[2024-01-24 10:58:06,467] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:58:06,471] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:58:06,471] [INFO] DQC Reference Directory: /var/lib/cwl/stg851add10-5723-4dcf-adb4-4b3483096e2a/dqc_reference
[2024-01-24 10:58:09,632] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:58:09,633] [INFO] Task started: Prodigal
[2024-01-24 10:58:09,633] [INFO] Running command: gunzip -c /var/lib/cwl/stgbb27a377-bb3e-462c-a1b0-352f76881b45/GCF_002217355.1_ASM221735v1_genomic.fna.gz | prodigal -d GCF_002217355.1_ASM221735v1_genomic.fna/cds.fna -a GCF_002217355.1_ASM221735v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:58:24,827] [INFO] Task succeeded: Prodigal
[2024-01-24 10:58:24,828] [INFO] Task started: HMMsearch
[2024-01-24 10:58:24,828] [INFO] Running command: hmmsearch --tblout GCF_002217355.1_ASM221735v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg851add10-5723-4dcf-adb4-4b3483096e2a/dqc_reference/reference_markers.hmm GCF_002217355.1_ASM221735v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:58:25,182] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:58:25,184] [INFO] Found 6/6 markers.
[2024-01-24 10:58:25,259] [INFO] Query marker FASTA was written to GCF_002217355.1_ASM221735v1_genomic.fna/markers.fasta
[2024-01-24 10:58:25,260] [INFO] Task started: Blastn
[2024-01-24 10:58:25,260] [INFO] Running command: blastn -query GCF_002217355.1_ASM221735v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg851add10-5723-4dcf-adb4-4b3483096e2a/dqc_reference/reference_markers.fasta -out GCF_002217355.1_ASM221735v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:25,993] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:25,998] [INFO] Selected 19 target genomes.
[2024-01-24 10:58:25,999] [INFO] Target genome list was writen to GCF_002217355.1_ASM221735v1_genomic.fna/target_genomes.txt
[2024-01-24 10:58:26,009] [INFO] Task started: fastANI
[2024-01-24 10:58:26,009] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb27a377-bb3e-462c-a1b0-352f76881b45/GCF_002217355.1_ASM221735v1_genomic.fna.gz --refList GCF_002217355.1_ASM221735v1_genomic.fna/target_genomes.txt --output GCF_002217355.1_ASM221735v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:47,291] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:47,291] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg851add10-5723-4dcf-adb4-4b3483096e2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:47,292] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg851add10-5723-4dcf-adb4-4b3483096e2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:47,311] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:58:47,311] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:47,312] [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 oncorhynchi	strain=CCUG 59446	GCA_002217355.1	728056	728056	type	True	100.0	1550	1551	95	conclusive
Flavobacterium plurextorum	strain=CCUG 60112	GCA_002217395.1	1114867	1114867	type	True	93.028	1387	1551	95	below_threshold
Flavobacterium panici		GCA_903819335.1	2654843	2654843	type	True	84.7201	1048	1551	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	84.5827	1026	1551	95	below_threshold
Flavobacterium johnsoniae	strain=ATCC 17061	GCA_002221975.1	986	986	type	True	84.3891	1100	1551	95	below_threshold
Flavobacterium defluvii	strain=DSM 17963	GCA_900129555.1	370979	370979	type	True	83.9947	991	1551	95	below_threshold
Flavobacterium chilense	strain=LMG 26360	GCA_001602525.1	946677	946677	type	True	83.6267	1090	1551	95	below_threshold
Flavobacterium chilense	strain=DSM 24724	GCA_900142685.1	946677	946677	type	True	83.5552	1103	1551	95	below_threshold
Flavobacterium cutihirudinis	strain=DSM 25795	GCA_003385895.1	1265740	1265740	type	True	83.5128	1052	1551	95	below_threshold
Flavobacterium hibernum	strain=ATCC 51468	GCA_002217315.1	37752	37752	type	True	83.449	1114	1551	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	83.1209	1022	1551	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	83.0469	991	1551	95	below_threshold
Flavobacterium nitrogenifigens	strain=NXU-44	GCA_003254565.1	1617283	1617283	type	True	83.0219	1047	1551	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	82.8451	1016	1551	95	below_threshold
Flavobacterium reichenbachii	strain=DSM 21791	GCA_002217435.1	362418	362418	type	True	82.6606	947	1551	95	below_threshold
Flavobacterium collinsii		GCA_902804485.1	1114861	1114861	type	True	82.0414	956	1551	95	below_threshold
Flavobacterium hydrophilum	strain=IMCC34758	GCA_003202405.1	2211445	2211445	type	True	81.6387	858	1551	95	below_threshold
Flavobacterium aquicola	strain=DSM 100880	GCA_003385115.1	1682742	1682742	type	True	78.8709	461	1551	95	below_threshold
