[2024-01-24 12:15:04,133] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:15:04,135] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:15:04,135] [INFO] DQC Reference Directory: /var/lib/cwl/stg39632840-3d97-47c6-84cc-9b552755e92b/dqc_reference
[2024-01-24 12:15:05,511] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:15:05,513] [INFO] Task started: Prodigal
[2024-01-24 12:15:05,513] [INFO] Running command: gunzip -c /var/lib/cwl/stgea1384f6-89dd-4edb-b3d7-44e706f06d21/GCF_021245985.1_ASM2124598v1_genomic.fna.gz | prodigal -d GCF_021245985.1_ASM2124598v1_genomic.fna/cds.fna -a GCF_021245985.1_ASM2124598v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:21,734] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:21,735] [INFO] Task started: HMMsearch
[2024-01-24 12:15:21,735] [INFO] Running command: hmmsearch --tblout GCF_021245985.1_ASM2124598v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg39632840-3d97-47c6-84cc-9b552755e92b/dqc_reference/reference_markers.hmm GCF_021245985.1_ASM2124598v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:21,968] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:21,969] [INFO] Found 6/6 markers.
[2024-01-24 12:15:22,012] [INFO] Query marker FASTA was written to GCF_021245985.1_ASM2124598v1_genomic.fna/markers.fasta
[2024-01-24 12:15:22,012] [INFO] Task started: Blastn
[2024-01-24 12:15:22,012] [INFO] Running command: blastn -query GCF_021245985.1_ASM2124598v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg39632840-3d97-47c6-84cc-9b552755e92b/dqc_reference/reference_markers.fasta -out GCF_021245985.1_ASM2124598v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:22,712] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:22,716] [INFO] Selected 19 target genomes.
[2024-01-24 12:15:22,716] [INFO] Target genome list was writen to GCF_021245985.1_ASM2124598v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:22,725] [INFO] Task started: fastANI
[2024-01-24 12:15:22,726] [INFO] Running command: fastANI --query /var/lib/cwl/stgea1384f6-89dd-4edb-b3d7-44e706f06d21/GCF_021245985.1_ASM2124598v1_genomic.fna.gz --refList GCF_021245985.1_ASM2124598v1_genomic.fna/target_genomes.txt --output GCF_021245985.1_ASM2124598v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:46,190] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:46,190] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg39632840-3d97-47c6-84cc-9b552755e92b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:46,190] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg39632840-3d97-47c6-84cc-9b552755e92b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:46,204] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:15:46,204] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:46,204] [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 soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	100.0	1710	1714	95	conclusive
Flavobacterium panici		GCA_903819335.1	2654843	2654843	type	True	90.8124	1369	1714	95	below_threshold
Flavobacterium defluvii	strain=DSM 17963	GCA_900129555.1	370979	370979	type	True	87.0706	1235	1714	95	below_threshold
Flavobacterium johnsoniae	strain=ATCC 17061	GCA_002221975.1	986	986	type	True	86.0767	1193	1714	95	below_threshold
Flavobacterium johnsoniae	strain=UW101; ATCC 17061	GCA_000016645.1	986	986	type	True	86.0153	1218	1714	95	below_threshold
Flavobacterium johnsoniae	strain=DSM 2064	GCA_900142355.1	986	986	type	True	85.9653	1232	1714	95	below_threshold
Flavobacterium plurextorum	strain=CCUG 60112	GCA_002217395.1	1114867	1114867	type	True	84.4099	1023	1714	95	below_threshold
Flavobacterium resistens	strain=DSM 19382	GCA_009674815.1	443612	443612	type	True	84.2759	1049	1714	95	below_threshold
Flavobacterium resistens	strain=DSM 19382	GCA_900182645.1	443612	443612	type	True	84.2244	1055	1714	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	84.0893	1185	1714	95	below_threshold
Flavobacterium chilense	strain=DSM 24724	GCA_900142685.1	946677	946677	type	True	83.8613	1093	1714	95	below_threshold
Flavobacterium chilense	strain=LMG 26360	GCA_001602525.1	946677	946677	type	True	83.8103	1106	1714	95	below_threshold
Flavobacterium daemonense	strain=JCM 19455	GCA_007341385.1	1393049	1393049	type	True	83.7665	1021	1714	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	83.5703	1081	1714	95	below_threshold
Flavobacterium pectinovorum	strain=DSM 6368	GCA_900142715.1	29533	29533	type	True	83.5076	1170	1714	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	83.0915	1079	1714	95	below_threshold
Flavobacterium reichenbachii	strain=DSM 21791	GCA_002217435.1	362418	362418	type	True	83.0842	1043	1714	95	below_threshold
