[2023-06-28 14:18:54,864] [INFO] DFAST_QC pipeline started.
[2023-06-28 14:18:54,866] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 14:18:54,866] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c7f5c01-acbe-429b-828a-0c60476c670a/dqc_reference
[2023-06-28 14:18:55,966] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 14:18:55,966] [INFO] Task started: Prodigal
[2023-06-28 14:18:55,966] [INFO] Running command: gunzip -c /var/lib/cwl/stg8eaf2395-8138-4c7c-948d-24d9fa004ee4/GCA_913061495.1_SRR3933287_bin.9_MetaBAT_v2.12.1_MAG_genomic.fna.gz | prodigal -d GCA_913061495.1_SRR3933287_bin.9_MetaBAT_v2.12.1_MAG_genomic.fna/cds.fna -a GCA_913061495.1_SRR3933287_bin.9_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 14:19:04,683] [INFO] Task succeeded: Prodigal
[2023-06-28 14:19:04,683] [INFO] Task started: HMMsearch
[2023-06-28 14:19:04,683] [INFO] Running command: hmmsearch --tblout GCA_913061495.1_SRR3933287_bin.9_MetaBAT_v2.12.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c7f5c01-acbe-429b-828a-0c60476c670a/dqc_reference/reference_markers.hmm GCA_913061495.1_SRR3933287_bin.9_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-28 14:19:04,888] [INFO] Task succeeded: HMMsearch
[2023-06-28 14:19:04,889] [INFO] Found 6/6 markers.
[2023-06-28 14:19:04,917] [INFO] Query marker FASTA was written to GCA_913061495.1_SRR3933287_bin.9_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta
[2023-06-28 14:19:04,918] [INFO] Task started: Blastn
[2023-06-28 14:19:04,918] [INFO] Running command: blastn -query GCA_913061495.1_SRR3933287_bin.9_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c7f5c01-acbe-429b-828a-0c60476c670a/dqc_reference/reference_markers.fasta -out GCA_913061495.1_SRR3933287_bin.9_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 14:19:05,545] [INFO] Task succeeded: Blastn
[2023-06-28 14:19:05,548] [INFO] Selected 28 target genomes.
[2023-06-28 14:19:05,549] [INFO] Target genome list was writen to GCA_913061495.1_SRR3933287_bin.9_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt
[2023-06-28 14:19:05,600] [INFO] Task started: fastANI
[2023-06-28 14:19:05,600] [INFO] Running command: fastANI --query /var/lib/cwl/stg8eaf2395-8138-4c7c-948d-24d9fa004ee4/GCA_913061495.1_SRR3933287_bin.9_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913061495.1_SRR3933287_bin.9_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt --output GCA_913061495.1_SRR3933287_bin.9_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 14:19:24,013] [INFO] Task succeeded: fastANI
[2023-06-28 14:19:24,013] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c7f5c01-acbe-429b-828a-0c60476c670a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 14:19:24,013] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c7f5c01-acbe-429b-828a-0c60476c670a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 14:19:24,028] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 14:19:24,029] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 14:19:24,029] [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 echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	79.0378	399	913	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	79.0323	400	913	95	below_threshold
Winogradskyella marina	strain=F6397	GCA_015645385.1	2785530	2785530	type	True	78.8059	365	913	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	78.8016	351	913	95	below_threshold
Winogradskyella ouciana	strain=ZXX205	GCA_009709615.1	2608631	2608631	type	True	78.7991	383	913	95	below_threshold
Winogradskyella schleiferi	strain=Z215	GCA_013394655.1	2686078	2686078	type	True	78.766	368	913	95	below_threshold
Winogradskyella eckloniae	strain=EC29	GCA_013249045.1	1089306	1089306	type	True	78.6507	318	913	95	below_threshold
Winogradskyella ludwigii	strain=HL116	GCA_013403985.1	2686076	2686076	type	True	78.5942	370	913	95	below_threshold
Winogradskyella helgolandensis	strain=Z963	GCA_013404085.1	2697010	2697010	type	True	78.5434	389	913	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	78.537	374	913	95	below_threshold
Winogradskyella endarachnes	strain=HL2-2	GCA_009741275.1	2681965	2681965	type	True	78.5222	358	913	95	below_threshold
Winogradskyella costae	strain=Z3138	GCA_013403865.1	2697008	2697008	type	True	78.5073	359	913	95	below_threshold
Winogradskyella psychrotolerans	strain=RS-3	GCA_000427335.1	1344585	1344585	type	True	78.3582	376	913	95	below_threshold
Marixanthomonas spongiae	strain=HN-E44	GCA_003095375.1	2174845	2174845	type	True	78.0757	64	913	95	below_threshold
Winogradskyella flava	strain=KCTC 52348	GCA_014243395.1	1884876	1884876	type	True	78.0117	300	913	95	below_threshold
Winogradskyella jejuensis	strain=DSM 25330	GCA_900129745.1	1089305	1089305	type	True	77.8848	235	913	95	below_threshold
Winogradskyella haliclonae	strain=CCM 8681	GCA_014635865.1	2048558	2048558	type	True	77.8039	239	913	95	below_threshold
Winogradskyella wandonensis	strain=CECT 8445	GCA_004346845.1	1442586	1442586	type	True	77.7657	220	913	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	77.6214	149	913	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.3318	177	913	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	77.2777	166	913	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	77.27	148	913	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	77.1627	134	913	95	below_threshold
Aquimarina sediminis	strain=w01	GCA_002895435.1	2070536	2070536	type	True	76.8333	69	913	95	below_threshold
Seonamhaeicola aphaedonensis	strain=CECT 8487	GCA_003386195.1	1461338	1461338	type	True	76.5644	134	913	95	below_threshold
Flavobacterium lutivivi	strain=CGMCC 1.15347	GCA_014642275.1	1677894	1677894	type	True	76.13	54	913	95	below_threshold
