[2024-01-25 19:00:35,538] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:00:35,539] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:00:35,539] [INFO] DQC Reference Directory: /var/lib/cwl/stge785af3b-4574-4581-a023-b8ac4dfc6b67/dqc_reference
[2024-01-25 19:00:36,655] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:00:36,656] [INFO] Task started: Prodigal
[2024-01-25 19:00:36,657] [INFO] Running command: gunzip -c /var/lib/cwl/stg36518b33-a27b-4c77-b5a2-a4d84ff43030/GCF_013404085.1_ASM1340408v1_genomic.fna.gz | prodigal -d GCF_013404085.1_ASM1340408v1_genomic.fna/cds.fna -a GCF_013404085.1_ASM1340408v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:00:48,532] [INFO] Task succeeded: Prodigal
[2024-01-25 19:00:48,533] [INFO] Task started: HMMsearch
[2024-01-25 19:00:48,533] [INFO] Running command: hmmsearch --tblout GCF_013404085.1_ASM1340408v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge785af3b-4574-4581-a023-b8ac4dfc6b67/dqc_reference/reference_markers.hmm GCF_013404085.1_ASM1340408v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:00:48,823] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:00:48,824] [INFO] Found 6/6 markers.
[2024-01-25 19:00:48,864] [INFO] Query marker FASTA was written to GCF_013404085.1_ASM1340408v1_genomic.fna/markers.fasta
[2024-01-25 19:00:48,864] [INFO] Task started: Blastn
[2024-01-25 19:00:48,864] [INFO] Running command: blastn -query GCF_013404085.1_ASM1340408v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge785af3b-4574-4581-a023-b8ac4dfc6b67/dqc_reference/reference_markers.fasta -out GCF_013404085.1_ASM1340408v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:00:49,529] [INFO] Task succeeded: Blastn
[2024-01-25 19:00:49,531] [INFO] Selected 14 target genomes.
[2024-01-25 19:00:49,532] [INFO] Target genome list was writen to GCF_013404085.1_ASM1340408v1_genomic.fna/target_genomes.txt
[2024-01-25 19:00:49,540] [INFO] Task started: fastANI
[2024-01-25 19:00:49,540] [INFO] Running command: fastANI --query /var/lib/cwl/stg36518b33-a27b-4c77-b5a2-a4d84ff43030/GCF_013404085.1_ASM1340408v1_genomic.fna.gz --refList GCF_013404085.1_ASM1340408v1_genomic.fna/target_genomes.txt --output GCF_013404085.1_ASM1340408v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:01:03,532] [INFO] Task succeeded: fastANI
[2024-01-25 19:01:03,533] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge785af3b-4574-4581-a023-b8ac4dfc6b67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:01:03,533] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge785af3b-4574-4581-a023-b8ac4dfc6b67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:01:03,544] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:01:03,544] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:01:03,544] [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
Winogradskyella helgolandensis	strain=Z963	GCA_013404085.1	2697010	2697010	type	True	100.0	1530	1532	95	conclusive
Winogradskyella thalassocola	strain=DSM 15363	GCA_900099995.1	262004	262004	type	True	86.3338	1134	1532	95	below_threshold
Winogradskyella costae	strain=Z3138	GCA_013403865.1	2697008	2697008	type	True	86.1584	1048	1532	95	below_threshold
Winogradskyella psychrotolerans	strain=RS-3	GCA_000427335.1	1344585	1344585	type	True	84.9731	1032	1532	95	below_threshold
Winogradskyella ludwigii	strain=HL116	GCA_013403985.1	2686076	2686076	type	True	83.5665	961	1532	95	below_threshold
Winogradskyella marina	strain=F6397	GCA_015645385.1	2785530	2785530	type	True	83.3718	967	1532	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	82.8015	928	1532	95	below_threshold
Winogradskyella vidalii	strain=HL634	GCA_013403955.1	2615024	2615024	type	True	81.6085	867	1532	95	below_threshold
Winogradskyella eckloniae	strain=EC29	GCA_013249045.1	1089306	1089306	type	True	79.9738	675	1532	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	77.8179	271	1532	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	77.4407	205	1532	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	77.3698	184	1532	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	77.2802	198	1532	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	77.1959	179	1532	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:01:03,556] [INFO] DFAST Taxonomy check result was written to GCF_013404085.1_ASM1340408v1_genomic.fna/tc_result.tsv
