[2024-01-24 12:51:05,226] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:51:05,228] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:51:05,228] [INFO] DQC Reference Directory: /var/lib/cwl/stg6edb3d36-fb89-43c2-86b6-b1079562367e/dqc_reference
[2024-01-24 12:51:06,420] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:51:06,421] [INFO] Task started: Prodigal
[2024-01-24 12:51:06,421] [INFO] Running command: gunzip -c /var/lib/cwl/stg6eb60aa5-4867-4343-8176-99e3e42696a5/GCF_015182285.1_ASM1518228v1_genomic.fna.gz | prodigal -d GCF_015182285.1_ASM1518228v1_genomic.fna/cds.fna -a GCF_015182285.1_ASM1518228v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:51:26,453] [INFO] Task succeeded: Prodigal
[2024-01-24 12:51:26,453] [INFO] Task started: HMMsearch
[2024-01-24 12:51:26,454] [INFO] Running command: hmmsearch --tblout GCF_015182285.1_ASM1518228v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6edb3d36-fb89-43c2-86b6-b1079562367e/dqc_reference/reference_markers.hmm GCF_015182285.1_ASM1518228v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:51:26,744] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:51:26,745] [INFO] Found 6/6 markers.
[2024-01-24 12:51:26,792] [INFO] Query marker FASTA was written to GCF_015182285.1_ASM1518228v1_genomic.fna/markers.fasta
[2024-01-24 12:51:26,792] [INFO] Task started: Blastn
[2024-01-24 12:51:26,792] [INFO] Running command: blastn -query GCF_015182285.1_ASM1518228v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6edb3d36-fb89-43c2-86b6-b1079562367e/dqc_reference/reference_markers.fasta -out GCF_015182285.1_ASM1518228v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:51:27,504] [INFO] Task succeeded: Blastn
[2024-01-24 12:51:27,508] [INFO] Selected 25 target genomes.
[2024-01-24 12:51:27,509] [INFO] Target genome list was writen to GCF_015182285.1_ASM1518228v1_genomic.fna/target_genomes.txt
[2024-01-24 12:51:27,521] [INFO] Task started: fastANI
[2024-01-24 12:51:27,522] [INFO] Running command: fastANI --query /var/lib/cwl/stg6eb60aa5-4867-4343-8176-99e3e42696a5/GCF_015182285.1_ASM1518228v1_genomic.fna.gz --refList GCF_015182285.1_ASM1518228v1_genomic.fna/target_genomes.txt --output GCF_015182285.1_ASM1518228v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:51:55,950] [INFO] Task succeeded: fastANI
[2024-01-24 12:51:55,951] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6edb3d36-fb89-43c2-86b6-b1079562367e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:51:55,952] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6edb3d36-fb89-43c2-86b6-b1079562367e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:51:55,975] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:51:55,975] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:51:55,975] [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 fluviale	strain=HYN0086	GCA_003312915.1	2249356	2249356	type	True	83.9538	1198	1952	95	below_threshold
Flavobacterium ustbae	strain=T13	GCA_003946915.1	2488790	2488790	type	True	83.6247	1176	1952	95	below_threshold
Flavobacterium sharifuzzamanii	strain=A7.6	GCA_003254585.1	2211133	2211133	type	True	83.1864	1151	1952	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	83.165	1213	1952	95	below_threshold
Flavobacterium chungbukense	strain=CS100	GCA_020805785.1	877464	877464	type	True	83.0916	1236	1952	95	below_threshold
Flavobacterium tistrianum	strain=GB 56.1	GCA_003254545.1	1685414	1685414	type	True	83.0882	1127	1952	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	83.0132	1211	1952	95	below_threshold
Flavobacterium anhuiense	strain=CGMCC 1.6859	GCA_900101855.1	459526	459526	suspected-type	True	82.9777	1179	1952	95	below_threshold
Flavobacterium quisquiliarum	strain=EA-12	GCA_019308285.1	1834436	1834436	type	True	82.9727	1236	1952	95	below_threshold
Flavobacterium johnsoniae	strain=DSM 2064	GCA_900142355.1	986	986	type	True	82.9149	1215	1952	95	below_threshold
Flavobacterium johnsoniae	strain=UW101; ATCC 17061	GCA_000016645.1	986	986	type	True	82.908	1227	1952	95	below_threshold
Flavobacterium johnsoniae	strain=ATCC 17061	GCA_002221975.1	986	986	type	True	82.8241	1228	1952	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	82.6481	1082	1952	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	82.3924	1175	1952	95	below_threshold
Flavobacterium defluvii	strain=DSM 17963	GCA_900129555.1	370979	370979	type	True	82.2861	1069	1952	95	below_threshold
Flavobacterium reichenbachii	strain=DSM 21791	GCA_002217435.1	362418	362418	type	True	82.2434	1166	1952	95	below_threshold
Flavobacterium plurextorum	strain=CCUG 60112	GCA_002217395.1	1114867	1114867	type	True	82.0609	1000	1952	95	below_threshold
Flavobacterium chilense	strain=LMG 26360	GCA_001602525.1	946677	946677	type	True	81.8852	1077	1952	95	below_threshold
Flavobacterium pectinovorum	strain=ATCC 19366	GCA_002217365.1	29533	29533	type	True	81.7584	1116	1952	95	below_threshold
Flavobacterium pectinovorum	strain=DSM 6368	GCA_900142715.1	29533	29533	type	True	81.702	1127	1952	95	below_threshold
Flavobacterium psychroterrae	strain=CCM 8827	GCA_018380615.1	2133767	2133767	type	True	81.3747	1059	1952	95	below_threshold
Flavobacterium collinsii		GCA_902804485.1	1114861	1114861	type	True	81.0726	854	1952	95	below_threshold
Flavobacterium salmonis	strain=CIP 111411	GCA_903819435.1	2654844	2654844	type	True	80.9902	920	1952	95	below_threshold
Flavobacterium tructae	strain=CCUG 60100	GCA_002217475.1	1114873	1114873	type	True	80.8999	845	1952	95	below_threshold
