA_018595675.2	2838157	2838157	type	True	79.4013	709	1620	95	below_threshold
Flavihumibacter stibioxidans	strain=YS-17	GCA_014332695.1	1834163	1834163	type	True	77.883	309	1620	95	below_threshold
Flavihumibacter solisilvae	strain=3-3	GCA_000814475.1	1349421	1349421	type	True	77.6187	244	1620	95	below_threshold
Flavihumibacter cheonanensis	strain=WS16	GCA_022352215.1	1442385	1442385	type	True	77.242	230	1620	95	below_threshold
Flavihumibacter rivuli	strain=IMCC34838	GCA_018595685.2	2838156	2838156	type	True	77.184	198	1620	95	below_threshold
Flavihumibacter petaseus	strain=NBRC 106054	GCA_000974785.1	549295	549295	type	True	77.1399	213	1620	95	below_threshold
Sediminibacterium goheungense	strain=DSM 28323	GCA_004361915.1	1086393	1086393	type	True	76.4555	64	1620	95	below_threshold
Filimonas effusa	strain=TTM-71	GCA_004118675.1	2508721	2508721	type	True	76.2966	50	1620	95	below_threshold
Niastella koreensis	strain=GR20-10	GCA_000246855.1	354356	354356	type	True	76.1329	88	1620	95	below_threshold
Niastella koreensis	strain=DSM 17620	GCA_002077985.1	354356	354356	type	True	76.0148	86	1620	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:46:13,932] [INFO] DFAST Taxonomy check result was written to GCF_020076305.1_ASM2007630v1_genomic.fna/tc_result.tsv
[2024-01-25 19:46:13,932] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:46:13,932] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:46:13,932] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf8c326c2-31db-44c0-abb5-136fd3f32048/dqc_reference/checkm_data
[2024-01-25 19:46:13,933] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:46:13,992] [INFO] Task started: CheckM
[2024-01-25 19:46:13,992] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020076305.1_ASM2007630v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020076305.1_ASM2007630v1_genomic.fna/checkm_input GCF_020076305.1_ASM2007630v1_genomic.fna/checkm_result
[2024-01-25 19:47:09,551] [INFO] Task succeeded: CheckM
[2024-01-25 19:47:09,553] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:47:09,569] [INFO] ===== Completeness check finished =====
[2024-01-25 19:47:09,569] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:47:09,570] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020076305.1_ASM2007630v1_genomic.fna/markers.fasta)
[2024-01-25 19:47:09,571] [INFO] Task started: Blastn
[2024-01-25 19:47:09,571] [INFO] Running command: blastn -query GCF_020076305.1_ASM2007630v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf8c326c2-31db-44c0-abb5-136fd3f32048/dqc_reference/reference_markers_gtdb.fasta -out GCF_020076305.1_ASM2007630v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:47:10,382] [INFO] Task succeeded: Blastn
[2024-01-25 19:47:10,384] [INFO] Selected 25 target genomes.
[2024-01-25 19:47:10,385] [INFO] Target genome list was writen to GCF_020076305.1_ASM2007630v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:47:10,396] [INFO] Task started: fastANI
[2024-01-25 19:47:10,396] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1d4a90d-1363-45a4-a028-20eac23aac26/GCF_020076305.1_ASM2007630v1_genomic.fna.gz --refList GCF_020076305.1_ASM2007630v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020076305.1_ASM2007630v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:47:28,787] [INFO] Task succeeded: fastANI
[2024-01-25 19:47:28,799] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:47:28,799] [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_018595675.1	s__Flavihumibacter sp018595675	79.481	703	1620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavihumibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014332695.1	s__Flavihumibacter stibioxidans	77.8824	307	1620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavihumibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000814475.1	s__Flavihumibacter solisilvae	77.6089	244	1620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavihumibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000814325.1	s__Flavihumibacter sp000814325	77.5475	245	1620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavihumibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018595685.1	s__Flavihumibacter sp018595685	77.1538	195	1620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavihumibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016787265.1	s__Flavihumibacter sp016787265	77.1429	222	1620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavihumibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000974785.1	s__Flavihumibacter petaseus	77.1287	213	1620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavihumibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002483205.1	s__Flavihumibacter sp002483205	77.1115	221	1620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavihumibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016185185.1	s__AWTP1-9 sp016185185	76.6219	59	1620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__AWTP1-9	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004361915.1	s__Sediminibacterium goheungense	76.4555	64	1620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018993145.1	s__Flavihumibacter sp018993145	76.4175	127	1620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavihumibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002400415.1	s__JJ008 sp002400415	76.3638	79	1620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000246855.1	s__Niastella koreensis	76.1329	88	1620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002336115.1	s__Lacibacter sp002336115	75.8611	57	1620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Lacibacter	95.0	99.94	99.94	0.95	0.95	2	-
GCA_002390845.1	s__Panacibacter sp002390845	75.8514	74	1620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Panacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016787085.1	s__VBAT01 sp016787085	75.6999	71	1620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__VBAT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016786805.1	s__JJ008 sp016786805	75.6748	58	1620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016715365.1	s__Ferruginibacter sp016715365	75.4415	60	1620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	98.79	98.54	0.91	0.89	5	-
GCA_003175935.1	s__Agriterribacter sp003175935	75.1937	53	1620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Agriterribacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:47:28,801] [INFO] GTDB search result was written to GCF_020076305.1_ASM2007630v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:47:28,801] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:47:28,804] [INFO] DFAST_QC result json was written to GCF_020076305.1_ASM2007630v1_genomic.fna/dqc_result.json
[2024-01-25 19:47:28,805] [INFO] DFAST_QC completed!
[2024-01-25 19:47:28,805] [INFO] Total running time: 0h1m53s