[2024-01-25 19:55:05,496] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:55:05,497] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:55:05,497] [INFO] DQC Reference Directory: /var/lib/cwl/stg1af057dd-a068-4929-bfef-c3873b252d2d/dqc_reference
[2024-01-25 19:55:06,634] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:55:06,635] [INFO] Task started: Prodigal
[2024-01-25 19:55:06,635] [INFO] Running command: gunzip -c /var/lib/cwl/stg5f67006b-690d-4b45-adda-09d65e7c3c0e/GCF_013403955.1_ASM1340395v1_genomic.fna.gz | prodigal -d GCF_013403955.1_ASM1340395v1_genomic.fna/cds.fna -a GCF_013403955.1_ASM1340395v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:55:17,481] [INFO] Task succeeded: Prodigal
[2024-01-25 19:55:17,482] [INFO] Task started: HMMsearch
[2024-01-25 19:55:17,482] [INFO] Running command: hmmsearch --tblout GCF_013403955.1_ASM1340395v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1af057dd-a068-4929-bfef-c3873b252d2d/dqc_reference/reference_markers.hmm GCF_013403955.1_ASM1340395v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:55:17,747] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:55:17,748] [INFO] Found 6/6 markers.
[2024-01-25 19:55:17,786] [INFO] Query marker FASTA was written to GCF_013403955.1_ASM1340395v1_genomic.fna/markers.fasta
[2024-01-25 19:55:17,787] [INFO] Task started: Blastn
[2024-01-25 19:55:17,787] [INFO] Running command: blastn -query GCF_013403955.1_ASM1340395v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1af057dd-a068-4929-bfef-c3873b252d2d/dqc_reference/reference_markers.fasta -out GCF_013403955.1_ASM1340395v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:55:18,444] [INFO] Task succeeded: Blastn
[2024-01-25 19:55:18,450] [INFO] Selected 18 target genomes.
[2024-01-25 19:55:18,451] [INFO] Target genome list was writen to GCF_013403955.1_ASM1340395v1_genomic.fna/target_genomes.txt
[2024-01-25 19:55:18,471] [INFO] Task started: fastANI
[2024-01-25 19:55:18,471] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f67006b-690d-4b45-adda-09d65e7c3c0e/GCF_013403955.1_ASM1340395v1_genomic.fna.gz --refList GCF_013403955.1_ASM1340395v1_genomic.fna/target_genomes.txt --output GCF_013403955.1_ASM1340395v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:55:34,508] [INFO] Task succeeded: fastANI
[2024-01-25 19:55:34,508] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1af057dd-a068-4929-bfef-c3873b252d2d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:55:34,508] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1af057dd-a068-4929-bfef-c3873b252d2d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:55:34,519] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:55:34,519] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:55:34,520] [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 vidalii	strain=HL634	GCA_013403955.1	2615024	2615024	type	True	100.0	1420	1420	95	conclusive
Winogradskyella helgolandensis	strain=Z963	GCA_013404085.1	2697010	2697010	type	True	81.7827	873	1420	95	below_threshold
Winogradskyella marina	strain=F6397	GCA_015645385.1	2785530	2785530	type	True	81.7245	800	1420	95	below_threshold
Winogradskyella undariae	strain=CCUG 63832	GCA_013285155.1	1285465	1285465	type	True	81.4707	835	1420	95	below_threshold
Winogradskyella wichelsiae	strain=Z738	GCA_013403925.1	2697007	2697007	type	True	81.4222	807	1420	95	below_threshold
Winogradskyella costae	strain=Z3138	GCA_013403865.1	2697008	2697008	type	True	81.1922	794	1420	95	below_threshold
Winogradskyella ludwigii	strain=HL116	GCA_013403985.1	2686076	2686076	type	True	80.9517	768	1420	95	below_threshold
Winogradskyella psychrotolerans	strain=RS-3	GCA_000427335.1	1344585	1344585	type	True	80.8979	819	1420	95	below_threshold
Winogradskyella thalassocola	strain=DSM 15363	GCA_900099995.1	262004	262004	type	True	80.7023	794	1420	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	80.2915	716	1420	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	79.9709	668	1420	95	below_threshold
Winogradskyella eckloniae	strain=EC29	GCA_013249045.1	1089306	1089306	type	True	79.6268	586	1420	95	below_threshold
Winogradskyella schleiferi	strain=Z215	GCA_013394655.1	2686078	2686078	type	True	79.4999	659	1420	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	78.1261	270	1420	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.2363	215	1420	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	77.02	207	1420	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	76.7599	184	1420	95	below_threshold