[2024-01-25 19:01:03,558] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:01:03,558] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:01:03,558] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge785af3b-4574-4581-a023-b8ac4dfc6b67/dqc_reference/checkm_data
[2024-01-25 19:01:03,559] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:01:03,605] [INFO] Task started: CheckM
[2024-01-25 19:01:03,606] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013404085.1_ASM1340408v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013404085.1_ASM1340408v1_genomic.fna/checkm_input GCF_013404085.1_ASM1340408v1_genomic.fna/checkm_result
[2024-01-25 19:01:40,300] [INFO] Task succeeded: CheckM
[2024-01-25 19:01:40,301] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:01:40,321] [INFO] ===== Completeness check finished =====
[2024-01-25 19:01:40,321] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:01:40,322] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013404085.1_ASM1340408v1_genomic.fna/markers.fasta)
[2024-01-25 19:01:40,322] [INFO] Task started: Blastn
[2024-01-25 19:01:40,322] [INFO] Running command: blastn -query GCF_013404085.1_ASM1340408v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge785af3b-4574-4581-a023-b8ac4dfc6b67/dqc_reference/reference_markers_gtdb.fasta -out GCF_013404085.1_ASM1340408v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:01:41,303] [INFO] Task succeeded: Blastn
[2024-01-25 19:01:41,306] [INFO] Selected 10 target genomes.
[2024-01-25 19:01:41,306] [INFO] Target genome list was writen to GCF_013404085.1_ASM1340408v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:01:41,327] [INFO] Task started: fastANI
[2024-01-25 19:01:41,327] [INFO] Running command: fastANI --query /var/lib/cwl/stg36518b33-a27b-4c77-b5a2-a4d84ff43030/GCF_013404085.1_ASM1340408v1_genomic.fna.gz --refList GCF_013404085.1_ASM1340408v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013404085.1_ASM1340408v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:01:52,123] [INFO] Task succeeded: fastANI
[2024-01-25 19:01:52,130] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:01:52,131] [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_013404085.1	s__Winogradskyella helgolandensis	100.0	1530	1532	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	98.14	98.14	0.94	0.94	2	conclusive
GCF_018860545.1	s__Winogradskyella psychrotolerans_A	88.6742	1162	1532	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900099995.1	s__Winogradskyella thalassocola	86.3339	1134	1532	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013403865.1	s__Winogradskyella costae	86.1762	1046	1532	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000427335.1	s__Winogradskyella psychrotolerans	84.9922	1030	1532	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013403915.1	s__Winogradskyella pacifica	84.8236	1007	1532	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	97.90	97.90	0.94	0.94	2	-
GCF_015645385.1	s__Winogradskyella sp015645385	83.3642	968	1532	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860565.1	s__Winogradskyella psychrotolerans_B	82.8789	906	1532	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003387355.1	s__Winogradskyella sediminis	82.8291	929	1532	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	98.63	98.63	0.93	0.93	2	-
GCF_003386165.1	s__Winogradskyella eximia	82.1878	895	1532	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:01:52,133] [INFO] GTDB search result was written to GCF_013404085.1_ASM1340408v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:01:52,134] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:01:52,145] [INFO] DFAST_QC result json was written to GCF_013404085.1_ASM1340408v1_genomic.fna/dqc_result.json
[2024-01-25 19:01:52,145] [INFO] DFAST_QC completed!
[2024-01-25 19:01:52,145] [INFO] Total running time: 0h1m17s