Flavobacterium branchiophilum	strain=DSM 24789	GCA_006716585.1	55197	55197	type	True	77.3172	171	1551	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:47,313] [INFO] DFAST Taxonomy check result was written to GCF_002217355.1_ASM221735v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:47,314] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:47,314] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:47,314] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg851add10-5723-4dcf-adb4-4b3483096e2a/dqc_reference/checkm_data
[2024-01-24 10:58:47,315] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:47,372] [INFO] Task started: CheckM
[2024-01-24 10:58:47,373] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002217355.1_ASM221735v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002217355.1_ASM221735v1_genomic.fna/checkm_input GCF_002217355.1_ASM221735v1_genomic.fna/checkm_result
[2024-01-24 10:59:34,610] [INFO] Task succeeded: CheckM
[2024-01-24 10:59:34,612] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:59:34,633] [INFO] ===== Completeness check finished =====
[2024-01-24 10:59:34,634] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:59:34,634] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002217355.1_ASM221735v1_genomic.fna/markers.fasta)
[2024-01-24 10:59:34,635] [INFO] Task started: Blastn
[2024-01-24 10:59:34,635] [INFO] Running command: blastn -query GCF_002217355.1_ASM221735v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg851add10-5723-4dcf-adb4-4b3483096e2a/dqc_reference/reference_markers_gtdb.fasta -out GCF_002217355.1_ASM221735v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:59:35,662] [INFO] Task succeeded: Blastn
[2024-01-24 10:59:35,666] [INFO] Selected 18 target genomes.
[2024-01-24 10:59:35,666] [INFO] Target genome list was writen to GCF_002217355.1_ASM221735v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:59:35,696] [INFO] Task started: fastANI
[2024-01-24 10:59:35,696] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb27a377-bb3e-462c-a1b0-352f76881b45/GCF_002217355.1_ASM221735v1_genomic.fna.gz --refList GCF_002217355.1_ASM221735v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002217355.1_ASM221735v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:57,568] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:57,595] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:57,595] [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_002217355.1	s__Flavobacterium oncorhynchi	100.0	1550	1551	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.71	96.71	0.90	0.90	2	conclusive
GCF_004119495.1	s__Flavobacterium sp004119495	94.6799	1377	1551	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002217395.1	s__Flavobacterium plurextorum	93.028	1387	1551	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.27	98.27	0.92	0.92	2	-
GCF_900129795.1	s__Flavobacterium sp900129795	84.7069	1053	1551	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	0.98	0.98	2	-
GCF_002210235.1	s__Flavobacterium sp002210235	84.6558	1042	1551	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.80	96.54	0.96	0.91	4	-
GCA_002482975.1	s__Flavobacterium sp002482975	84.4706	1048	1551	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001879205.1	s__Flavobacterium johnsoniae_A	84.2254	1130	1551	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900182645.1	s__Flavobacterium resistens	83.7235	1013	1551	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCF_003385895.1	s__Flavobacterium cutihirudinis	83.5056	1053	1551	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002754195.1	s__Flavobacterium sp002754195	83.2746	1080	1551	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018383905.1	s__Flavobacterium branchiicola	83.2626	1057	1551	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000708595.2	s__Flavobacterium sp000708595	83.2531	942	1551	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.30	98.27	0.95	0.93	3	-
GCF_009664855.1	s__Flavobacterium sp009664855	82.8678	1007	1551	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.90	98.90	0.89	0.89	2	-
GCF_003105115.1	s__Flavobacterium sp003105115	82.4491	866	1551	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902804485.1	s__Flavobacterium collinsii	82.0347	957	1551	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003202405.1	s__Flavobacterium hydrophilum	81.6467	857	1551	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903469665.1	s__Flavobacterium sp903469665	81.5575	882	1551	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003385115.1	s__Flavobacterium aquicola	78.876	460	1551	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 10:59:57,597] [INFO] GTDB search result was written to GCF_002217355.1_ASM221735v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:57,597] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:57,602] [INFO] DFAST_QC result json was written to GCF_002217355.1_ASM221735v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:57,602] [INFO] DFAST_QC completed!
[2024-01-24 10:59:57,602] [INFO] Total running time: 0h1m51s