[2024-01-24 13:01:12,406] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:12,408] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:12,408] [INFO] DQC Reference Directory: /var/lib/cwl/stgd39f977e-3411-4b70-a478-e6d77fde06f5/dqc_reference
[2024-01-24 13:01:13,885] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:13,886] [INFO] Task started: Prodigal
[2024-01-24 13:01:13,886] [INFO] Running command: gunzip -c /var/lib/cwl/stgd5e4e3c9-3237-4bb6-a2ad-4a2f8845063f/GCF_003688495.1_ASM368849v1_genomic.fna.gz | prodigal -d GCF_003688495.1_ASM368849v1_genomic.fna/cds.fna -a GCF_003688495.1_ASM368849v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:24,908] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:24,909] [INFO] Task started: HMMsearch
[2024-01-24 13:01:24,909] [INFO] Running command: hmmsearch --tblout GCF_003688495.1_ASM368849v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd39f977e-3411-4b70-a478-e6d77fde06f5/dqc_reference/reference_markers.hmm GCF_003688495.1_ASM368849v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:25,199] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:25,201] [INFO] Found 6/6 markers.
[2024-01-24 13:01:25,231] [INFO] Query marker FASTA was written to GCF_003688495.1_ASM368849v1_genomic.fna/markers.fasta
[2024-01-24 13:01:25,231] [INFO] Task started: Blastn
[2024-01-24 13:01:25,231] [INFO] Running command: blastn -query GCF_003688495.1_ASM368849v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd39f977e-3411-4b70-a478-e6d77fde06f5/dqc_reference/reference_markers.fasta -out GCF_003688495.1_ASM368849v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:25,924] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:25,932] [INFO] Selected 20 target genomes.
[2024-01-24 13:01:25,932] [INFO] Target genome list was writen to GCF_003688495.1_ASM368849v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:25,940] [INFO] Task started: fastANI
[2024-01-24 13:01:25,940] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5e4e3c9-3237-4bb6-a2ad-4a2f8845063f/GCF_003688495.1_ASM368849v1_genomic.fna.gz --refList GCF_003688495.1_ASM368849v1_genomic.fna/target_genomes.txt --output GCF_003688495.1_ASM368849v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:41,692] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:41,692] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd39f977e-3411-4b70-a478-e6d77fde06f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:41,692] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd39f977e-3411-4b70-a478-e6d77fde06f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:41,708] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:01:41,708] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:01:41,708] [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
Flavobacterium weaverense	strain=DSM 19727	GCA_003688495.1	271156	271156	type	True	100.0	1125	1125	95	conclusive
Flavobacterium flabelliforme	strain=P4023	GCA_017948675.1	2816119	2816119	type	True	82.6761	736	1125	95	below_threshold
Flavobacterium segetis	strain=DSM 19741	GCA_900129575.1	271157	271157	type	True	81.0818	611	1125	95	below_threshold
Flavobacterium xanthum	strain=DSM 3661	GCA_900142695.1	69322	69322	type	True	80.4147	565	1125	95	below_threshold
Flavobacterium micromati	strain=DSM 17659	GCA_900129585.1	229205	229205	type	True	80.2951	557	1125	95	below_threshold
Flavobacterium psychrolimnae	strain=LMG 22018	GCA_003312425.1	249351	249351	type	True	80.2647	584	1125	95	below_threshold
Flavobacterium fryxellicola	strain=DSM 16209	GCA_001637185.1	249352	249352	type	True	80.2057	584	1125	95	below_threshold
Flavobacterium sandaracinum	strain=LB-D12	GCA_004349135.1	2541733	2541733	type	True	80.182	594	1125	95	below_threshold
Flavobacterium fryxellicola	strain=DSM 16209	GCA_900143245.1	249352	249352	type	True	80.182	583	1125	95	below_threshold
Flavobacterium limicola	strain=DSM 15094	GCA_003634755.1	180441	180441	type	True	80.182	545	1125	95	below_threshold
Flavobacterium petrolei	strain=Kopri-42	GCA_003314435.2	2259594	2259594	type	True	80.1465	568	1125	95	below_threshold
Flavobacterium caseinilyticum	strain=AT-3-2	GCA_004349085.1	2541732	2541732	type	True	79.8869	506	1125	95	below_threshold
Flavobacterium urumqiense	strain=CGMCC 1.9230	GCA_900108015.1	935224	935224	type	True	79.6537	505	1125	95	below_threshold
Flavobacterium xinjiangense	strain=CGMCC 1.2749	GCA_900142885.1	178356	178356	type	True	79.6121	527	1125	95	below_threshold
Flavobacterium hiemivividum	strain=TSA-D2	GCA_004349145.1	2541734	2541734	type	True	79.5504	444	1125	95	below_threshold
Flavobacterium taihuense	strain=NAS39	GCA_019351435.1	2857508	2857508	type	True	78.5308	338	1125	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	78.1999	339	1125	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	78.1793	327	1125	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	78.0698	340	1125	95	below_threshold