Hyunsoonleella aquatilis	strain=SJ7	GCA_014270105.1	2762758	2762758	type	True	76.6196	102	1420	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:55:34,521] [INFO] DFAST Taxonomy check result was written to GCF_013403955.1_ASM1340395v1_genomic.fna/tc_result.tsv
[2024-01-25 19:55:34,521] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:55:34,521] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:55:34,522] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1af057dd-a068-4929-bfef-c3873b252d2d/dqc_reference/checkm_data
[2024-01-25 19:55:34,522] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:55:34,564] [INFO] Task started: CheckM
[2024-01-25 19:55:34,565] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013403955.1_ASM1340395v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013403955.1_ASM1340395v1_genomic.fna/checkm_input GCF_013403955.1_ASM1340395v1_genomic.fna/checkm_result
[2024-01-25 19:56:08,725] [INFO] Task succeeded: CheckM
[2024-01-25 19:56:08,726] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:56:08,743] [INFO] ===== Completeness check finished =====
[2024-01-25 19:56:08,743] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:56:08,744] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013403955.1_ASM1340395v1_genomic.fna/markers.fasta)
[2024-01-25 19:56:08,744] [INFO] Task started: Blastn
[2024-01-25 19:56:08,744] [INFO] Running command: blastn -query GCF_013403955.1_ASM1340395v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1af057dd-a068-4929-bfef-c3873b252d2d/dqc_reference/reference_markers_gtdb.fasta -out GCF_013403955.1_ASM1340395v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:56:09,716] [INFO] Task succeeded: Blastn
[2024-01-25 19:56:09,719] [INFO] Selected 16 target genomes.
[2024-01-25 19:56:09,719] [INFO] Target genome list was writen to GCF_013403955.1_ASM1340395v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:56:09,733] [INFO] Task started: fastANI
[2024-01-25 19:56:09,733] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f67006b-690d-4b45-adda-09d65e7c3c0e/GCF_013403955.1_ASM1340395v1_genomic.fna.gz --refList GCF_013403955.1_ASM1340395v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013403955.1_ASM1340395v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:56:23,601] [INFO] Task succeeded: fastANI
[2024-01-25 19:56:23,610] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:56:23,611] [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_013403955.1	s__Winogradskyella vidalii	100.0	1420	1420	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_013404085.1	s__Winogradskyella helgolandensis	81.7706	876	1420	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	98.14	98.14	0.94	0.94	2	-
GCF_015645385.1	s__Winogradskyella sp015645385	81.7229	801	1420	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860545.1	s__Winogradskyella psychrotolerans_A	81.5575	799	1420	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013285155.1	s__Winogradskyella undariae	81.4427	836	1420	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	97.00	96.07	0.88	0.85	4	-
GCF_013403925.1	s__Winogradskyella wichelsiae	81.3997	810	1420	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	81.2032	793	1420	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	80.9588	766	1420	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	80.9399	787	1420	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	97.90	97.90	0.94	0.94	2	-
GCF_018860565.1	s__Winogradskyella psychrotolerans_B	80.9139	752	1420	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	80.9061	818	1420	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	80.679	797	1420	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	80.5283	768	1420	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	80.2854	717	1420	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	98.63	98.63	0.93	0.93	2	-
GCF_013249065.1	s__Winogradskyella litoriviva	79.9772	668	1420	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	79.6079	589	1420	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 19:56:23,612] [INFO] GTDB search result was written to GCF_013403955.1_ASM1340395v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:56:23,613] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:56:23,616] [INFO] DFAST_QC result json was written to GCF_013403955.1_ASM1340395v1_genomic.fna/dqc_result.json
[2024-01-25 19:56:23,616] [INFO] DFAST_QC completed!
[2024-01-25 19:56:23,616] [INFO] Total running time: 0h1m18s