Flavobacterium tructae	strain=CCUG 60100	GCA_002217475.1	1114873	1114873	type	True	81.9929	892	1714	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	76.9361	203	1714	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:46,206] [INFO] DFAST Taxonomy check result was written to GCF_021245985.1_ASM2124598v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:46,208] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:46,208] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:46,208] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg39632840-3d97-47c6-84cc-9b552755e92b/dqc_reference/checkm_data
[2024-01-24 12:15:46,209] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:46,257] [INFO] Task started: CheckM
[2024-01-24 12:15:46,257] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021245985.1_ASM2124598v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021245985.1_ASM2124598v1_genomic.fna/checkm_input GCF_021245985.1_ASM2124598v1_genomic.fna/checkm_result
[2024-01-24 12:16:33,037] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:33,039] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:33,058] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:33,058] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:33,058] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021245985.1_ASM2124598v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:33,059] [INFO] Task started: Blastn
[2024-01-24 12:16:33,059] [INFO] Running command: blastn -query GCF_021245985.1_ASM2124598v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg39632840-3d97-47c6-84cc-9b552755e92b/dqc_reference/reference_markers_gtdb.fasta -out GCF_021245985.1_ASM2124598v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:33,982] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:33,985] [INFO] Selected 15 target genomes.
[2024-01-24 12:16:33,985] [INFO] Target genome list was writen to GCF_021245985.1_ASM2124598v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:33,994] [INFO] Task started: fastANI
[2024-01-24 12:16:33,994] [INFO] Running command: fastANI --query /var/lib/cwl/stgea1384f6-89dd-4edb-b3d7-44e706f06d21/GCF_021245985.1_ASM2124598v1_genomic.fna.gz --refList GCF_021245985.1_ASM2124598v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021245985.1_ASM2124598v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:52,634] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:52,646] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:16:52,647] [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_900129795.1	s__Flavobacterium sp900129795	91.3522	1439	1714	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	90.7768	1395	1714	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	90.7426	1339	1714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428525.1	s__Flavobacterium sp001428525	90.407	1364	1714	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	87.0469	1238	1714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001429765.1	s__Flavobacterium sp001429765	86.4803	1227	1714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.48	98.48	0.97	0.97	2	-
GCF_000016645.1	s__Flavobacterium johnsoniae	86.0153	1218	1714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.23	96.72	0.94	0.86	7	-
GCF_001879205.1	s__Flavobacterium johnsoniae_A	85.9037	1208	1714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009711135.1	s__Flavobacterium sp009711135	84.2649	1072	1714	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	84.2223	1055	1714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCF_004362055.1	s__Flavobacterium sp004362055	84.056	1042	1714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001602525.1	s__Flavobacterium chilense	83.802	1107	1714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.30	96.61	0.93	0.86	3	-
GCF_004352915.1	s__Flavobacterium zhairuonense	83.569	1054	1714	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	83.3756	1113	1714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002217475.1	s__Flavobacterium tructae	82.0037	890	1714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.59	96.94	0.94	0.93	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:52,648] [INFO] GTDB search result was written to GCF_021245985.1_ASM2124598v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:52,649] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:52,652] [INFO] DFAST_QC result json was written to GCF_021245985.1_ASM2124598v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:52,652] [INFO] DFAST_QC completed!
[2024-01-24 12:16:52,652] [INFO] Total running time: 0h1m49s