Flavobacterium litorale	strain=WSW3-B6	GCA_019613795.1	2856519	2856519	type	True	76.9447	64	1125	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:41,710] [INFO] DFAST Taxonomy check result was written to GCF_003688495.1_ASM368849v1_genomic.fna/tc_result.tsv
[2024-01-24 13:01:41,711] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:41,711] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:41,712] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd39f977e-3411-4b70-a478-e6d77fde06f5/dqc_reference/checkm_data
[2024-01-24 13:01:41,713] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:41,749] [INFO] Task started: CheckM
[2024-01-24 13:01:41,749] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003688495.1_ASM368849v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003688495.1_ASM368849v1_genomic.fna/checkm_input GCF_003688495.1_ASM368849v1_genomic.fna/checkm_result
[2024-01-24 13:02:17,209] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:17,210] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:17,229] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:17,229] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:17,230] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003688495.1_ASM368849v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:17,230] [INFO] Task started: Blastn
[2024-01-24 13:02:17,230] [INFO] Running command: blastn -query GCF_003688495.1_ASM368849v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd39f977e-3411-4b70-a478-e6d77fde06f5/dqc_reference/reference_markers_gtdb.fasta -out GCF_003688495.1_ASM368849v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:18,165] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:18,169] [INFO] Selected 15 target genomes.
[2024-01-24 13:02:18,169] [INFO] Target genome list was writen to GCF_003688495.1_ASM368849v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:18,179] [INFO] Task started: fastANI
[2024-01-24 13:02:18,180] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5e4e3c9-3237-4bb6-a2ad-4a2f8845063f/GCF_003688495.1_ASM368849v1_genomic.fna.gz --refList GCF_003688495.1_ASM368849v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003688495.1_ASM368849v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:29,022] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:29,034] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:02:29,035] [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_003688495.1	s__Flavobacterium weaverense	100.0	1125	1125	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014281985.1	s__Flavobacterium sp014281985	82.4852	734	1125	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.07	98.07	0.91	0.91	2	-
GCF_900129575.1	s__Flavobacterium segetis	81.0854	610	1125	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142695.1	s__Flavobacterium xanthum	80.4358	563	1125	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.99	97.99	0.90	0.90	2	-
GCF_900129585.1	s__Flavobacterium micromati	80.3055	556	1125	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003312425.1	s__Flavobacterium psychrolimnae	80.2775	582	1125	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900143245.1	s__Flavobacterium fryxellicola	80.192	582	1125	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000812945.1	s__Flavobacterium sp000812945	80.1776	507	1125	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003314435.2	s__Flavobacterium petrolei	80.1565	567	1125	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.35	97.35	0.87	0.87	2	-
GCF_017875765.1	s__Flavobacterium sp017875765	80.1038	495	1125	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.17	98.17	0.94	0.94	2	-
GCF_000744835.1	s__Flavobacterium sp000744835	79.9256	515	1125	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108015.1	s__Flavobacterium urumqiense	79.6494	504	1125	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142885.1	s__Flavobacterium xinjiangense	79.5953	528	1125	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004349145.1	s__Flavobacterium hiemivividum	79.5448	445	1125	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	95.37	95.37	0.86	0.86	2	-
GCF_003668995.1	s__Flavobacterium sp003668995	78.6329	420	1125	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:02:29,036] [INFO] GTDB search result was written to GCF_003688495.1_ASM368849v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:29,037] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:29,041] [INFO] DFAST_QC result json was written to GCF_003688495.1_ASM368849v1_genomic.fna/dqc_result.json
[2024-01-24 13:02:29,041] [INFO] DFAST_QC completed!
[2024-01-24 13:02:29,041] [INFO] Total running time: 0h1m17s