Flavobacterium oreochromis	strain=Costa Rica 04-02-TN	GCA_019565455.1	2906078	2906078	type	True	76.9313	167	1952	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:51:55,977] [INFO] DFAST Taxonomy check result was written to GCF_015182285.1_ASM1518228v1_genomic.fna/tc_result.tsv
[2024-01-24 12:51:55,978] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:51:55,978] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:51:55,978] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6edb3d36-fb89-43c2-86b6-b1079562367e/dqc_reference/checkm_data
[2024-01-24 12:51:55,979] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:51:56,040] [INFO] Task started: CheckM
[2024-01-24 12:51:56,041] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015182285.1_ASM1518228v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015182285.1_ASM1518228v1_genomic.fna/checkm_input GCF_015182285.1_ASM1518228v1_genomic.fna/checkm_result
[2024-01-24 12:52:54,042] [INFO] Task succeeded: CheckM
[2024-01-24 12:52:54,043] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:52:54,065] [INFO] ===== Completeness check finished =====
[2024-01-24 12:52:54,065] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:52:54,066] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015182285.1_ASM1518228v1_genomic.fna/markers.fasta)
[2024-01-24 12:52:54,066] [INFO] Task started: Blastn
[2024-01-24 12:52:54,066] [INFO] Running command: blastn -query GCF_015182285.1_ASM1518228v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6edb3d36-fb89-43c2-86b6-b1079562367e/dqc_reference/reference_markers_gtdb.fasta -out GCF_015182285.1_ASM1518228v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:52:55,012] [INFO] Task succeeded: Blastn
[2024-01-24 12:52:55,015] [INFO] Selected 22 target genomes.
[2024-01-24 12:52:55,015] [INFO] Target genome list was writen to GCF_015182285.1_ASM1518228v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:52:55,087] [INFO] Task started: fastANI
[2024-01-24 12:52:55,087] [INFO] Running command: fastANI --query /var/lib/cwl/stg6eb60aa5-4867-4343-8176-99e3e42696a5/GCF_015182285.1_ASM1518228v1_genomic.fna.gz --refList GCF_015182285.1_ASM1518228v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015182285.1_ASM1518228v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:53:21,091] [INFO] Task succeeded: fastANI
[2024-01-24 12:53:21,114] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:53:21,114] [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_015182285.1	s__Flavobacterium sp015182285	100.0	1950	1952	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_001429295.1	s__Flavobacterium sp001429295	83.9832	1224	1952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.90	97.90	0.95	0.95	2	-
GCF_003312915.1	s__Flavobacterium sp003312915	83.9673	1199	1952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946915.1	s__Flavobacterium sp003946915	83.6039	1179	1952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002304005.1	s__Flavobacterium sp002304005	83.5328	1214	1952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254585.1	s__Flavobacterium sharifuzzamanii	83.1861	1151	1952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016405855.1	s__Flavobacterium sp002399805	83.1786	1192	1952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.61	96.61	0.90	0.90	2	-
GCF_900101855.1	s__Flavobacterium anhuiense	82.9927	1177	1952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.61	97.43	0.90	0.88	4	-
GCA_017744675.1	s__Flavobacterium sp017744675	82.9397	1155	1952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207905.1	s__Flavobacterium notoginsengisoli	82.9207	1223	1952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000016645.1	s__Flavobacterium johnsoniae	82.9205	1226	1952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.23	96.72	0.94	0.86	7	-
GCF_004362055.1	s__Flavobacterium sp004362055	82.3438	1063	1952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129555.1	s__Flavobacterium defluvii	82.2794	1070	1952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017833855.1	s__Flavobacterium sp017833855	82.2652	1054	1952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002217435.1	s__Flavobacterium reichenbachii	82.265	1164	1952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.98	99.98	0.99	0.99	2	-
GCF_002217395.1	s__Flavobacterium plurextorum	82.068	998	1952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.27	98.27	0.92	0.92	2	-
GCF_003105115.1	s__Flavobacterium sp003105115	81.9321	963	1952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003688345.1	s__Flavobacterium sp003688345	81.8573	1092	1952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900142715.1	s__Flavobacterium pectinovorum	81.7275	1123	1952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.30	96.60	0.94	0.89	3	-
GCF_018380615.1	s__Flavobacterium psychroterrae	81.3658	1060	1952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000735715.2	s__Flavobacterium chungangense	81.0767	924	1952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.81	95.16	0.89	0.84	4	-
GCF_903469665.1	s__Flavobacterium sp903469665	80.9883	825	1952	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 12:53:21,116] [INFO] GTDB search result was written to GCF_015182285.1_ASM1518228v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:53:21,117] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:53:21,121] [INFO] DFAST_QC result json was written to GCF_015182285.1_ASM1518228v1_genomic.fna/dqc_result.json
[2024-01-24 12:53:21,121] [INFO] DFAST_QC completed!
[2024-01-24 12:53:21,121] [INFO] Total running time: 0h2m16s