[2024-01-24 13:54:03,964] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:54:03,966] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:54:03,966] [INFO] DQC Reference Directory: /var/lib/cwl/stgc2ca5c1c-dffb-4447-a518-2cc9d153a7e5/dqc_reference
[2024-01-24 13:54:05,636] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:54:05,638] [INFO] Task started: Prodigal
[2024-01-24 13:54:05,638] [INFO] Running command: gunzip -c /var/lib/cwl/stg3664daa3-e647-4a49-b7e5-611afdfb93bf/GCF_013403975.1_ASM1340397v1_genomic.fna.gz | prodigal -d GCF_013403975.1_ASM1340397v1_genomic.fna/cds.fna -a GCF_013403975.1_ASM1340397v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:54:19,486] [INFO] Task succeeded: Prodigal
[2024-01-24 13:54:19,486] [INFO] Task started: HMMsearch
[2024-01-24 13:54:19,486] [INFO] Running command: hmmsearch --tblout GCF_013403975.1_ASM1340397v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc2ca5c1c-dffb-4447-a518-2cc9d153a7e5/dqc_reference/reference_markers.hmm GCF_013403975.1_ASM1340397v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:54:19,810] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:54:19,812] [INFO] Found 6/6 markers.
[2024-01-24 13:54:19,872] [INFO] Query marker FASTA was written to GCF_013403975.1_ASM1340397v1_genomic.fna/markers.fasta
[2024-01-24 13:54:19,873] [INFO] Task started: Blastn
[2024-01-24 13:54:19,873] [INFO] Running command: blastn -query GCF_013403975.1_ASM1340397v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2ca5c1c-dffb-4447-a518-2cc9d153a7e5/dqc_reference/reference_markers.fasta -out GCF_013403975.1_ASM1340397v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:54:20,709] [INFO] Task succeeded: Blastn
[2024-01-24 13:54:20,713] [INFO] Selected 21 target genomes.
[2024-01-24 13:54:20,714] [INFO] Target genome list was writen to GCF_013403975.1_ASM1340397v1_genomic.fna/target_genomes.txt
[2024-01-24 13:54:20,745] [INFO] Task started: fastANI
[2024-01-24 13:54:20,746] [INFO] Running command: fastANI --query /var/lib/cwl/stg3664daa3-e647-4a49-b7e5-611afdfb93bf/GCF_013403975.1_ASM1340397v1_genomic.fna.gz --refList GCF_013403975.1_ASM1340397v1_genomic.fna/target_genomes.txt --output GCF_013403975.1_ASM1340397v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:54:35,629] [INFO] Task succeeded: fastANI
[2024-01-24 13:54:35,630] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc2ca5c1c-dffb-4447-a518-2cc9d153a7e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:54:35,630] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc2ca5c1c-dffb-4447-a518-2cc9d153a7e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:54:35,646] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:54:35,646] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:54:35,647] [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 ursingii	strain=HL4150	GCA_013403975.1	2686079	2686079	type	True	100.0	1149	1149	95	conclusive
Winogradskyella ouciana	strain=ZXX205	GCA_009709615.1	2608631	2608631	type	True	79.2377	409	1149	95	below_threshold
Winogradskyella schleiferi	strain=Z215	GCA_013394655.1	2686078	2686078	type	True	78.9374	394	1149	95	below_threshold
Winogradskyella forsetii	strain=HL857	GCA_013394595.1	2686077	2686077	type	True	78.542	385	1149	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	78.4221	424	1149	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	78.4221	424	1149	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	78.2975	337	1149	95	below_threshold
Winogradskyella marina	strain=F6397	GCA_015645385.1	2785530	2785530	type	True	78.15	355	1149	95	below_threshold
Winogradskyella endarachnes	strain=HL2-2	GCA_009741275.1	2681965	2681965	type	True	78.116	368	1149	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	78.0831	356	1149	95	below_threshold
Winogradskyella ludwigii	strain=HL116	GCA_013403985.1	2686076	2686076	type	True	78.0543	366	1149	95	below_threshold
Winogradskyella eckloniae	strain=EC29	GCA_013249045.1	1089306	1089306	type	True	78.0222	328	1149	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	77.5086	197	1149	95	below_threshold
Winogradskyella haliclonae	strain=CCM 8681	GCA_014635865.1	2048558	2048558	type	True	77.4727	252	1149	95	below_threshold
Hyunsoonleella aquatilis	strain=SJ7	GCA_014270105.1	2762758	2762758	type	True	77.2274	104	1149	95	below_threshold
Psychroserpens mesophilus	strain=JCM 13413	GCA_000826645.1	325473	325473	type	True	77.2092	222	1149	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	77.1352	157	1149	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	77.1349	157	1149	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.9746	139	1149	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	76.9658	117	1149	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	76.8559	142	1149	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:54:35,648] [INFO] DFAST Taxonomy check result was written to GCF_013403975.1_ASM1340397v1_genomic.fna/tc_result.tsv
