[2024-01-25 19:39:20,773] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:39:20,775] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:39:20,776] [INFO] DQC Reference Directory: /var/lib/cwl/stg887c7cdc-cd94-4198-97fa-265ac663d1e1/dqc_reference
[2024-01-25 19:39:21,895] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:39:21,896] [INFO] Task started: Prodigal
[2024-01-25 19:39:21,896] [INFO] Running command: gunzip -c /var/lib/cwl/stgec03d4ec-ba5e-4f14-91d8-dc866dadd9ac/GCF_022012415.1_ASM2201241v1_genomic.fna.gz | prodigal -d GCF_022012415.1_ASM2201241v1_genomic.fna/cds.fna -a GCF_022012415.1_ASM2201241v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:39:50,653] [INFO] Task succeeded: Prodigal
[2024-01-25 19:39:50,654] [INFO] Task started: HMMsearch
[2024-01-25 19:39:50,654] [INFO] Running command: hmmsearch --tblout GCF_022012415.1_ASM2201241v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg887c7cdc-cd94-4198-97fa-265ac663d1e1/dqc_reference/reference_markers.hmm GCF_022012415.1_ASM2201241v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:39:51,077] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:39:51,078] [INFO] Found 6/6 markers.
[2024-01-25 19:39:51,130] [INFO] Query marker FASTA was written to GCF_022012415.1_ASM2201241v1_genomic.fna/markers.fasta
[2024-01-25 19:39:51,131] [INFO] Task started: Blastn
[2024-01-25 19:39:51,131] [INFO] Running command: blastn -query GCF_022012415.1_ASM2201241v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg887c7cdc-cd94-4198-97fa-265ac663d1e1/dqc_reference/reference_markers.fasta -out GCF_022012415.1_ASM2201241v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:39:51,713] [INFO] Task succeeded: Blastn
[2024-01-25 19:39:51,716] [INFO] Selected 30 target genomes.
[2024-01-25 19:39:51,716] [INFO] Target genome list was writen to GCF_022012415.1_ASM2201241v1_genomic.fna/target_genomes.txt
[2024-01-25 19:39:51,738] [INFO] Task started: fastANI
[2024-01-25 19:39:51,738] [INFO] Running command: fastANI --query /var/lib/cwl/stgec03d4ec-ba5e-4f14-91d8-dc866dadd9ac/GCF_022012415.1_ASM2201241v1_genomic.fna.gz --refList GCF_022012415.1_ASM2201241v1_genomic.fna/target_genomes.txt --output GCF_022012415.1_ASM2201241v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:40:20,352] [INFO] Task succeeded: fastANI
[2024-01-25 19:40:20,355] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg887c7cdc-cd94-4198-97fa-265ac663d1e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:40:20,356] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg887c7cdc-cd94-4198-97fa-265ac663d1e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:40:20,370] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:40:20,370] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:40:20,370] [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
Terrimonas ferruginea	strain=DSM 30193	GCA_000425585.1	249	249	type	True	77.0687	194	2356	95	below_threshold
Pseudobacter ginsenosidimutans	strain=Gsoil 221	GCA_007970185.1	661488	661488	type	True	76.5819	121	2356	95	below_threshold
Niabella soli	strain=JS13-8; DSM 19437	GCA_000243115.3	446683	446683	type	True	76.5475	66	2356	95	below_threshold
Pseudobacter ginsenosidimutans	strain=DSM 18116	GCA_004291315.1	661488	661488	type	True	76.4854	122	2356	95	below_threshold
Paraflavitalea devenefica	strain=X16	GCA_011759375.1	2716334	2716334	type	True	76.3896	103	2356	95	below_threshold
Chitinophaga ginsengisoli	strain=DSM 18107	GCA_003014595.1	363837	363837	type	True	76.3622	70	2356	95	below_threshold
Niabella hibiscisoli	strain=THG-DN5.5	GCA_022512515.1	1825928	1825928	type	True	76.3107	67	2356	95	below_threshold
Chitinophaga agrisoli	strain=BN140078	GCA_008386695.1	2607653	2607653	type	True	76.28	67	2356	95	below_threshold
Lacibacter cauensis	strain=CGMCC 1.7271	GCA_007830055.1	510947	510947	type	True	76.2768	86	2356	95	below_threshold
Niabella beijingensis	strain=3A5MI-3	GCA_020034665.1	2872700	2872700	type	True	76.2579	97	2356	95	below_threshold
Chitinophaga rhizophila	strain=B61	GCA_019492185.1	2866212	2866212	type	True	76.2458	56	2356	95	below_threshold
Niabella pedocola	strain=JCM 31011	GCA_021044425.1	1752077	1752077	type	True	76.2274	82	2356	95	below_threshold
Flavisolibacter nicotianae	strain=X7X	GCA_003628535.1	2364882	2364882	type	True	76.1183	80	2356	95	below_threshold
Niabella drilacis	strain=DSM 25811	GCA_900101395.1	1285928	1285928	type	True	76.1181	78	2356	95	below_threshold
Sediminibacterium ginsengisoli	strain=DSM 22335	GCA_900167075.1	413434	413434	type	True	76.1162	110	2356	95	below_threshold
Flavihumibacter rivuli	strain=IMCC34838	GCA_018595685.2	2838156	2838156	type	True	76.1153	77	2356	95	below_threshold
Flavihumibacter cheonanensis	strain=WS16	GCA_022352215.1	1442385	1442385	type	True	76.067	65	2356	95	below_threshold
Cnuella takakiae	strain=DSM 26897	GCA_900129015.1	1302690	1302690	type	True	76.0357	78	2356	95	below_threshold
Cnuella takakiae	strain=RG1-1	GCA_001953305.1	1302690	1302690	type	True	75.968	80	2356	95	below_threshold
Chitinophaga terrae (ex Kim and Jung 2007)	strain=DSM 23920	GCA_900107795.1	408074	408074	type	True	75.9605	62	2356	95	below_threshold
Deminuibacter soli	strain=K23C18032701	GCA_003412455.1	2291815	2291815	type	True	75.9371	88	2356	95	below_threshold
Filimonas effusa	strain=TTM-71	GCA_004118675.1	2508721	2508721	type	True	75.929	69	2356	95	below_threshold
Chitinophaga varians	strain=KACC 19415	GCA_014529945.1	2202339	2202339	type	True	75.6841	78	2356	95	below_threshold
