[2024-01-24 14:13:18,728] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:13:18,731] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:13:18,731] [INFO] DQC Reference Directory: /var/lib/cwl/stgacc71aa8-df24-41b6-b7b5-9c0220c2d0c9/dqc_reference
[2024-01-24 14:13:20,024] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:13:20,024] [INFO] Task started: Prodigal
[2024-01-24 14:13:20,025] [INFO] Running command: gunzip -c /var/lib/cwl/stg25c6f46f-dfc9-4ed7-892f-06efa0a208f2/GCF_006385255.1_ASM638525v1_genomic.fna.gz | prodigal -d GCF_006385255.1_ASM638525v1_genomic.fna/cds.fna -a GCF_006385255.1_ASM638525v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:13:36,678] [INFO] Task succeeded: Prodigal
[2024-01-24 14:13:36,678] [INFO] Task started: HMMsearch
[2024-01-24 14:13:36,678] [INFO] Running command: hmmsearch --tblout GCF_006385255.1_ASM638525v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgacc71aa8-df24-41b6-b7b5-9c0220c2d0c9/dqc_reference/reference_markers.hmm GCF_006385255.1_ASM638525v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:13:36,967] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:13:36,968] [INFO] Found 6/6 markers.
[2024-01-24 14:13:37,007] [INFO] Query marker FASTA was written to GCF_006385255.1_ASM638525v1_genomic.fna/markers.fasta
[2024-01-24 14:13:37,007] [INFO] Task started: Blastn
[2024-01-24 14:13:37,007] [INFO] Running command: blastn -query GCF_006385255.1_ASM638525v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgacc71aa8-df24-41b6-b7b5-9c0220c2d0c9/dqc_reference/reference_markers.fasta -out GCF_006385255.1_ASM638525v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:37,737] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:37,740] [INFO] Selected 10 target genomes.
[2024-01-24 14:13:37,740] [INFO] Target genome list was writen to GCF_006385255.1_ASM638525v1_genomic.fna/target_genomes.txt
[2024-01-24 14:13:37,745] [INFO] Task started: fastANI
[2024-01-24 14:13:37,745] [INFO] Running command: fastANI --query /var/lib/cwl/stg25c6f46f-dfc9-4ed7-892f-06efa0a208f2/GCF_006385255.1_ASM638525v1_genomic.fna.gz --refList GCF_006385255.1_ASM638525v1_genomic.fna/target_genomes.txt --output GCF_006385255.1_ASM638525v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:13:45,485] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:45,486] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgacc71aa8-df24-41b6-b7b5-9c0220c2d0c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:13:45,486] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgacc71aa8-df24-41b6-b7b5-9c0220c2d0c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:13:45,494] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:13:45,495] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:13:45,495] [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 microcysteis	strain=MaA-Y11	GCA_006385255.1	2596891	2596891	type	True	100.0	1335	1338	95	conclusive
Flavobacterium lindanitolerans	strain=DSM 21886	GCA_003663835.1	428988	428988	type	True	87.1592	1053	1338	95	below_threshold
Flavobacterium lindanitolerans	strain=IP-10	GCA_002846575.1	428988	428988	type	True	87.1199	1058	1338	95	below_threshold
Flavobacterium gossypii	strain=DSM 100397	GCA_014138495.1	1646119	1646119	type	True	81.8321	846	1338	95	below_threshold
Flavobacterium endophyticum	strain=DSM 29537	GCA_003634455.1	1540163	1540163	type	True	81.7801	852	1338	95	below_threshold
Flavobacterium amniphilum	strain=KYPY10	GCA_023634845.1	1834035	1834035	type	True	77.5904	147	1338	95	below_threshold
Flavobacterium taihuense	strain=NAS39	GCA_019351435.1	2857508	2857508	type	True	77.3526	192	1338	95	below_threshold
Flavobacterium alkalisoli	strain=XS-5	GCA_008000935.1	2602769	2602769	type	True	77.0518	139	1338	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	76.2144	51	1338	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:13:45,496] [INFO] DFAST Taxonomy check result was written to GCF_006385255.1_ASM638525v1_genomic.fna/tc_result.tsv
[2024-01-24 14:13:45,497] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:13:45,497] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:13:45,497] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgacc71aa8-df24-41b6-b7b5-9c0220c2d0c9/dqc_reference/checkm_data
[2024-01-24 14:13:45,498] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:13:45,544] [INFO] Task started: CheckM
[2024-01-24 14:13:45,544] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006385255.1_ASM638525v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006385255.1_ASM638525v1_genomic.fna/checkm_input GCF_006385255.1_ASM638525v1_genomic.fna/checkm_result
[2024-01-24 14:14:34,121] [INFO] Task succeeded: CheckM
[2024-01-24 14:14:34,122] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:14:34,144] [INFO] ===== Completeness check finished =====
[2024-01-24 14:14:34,145] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:14:34,145] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006385255.1_ASM638525v1_genomic.fna/markers.fasta)
[2024-01-24 14:14:34,145] [INFO] Task started: Blastn
[2024-01-24 14:14:34,146] [INFO] Running command: blastn -query GCF_006385255.1_ASM638525v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgacc71aa8-df24-41b6-b7b5-9c0220c2d0c9/dqc_reference/reference_markers_gtdb.fasta -out GCF_006385255.1_ASM638525v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:35,047] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:35,051] [INFO] Selected 11 target genomes.
[2024-01-24 14:14:35,051] [INFO] Target genome list was writen to GCF_006385255.1_ASM638525v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:14:35,062] [INFO] Task started: fastANI
[2024-01-24 14:14:35,062] [INFO] Running command: fastANI --query /var/lib/cwl/stg25c6f46f-dfc9-4ed7-892f-06efa0a208f2/GCF_006385255.1_ASM638525v1_genomic.fna.gz --refList GCF_006385255.1_ASM638525v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006385255.1_ASM638525v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:14:43,454] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:43,466] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:14:43,466] [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_006385255.1	s__Flavobacterium microcysteis	100.0	1335	1338	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_002846575.1	s__Flavobacterium lindanitolerans	87.1199	1058	1338	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.86	97.14	0.91	0.85	11	-
GCF_003634455.1	s__Flavobacterium endophyticum	81.7801	852	1338	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.19	97.19	0.95	0.95	2	-
GCF_003865365.1	s__Flavobacterium macacae	79.179	439	1338	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422705.1	s__Flavobacterium soli	78.2072	299	1338	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002210235.1	s__Flavobacterium sp002210235	77.7894	221	1338	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.80	96.54	0.96	0.91	4	-
GCF_003076475.1	s__Flavobacterium kingsejongi	77.6879	232	1338	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017875765.1	s__Flavobacterium sp017875765	77.679	186	1338	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.17	98.17	0.94	0.94	2	-
GCA_002352205.1	s__Flavobacterium sp002352205	77.523	166	1338	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.95	99.95	0.86	0.86	2	-
GCF_004349315.1	s__Flavobacterium sp004349315	77.5042	207	1338	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.48	98.48	0.90	0.90	2	-
GCA_002482975.1	s__Flavobacterium sp002482975	77.4372	230	1338	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 14:14:43,468] [INFO] GTDB search result was written to GCF_006385255.1_ASM638525v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:14:43,468] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:14:43,472] [INFO] DFAST_QC result json was written to GCF_006385255.1_ASM638525v1_genomic.fna/dqc_result.json
[2024-01-24 14:14:43,472] [INFO] DFAST_QC completed!
[2024-01-24 14:14:43,472] [INFO] Total running time: 0h1m25s