[2024-01-24 13:54:35,649] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:54:35,649] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:54:35,649] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc2ca5c1c-dffb-4447-a518-2cc9d153a7e5/dqc_reference/checkm_data
[2024-01-24 13:54:35,650] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:54:35,687] [INFO] Task started: CheckM
[2024-01-24 13:54:35,687] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013403975.1_ASM1340397v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013403975.1_ASM1340397v1_genomic.fna/checkm_input GCF_013403975.1_ASM1340397v1_genomic.fna/checkm_result
[2024-01-24 13:55:18,543] [INFO] Task succeeded: CheckM
[2024-01-24 13:55:18,544] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:55:18,569] [INFO] ===== Completeness check finished =====
[2024-01-24 13:55:18,570] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:55:18,570] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013403975.1_ASM1340397v1_genomic.fna/markers.fasta)
[2024-01-24 13:55:18,571] [INFO] Task started: Blastn
[2024-01-24 13:55:18,571] [INFO] Running command: blastn -query GCF_013403975.1_ASM1340397v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2ca5c1c-dffb-4447-a518-2cc9d153a7e5/dqc_reference/reference_markers_gtdb.fasta -out GCF_013403975.1_ASM1340397v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:19,527] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:19,530] [INFO] Selected 18 target genomes.
[2024-01-24 13:55:19,530] [INFO] Target genome list was writen to GCF_013403975.1_ASM1340397v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:55:19,564] [INFO] Task started: fastANI
[2024-01-24 13:55:19,564] [INFO] Running command: fastANI --query /var/lib/cwl/stg3664daa3-e647-4a49-b7e5-611afdfb93bf/GCF_013403975.1_ASM1340397v1_genomic.fna.gz --refList GCF_013403975.1_ASM1340397v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013403975.1_ASM1340397v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:55:32,412] [INFO] Task succeeded: fastANI
[2024-01-24 13:55:32,430] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:55:32,430] [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	100.0	1149	1149	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_009709615.1	s__Winogradskyella ouciana	79.2377	409	1149	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	97.22	97.22	0.91	0.91	2	-
GCF_013394655.1	s__Winogradskyella schleiferi	78.9374	394	1149	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013394595.1	s__Winogradskyella forsetii	78.5419	384	1149	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	97.73	96.59	0.91	0.86	4	-
GCF_014297365.1	s__Winogradskyella echinorum	78.4166	424	1149	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	78.4058	364	1149	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	78.3116	382	1149	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	78.2972	369	1149	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	78.1982	360	1149	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	78.1229	357	1149	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	78.1098	369	1149	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	78.0831	356	1149	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	78.0543	366	1149	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	78.0222	328	1149	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364335.1	s__Winogradskyella sp002364335	77.9791	351	1149	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014635865.1	s__Winogradskyella haliclonae	77.4727	252	1149	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000826645.1	s__Psychroserpens mesophilus	77.2217	221	1149	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202225.1	s__Algibacter_B amylolyticus	77.1512	157	1149	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	100.00	100.00	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:55:32,432] [INFO] GTDB search result was written to GCF_013403975.1_ASM1340397v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:55:32,432] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:55:32,436] [INFO] DFAST_QC result json was written to GCF_013403975.1_ASM1340397v1_genomic.fna/dqc_result.json
[2024-01-24 13:55:32,437] [INFO] DFAST_QC completed!
[2024-01-24 13:55:32,437] [INFO] Total running time: 0h1m28s