[2024-01-25 18:07:50,365] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:07:50,367] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:07:50,367] [INFO] DQC Reference Directory: /var/lib/cwl/stgb3a75bf6-8abf-49a0-b63b-28df719d232c/dqc_reference
[2024-01-25 18:07:51,472] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:07:51,473] [INFO] Task started: Prodigal
[2024-01-25 18:07:51,474] [INFO] Running command: gunzip -c /var/lib/cwl/stgdd81bcd9-f7f7-44bb-b8ca-42de9d77e51f/GCF_009674815.1_ASM967481v1_genomic.fna.gz | prodigal -d GCF_009674815.1_ASM967481v1_genomic.fna/cds.fna -a GCF_009674815.1_ASM967481v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:08:06,049] [INFO] Task succeeded: Prodigal
[2024-01-25 18:08:06,049] [INFO] Task started: HMMsearch
[2024-01-25 18:08:06,049] [INFO] Running command: hmmsearch --tblout GCF_009674815.1_ASM967481v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb3a75bf6-8abf-49a0-b63b-28df719d232c/dqc_reference/reference_markers.hmm GCF_009674815.1_ASM967481v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:08:06,375] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:08:06,378] [INFO] Found 6/6 markers.
[2024-01-25 18:08:06,420] [INFO] Query marker FASTA was written to GCF_009674815.1_ASM967481v1_genomic.fna/markers.fasta
[2024-01-25 18:08:06,421] [INFO] Task started: Blastn
[2024-01-25 18:08:06,421] [INFO] Running command: blastn -query GCF_009674815.1_ASM967481v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3a75bf6-8abf-49a0-b63b-28df719d232c/dqc_reference/reference_markers.fasta -out GCF_009674815.1_ASM967481v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:08:07,095] [INFO] Task succeeded: Blastn
[2024-01-25 18:08:07,098] [INFO] Selected 14 target genomes.
[2024-01-25 18:08:07,098] [INFO] Target genome list was writen to GCF_009674815.1_ASM967481v1_genomic.fna/target_genomes.txt
[2024-01-25 18:08:07,126] [INFO] Task started: fastANI
[2024-01-25 18:08:07,126] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd81bcd9-f7f7-44bb-b8ca-42de9d77e51f/GCF_009674815.1_ASM967481v1_genomic.fna.gz --refList GCF_009674815.1_ASM967481v1_genomic.fna/target_genomes.txt --output GCF_009674815.1_ASM967481v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:08:23,635] [INFO] Task succeeded: fastANI
[2024-01-25 18:08:23,636] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb3a75bf6-8abf-49a0-b63b-28df719d232c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:08:23,636] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb3a75bf6-8abf-49a0-b63b-28df719d232c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:08:23,646] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:08:23,646] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:08:23,646] [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 resistens	strain=DSM 19382	GCA_009674815.1	443612	443612	type	True	100.0	1658	1658	95	conclusive
Flavobacterium resistens	strain=DSM 19382	GCA_900182645.1	443612	443612	type	True	99.9821	1652	1658	95	conclusive
Flavobacterium zhairuonense	strain=A5.7	GCA_004352915.1	2493631	2493631	type	True	87.8131	1376	1658	95	below_threshold
Flavobacterium denitrificans	strain=DSM 15936	GCA_000425445.1	281361	281361	type	True	87.2213	1284	1658	95	below_threshold
Flavobacterium daemonense	strain=JCM 19455	GCA_007341385.1	1393049	1393049	type	True	86.8809	1261	1658	95	below_threshold
Flavobacterium cutihirudinis	strain=DSM 25795	GCA_003385895.1	1265740	1265740	type	True	85.9263	1129	1658	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	84.1865	1056	1658	95	below_threshold
Flavobacterium johnsoniae	strain=ATCC 17061	GCA_002221975.1	986	986	type	True	83.9168	1115	1658	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	83.6197	1101	1658	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	83.4691	1044	1658	95	below_threshold
Flavobacterium crocinum	strain=HYN0056	GCA_003122385.1	2183896	2183896	type	True	83.4182	1095	1658	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	83.3885	1072	1658	95	below_threshold
Flavobacterium chilense	strain=LMG 26360	GCA_001602525.1	946677	946677	type	True	83.1231	1083	1658	95	below_threshold
Flavobacterium jumunjinense	strain=HME7102	GCA_021650975.2	998845	998845	type	True	77.0095	236	1658	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:08:23,649] [INFO] DFAST Taxonomy check result was written to GCF_009674815.1_ASM967481v1_genomic.fna/tc_result.tsv
