[2024-01-24 11:12:57,079] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:57,082] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:57,082] [INFO] DQC Reference Directory: /var/lib/cwl/stgb16d5b22-8141-4f2d-bac1-e5ebf6bc52c4/dqc_reference
[2024-01-24 11:12:58,433] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:58,434] [INFO] Task started: Prodigal
[2024-01-24 11:12:58,434] [INFO] Running command: gunzip -c /var/lib/cwl/stg94e4d44a-99fe-45d0-92fd-33c782c97b64/GCF_013249065.1_ASM1324906v1_genomic.fna.gz | prodigal -d GCF_013249065.1_ASM1324906v1_genomic.fna/cds.fna -a GCF_013249065.1_ASM1324906v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:09,739] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:09,740] [INFO] Task started: HMMsearch
[2024-01-24 11:13:09,740] [INFO] Running command: hmmsearch --tblout GCF_013249065.1_ASM1324906v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb16d5b22-8141-4f2d-bac1-e5ebf6bc52c4/dqc_reference/reference_markers.hmm GCF_013249065.1_ASM1324906v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:10,059] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:10,060] [INFO] Found 6/6 markers.
[2024-01-24 11:13:10,093] [INFO] Query marker FASTA was written to GCF_013249065.1_ASM1324906v1_genomic.fna/markers.fasta
[2024-01-24 11:13:10,093] [INFO] Task started: Blastn
[2024-01-24 11:13:10,093] [INFO] Running command: blastn -query GCF_013249065.1_ASM1324906v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb16d5b22-8141-4f2d-bac1-e5ebf6bc52c4/dqc_reference/reference_markers.fasta -out GCF_013249065.1_ASM1324906v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:10,842] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:10,845] [INFO] Selected 15 target genomes.
[2024-01-24 11:13:10,846] [INFO] Target genome list was writen to GCF_013249065.1_ASM1324906v1_genomic.fna/target_genomes.txt
[2024-01-24 11:13:10,854] [INFO] Task started: fastANI
[2024-01-24 11:13:10,854] [INFO] Running command: fastANI --query /var/lib/cwl/stg94e4d44a-99fe-45d0-92fd-33c782c97b64/GCF_013249065.1_ASM1324906v1_genomic.fna.gz --refList GCF_013249065.1_ASM1324906v1_genomic.fna/target_genomes.txt --output GCF_013249065.1_ASM1324906v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:23,472] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:23,472] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb16d5b22-8141-4f2d-bac1-e5ebf6bc52c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:23,472] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb16d5b22-8141-4f2d-bac1-e5ebf6bc52c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:23,487] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:13:23,487] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:23,487] [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 litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	100.0	1277	1277	95	conclusive
Winogradskyella endarachnes	strain=HL2-2	GCA_009741275.1	2681965	2681965	type	True	84.1197	888	1277	95	below_threshold
Winogradskyella eckloniae	strain=EC29	GCA_013249045.1	1089306	1089306	type	True	82.0512	789	1277	95	below_threshold
Winogradskyella ludwigii	strain=HL116	GCA_013403985.1	2686076	2686076	type	True	81.0648	742	1277	95	below_threshold
Winogradskyella thalassocola	strain=DSM 15363	GCA_900099995.1	262004	262004	type	True	80.9211	735	1277	95	below_threshold
Winogradskyella helgolandensis	strain=Z963	GCA_013404085.1	2697010	2697010	type	True	80.5693	772	1277	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	80.2937	653	1277	95	below_threshold
Winogradskyella costae	strain=Z3138	GCA_013403865.1	2697008	2697008	type	True	80.1969	667	1277	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	80.1196	674	1277	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	80.1129	676	1277	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	78.2116	305	1277	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	77.7884	305	1277	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	77.6151	230	1277	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	77.3711	211	1277	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	77.2873	209	1277	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:23,489] [INFO] DFAST Taxonomy check result was written to GCF_013249065.1_ASM1324906v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:23,489] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:23,489] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:23,490] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb16d5b22-8141-4f2d-bac1-e5ebf6bc52c4/dqc_reference/checkm_data
[2024-01-24 11:13:23,491] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:23,534] [INFO] Task started: CheckM
[2024-01-24 11:13:23,535] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013249065.1_ASM1324906v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013249065.1_ASM1324906v1_genomic.fna/checkm_input GCF_013249065.1_ASM1324906v1_genomic.fna/checkm_result
[2024-01-24 11:14:00,598] [INFO] Task succeeded: CheckM
[2024-01-24 11:14:00,600] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:14:00,622] [INFO] ===== Completeness check finished =====
[2024-01-24 11:14:00,623] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:14:00,623] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013249065.1_ASM1324906v1_genomic.fna/markers.fasta)
[2024-01-24 11:14:00,624] [INFO] Task started: Blastn
[2024-01-24 11:14:00,624] [INFO] Running command: blastn -query GCF_013249065.1_ASM1324906v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb16d5b22-8141-4f2d-bac1-e5ebf6bc52c4/dqc_reference/reference_markers_gtdb.fasta -out GCF_013249065.1_ASM1324906v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:14:01,606] [INFO] Task succeeded: Blastn
[2024-01-24 11:14:01,610] [INFO] Selected 11 target genomes.
[2024-01-24 11:14:01,610] [INFO] Target genome list was writen to GCF_013249065.1_ASM1324906v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:14:01,619] [INFO] Task started: fastANI
[2024-01-24 11:14:01,619] [INFO] Running command: fastANI --query /var/lib/cwl/stg94e4d44a-99fe-45d0-92fd-33c782c97b64/GCF_013249065.1_ASM1324906v1_genomic.fna.gz --refList GCF_013249065.1_ASM1324906v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013249065.1_ASM1324906v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:11,286] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:11,303] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:14:11,303] [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_013249065.1	s__Winogradskyella litoriviva	100.0	1277	1277	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009741275.1	s__Winogradskyella endarachnes	84.1306	888	1277	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386165.1	s__Winogradskyella eximia	82.3181	817	1277	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013249045.1	s__Winogradskyella eckloniae	82.0583	789	1277	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	81.1056	752	1277	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013403985.1	s__Winogradskyella ludwigii	81.0729	741	1277	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	80.9156	736	1277	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013404085.1	s__Winogradskyella helgolandensis	80.5793	771	1277	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	98.14	98.14	0.94	0.94	2	-
GCF_013403915.1	s__Winogradskyella pacifica	80.5409	685	1277	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	97.90	97.90	0.94	0.94	2	-
GCF_014297365.1	s__Winogradskyella echinorum	80.118	676	1277	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016744625.1	s__Winogradskyella sp016744625	79.626	583	1277	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:14:11,305] [INFO] GTDB search result was written to GCF_013249065.1_ASM1324906v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:11,305] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:11,308] [INFO] DFAST_QC result json was written to GCF_013249065.1_ASM1324906v1_genomic.fna/dqc_result.json
[2024-01-24 11:14:11,309] [INFO] DFAST_QC completed!
[2024-01-24 11:14:11,309] [INFO] Total running time: 0h1m14s