Aurantibacter crassamenti	strain=HG732	GCA_016811105.1	1837375	1837375	type	True	75.9377	87	913	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 14:19:24,031] [INFO] DFAST Taxonomy check result was written to GCA_913061495.1_SRR3933287_bin.9_MetaBAT_v2.12.1_MAG_genomic.fna/tc_result.tsv
[2023-06-28 14:19:24,031] [INFO] ===== Taxonomy check completed =====
[2023-06-28 14:19:24,031] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 14:19:24,032] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c7f5c01-acbe-429b-828a-0c60476c670a/dqc_reference/checkm_data
[2023-06-28 14:19:24,032] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 14:19:24,066] [INFO] Task started: CheckM
[2023-06-28 14:19:24,066] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_913061495.1_SRR3933287_bin.9_MetaBAT_v2.12.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_913061495.1_SRR3933287_bin.9_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_input GCA_913061495.1_SRR3933287_bin.9_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_result
[2023-06-28 14:19:53,052] [INFO] Task succeeded: CheckM
[2023-06-28 14:19:53,053] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 14:19:53,073] [INFO] ===== Completeness check finished =====
[2023-06-28 14:19:53,073] [INFO] ===== Start GTDB Search =====
[2023-06-28 14:19:53,074] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_913061495.1_SRR3933287_bin.9_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta)
[2023-06-28 14:19:53,075] [INFO] Task started: Blastn
[2023-06-28 14:19:53,075] [INFO] Running command: blastn -query GCA_913061495.1_SRR3933287_bin.9_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c7f5c01-acbe-429b-828a-0c60476c670a/dqc_reference/reference_markers_gtdb.fasta -out GCA_913061495.1_SRR3933287_bin.9_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 14:19:53,956] [INFO] Task succeeded: Blastn
[2023-06-28 14:19:53,960] [INFO] Selected 28 target genomes.
[2023-06-28 14:19:53,960] [INFO] Target genome list was writen to GCA_913061495.1_SRR3933287_bin.9_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 14:19:53,982] [INFO] Task started: fastANI
[2023-06-28 14:19:53,982] [INFO] Running command: fastANI --query /var/lib/cwl/stg8eaf2395-8138-4c7c-948d-24d9fa004ee4/GCA_913061495.1_SRR3933287_bin.9_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913061495.1_SRR3933287_bin.9_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_913061495.1_SRR3933287_bin.9_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 14:20:13,025] [INFO] Task succeeded: fastANI
[2023-06-28 14:20:13,040] [INFO] Found 26 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 14:20:13,040] [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_013403975.1	s__Winogradskyella ursingii	79.6708	415	913	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014297365.1	s__Winogradskyella echinorum	79.0207	401	913	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	78.8839	377	913	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015645385.1	s__Winogradskyella sp015645385	78.817	364	913	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000171875.1	s__Winogradskyella sp000171875	78.804	367	913	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	78.7899	352	913	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	98.63	98.63	0.93	0.93	2	-
GCF_013394655.1	s__Winogradskyella schleiferi	78.766	368	913	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	78.6704	394	913	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	78.6639	317	913	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	78.5942	370	913	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	78.5638	385	913	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009741275.1	s__Winogradskyella endarachnes	78.5222	358	913	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013249065.1	s__Winogradskyella litoriviva	78.5154	376	913	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	78.5073	359	913	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	78.3654	376	913	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	78.3584	383	913	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	97.90	97.90	0.94	0.94	2	-
GCF_019203985.1	s__Winogradskyella sp019203985	78.2617	335	913	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002682935.1	s__Winogradskyella sp002682935	78.1449	331	913	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013213835.1	s__Winogradskyella sp013213835	78.0848	234	913	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014243395.1	s__Winogradskyella flava	78.0117	300	913	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004346845.1	s__Winogradskyella wandonensis	77.7657	220	913	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002162685.1	s__Psychroserpens sp002162685	77.634	241	913	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001874145.1	s__Lacinutrix sp001874145	77.384	217	913	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358095.2	s__Seonamhaeicola sp004358095	76.882	133	913	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002895435.1	s__Aquimarina sediminis	76.8333	69	913	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386195.1	s__Seonamhaeicola aphaedonensis	76.5644	134	913	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 14:20:13,041] [INFO] GTDB search result was written to GCA_913061495.1_SRR3933287_bin.9_MetaBAT_v2.12.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-28 14:20:13,042] [INFO] ===== GTDB Search completed =====
[2023-06-28 14:20:13,046] [INFO] DFAST_QC result json was written to GCA_913061495.1_SRR3933287_bin.9_MetaBAT_v2.12.1_MAG_genomic.fna/dqc_result.json
[2023-06-28 14:20:13,046] [INFO] DFAST_QC completed!
[2023-06-28 14:20:13,046] [INFO] Total running time: 0h1m18s