[2024-01-25 18:08:23,650] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:08:23,650] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:08:23,650] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb3a75bf6-8abf-49a0-b63b-28df719d232c/dqc_reference/checkm_data
[2024-01-25 18:08:23,651] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:08:23,700] [INFO] Task started: CheckM
[2024-01-25 18:08:23,700] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009674815.1_ASM967481v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009674815.1_ASM967481v1_genomic.fna/checkm_input GCF_009674815.1_ASM967481v1_genomic.fna/checkm_result
[2024-01-25 18:09:08,320] [INFO] Task succeeded: CheckM
[2024-01-25 18:09:08,321] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:09:08,338] [INFO] ===== Completeness check finished =====
[2024-01-25 18:09:08,338] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:09:08,338] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009674815.1_ASM967481v1_genomic.fna/markers.fasta)
[2024-01-25 18:09:08,339] [INFO] Task started: Blastn
[2024-01-25 18:09:08,339] [INFO] Running command: blastn -query GCF_009674815.1_ASM967481v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3a75bf6-8abf-49a0-b63b-28df719d232c/dqc_reference/reference_markers_gtdb.fasta -out GCF_009674815.1_ASM967481v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:09:09,288] [INFO] Task succeeded: Blastn
[2024-01-25 18:09:09,292] [INFO] Selected 13 target genomes.
[2024-01-25 18:09:09,292] [INFO] Target genome list was writen to GCF_009674815.1_ASM967481v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:09:09,311] [INFO] Task started: fastANI
[2024-01-25 18:09:09,311] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd81bcd9-f7f7-44bb-b8ca-42de9d77e51f/GCF_009674815.1_ASM967481v1_genomic.fna.gz --refList GCF_009674815.1_ASM967481v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009674815.1_ASM967481v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:09:24,865] [INFO] Task succeeded: fastANI
[2024-01-25 18:09:24,874] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:09:24,875] [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_900182645.1	s__Flavobacterium resistens	99.9821	1652	1658	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.98	99.98	1.00	1.00	2	conclusive
GCF_000745775.1	s__Flavobacterium sp000745775	94.4112	1481	1658	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	87.83	1399	1658	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004352915.1	s__Flavobacterium zhairuonense	87.8227	1375	1658	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425445.1	s__Flavobacterium denitrificans	87.2213	1284	1658	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362055.1	s__Flavobacterium sp004362055	87.1033	1283	1658	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007341385.1	s__Flavobacterium daemonense	86.8872	1260	1658	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003385895.1	s__Flavobacterium cutihirudinis	85.9444	1127	1658	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013388355.1	s__Flavobacterium sp013388355	84.1789	844	1658	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002217355.1	s__Flavobacterium oncorhynchi	83.8697	987	1658	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.71	96.71	0.90	0.90	2	-
GCF_002217395.1	s__Flavobacterium plurextorum	83.684	1006	1658	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.27	98.27	0.92	0.92	2	-
GCF_001429295.1	s__Flavobacterium sp001429295	83.5972	1057	1658	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.90	97.90	0.95	0.95	2	-
GCF_017833855.1	s__Flavobacterium sp017833855	83.1897	1029	1658	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:09:24,877] [INFO] GTDB search result was written to GCF_009674815.1_ASM967481v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:09:24,878] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:09:24,881] [INFO] DFAST_QC result json was written to GCF_009674815.1_ASM967481v1_genomic.fna/dqc_result.json
[2024-01-25 18:09:24,881] [INFO] DFAST_QC completed!
[2024-01-25 18:09:24,881] [INFO] Total running time: 0h1m35s