Chitinophaga filiformis	strain=DSM 527	GCA_900102545.1	104663	104663	type	True	75.6108	82	2356	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:40:20,372] [INFO] DFAST Taxonomy check result was written to GCF_022012415.1_ASM2201241v1_genomic.fna/tc_result.tsv
[2024-01-25 19:40:20,372] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:40:20,372] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:40:20,373] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg887c7cdc-cd94-4198-97fa-265ac663d1e1/dqc_reference/checkm_data
[2024-01-25 19:40:20,373] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:40:20,441] [INFO] Task started: CheckM
[2024-01-25 19:40:20,442] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022012415.1_ASM2201241v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022012415.1_ASM2201241v1_genomic.fna/checkm_input GCF_022012415.1_ASM2201241v1_genomic.fna/checkm_result
[2024-01-25 19:41:40,773] [INFO] Task succeeded: CheckM
[2024-01-25 19:41:40,774] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:41:40,802] [INFO] ===== Completeness check finished =====
[2024-01-25 19:41:40,802] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:41:40,803] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022012415.1_ASM2201241v1_genomic.fna/markers.fasta)
[2024-01-25 19:41:40,803] [INFO] Task started: Blastn
[2024-01-25 19:41:40,803] [INFO] Running command: blastn -query GCF_022012415.1_ASM2201241v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg887c7cdc-cd94-4198-97fa-265ac663d1e1/dqc_reference/reference_markers_gtdb.fasta -out GCF_022012415.1_ASM2201241v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:41:41,639] [INFO] Task succeeded: Blastn
[2024-01-25 19:41:41,642] [INFO] Selected 19 target genomes.
[2024-01-25 19:41:41,642] [INFO] Target genome list was writen to GCF_022012415.1_ASM2201241v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:41:41,698] [INFO] Task started: fastANI
[2024-01-25 19:41:41,698] [INFO] Running command: fastANI --query /var/lib/cwl/stgec03d4ec-ba5e-4f14-91d8-dc866dadd9ac/GCF_022012415.1_ASM2201241v1_genomic.fna.gz --refList GCF_022012415.1_ASM2201241v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022012415.1_ASM2201241v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:41:59,800] [INFO] Task succeeded: fastANI
[2024-01-25 19:41:59,811] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:41:59,812] [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_003243445.1	s__46-32 sp003243445	79.4622	818	2356	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__46-32	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898405.1	s__46-32 sp001898405	78.2052	582	2356	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__46-32	95.0	98.21	96.99	0.89	0.84	4	-
GCF_000425585.1	s__Terrimonas ferruginea	77.0795	195	2356	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Terrimonas	95.0	95.38	95.33	0.94	0.93	4	-
GCA_016786805.1	s__JJ008 sp016786805	76.845	123	2356	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826165.1	s__JJ008 sp902826165	76.8105	186	2356	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004173355.1	s__46-32 sp004173355	76.7913	163	2356	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__46-32	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898485.1	s__46-32 sp001898485	76.75	216	2356	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__46-32	95.0	99.14	98.30	0.96	0.92	3	-
GCA_017998385.1	s__46-32 sp017998385	76.6824	171	2356	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__46-32	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016720825.1	s__JJ008 sp016720825	76.6608	117	2356	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	98.65	98.65	0.92	0.92	2	-
GCA_016719165.1	s__JJ008 sp016719165	76.6171	111	2356	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	97.96	97.46	0.92	0.92	3	-
GCA_016706055.1	s__JJ008 sp016706055	76.4387	97	2356	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	99.30	99.30	0.94	0.94	2	-
GCA_004173255.1	s__46-32 sp004173255	76.4335	147	2356	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__46-32	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016787125.1	s__JJ008 sp016787125	76.3623	103	2356	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016787135.1	s__VBAT01 sp016787135	76.2446	168	2356	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__VBAT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018267535.1	s__JAFDYH01 sp018267535	76.1581	71	2356	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JAFDYH01	95.0	98.33	98.33	0.81	0.81	2	-
GCF_003628535.1	s__Flavisolibacter nicotianae	76.1183	80	2356	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016125075.1	s__SpSt-398 sp016125075	76.1048	86	2356	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__SpSt-398	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016710165.1	s__Ferruginibacter sp016710165	75.9587	62	2356	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	99.37	99.37	0.98	0.98	3	-
GCA_003963365.1	s__AWTP1-9 sp003963365	75.892	71	2356	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__AWTP1-9	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:41:59,813] [INFO] GTDB search result was written to GCF_022012415.1_ASM2201241v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:41:59,813] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:41:59,817] [INFO] DFAST_QC result json was written to GCF_022012415.1_ASM2201241v1_genomic.fna/dqc_result.json
[2024-01-25 19:41:59,817] [INFO] DFAST_QC completed!
[2024-01-25 19:41:59,817] [INFO] Total running time: 0h2m39s