[2024-01-24 12:06:13,094] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:13,097] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:13,097] [INFO] DQC Reference Directory: /var/lib/cwl/stgd70122cd-ae1b-4f81-9954-ba5225d226a4/dqc_reference
[2024-01-24 12:06:14,424] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:14,425] [INFO] Task started: Prodigal
[2024-01-24 12:06:14,425] [INFO] Running command: gunzip -c /var/lib/cwl/stg61ac87ae-08f3-432c-91bc-866df74871db/GCF_013403865.1_ASM1340386v1_genomic.fna.gz | prodigal -d GCF_013403865.1_ASM1340386v1_genomic.fna/cds.fna -a GCF_013403865.1_ASM1340386v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:27,340] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:27,340] [INFO] Task started: HMMsearch
[2024-01-24 12:06:27,340] [INFO] Running command: hmmsearch --tblout GCF_013403865.1_ASM1340386v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd70122cd-ae1b-4f81-9954-ba5225d226a4/dqc_reference/reference_markers.hmm GCF_013403865.1_ASM1340386v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:27,688] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:27,689] [INFO] Found 6/6 markers.
[2024-01-24 12:06:27,729] [INFO] Query marker FASTA was written to GCF_013403865.1_ASM1340386v1_genomic.fna/markers.fasta
[2024-01-24 12:06:27,729] [INFO] Task started: Blastn
[2024-01-24 12:06:27,730] [INFO] Running command: blastn -query GCF_013403865.1_ASM1340386v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd70122cd-ae1b-4f81-9954-ba5225d226a4/dqc_reference/reference_markers.fasta -out GCF_013403865.1_ASM1340386v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:28,459] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:28,462] [INFO] Selected 15 target genomes.
[2024-01-24 12:06:28,463] [INFO] Target genome list was writen to GCF_013403865.1_ASM1340386v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:28,471] [INFO] Task started: fastANI
[2024-01-24 12:06:28,471] [INFO] Running command: fastANI --query /var/lib/cwl/stg61ac87ae-08f3-432c-91bc-866df74871db/GCF_013403865.1_ASM1340386v1_genomic.fna.gz --refList GCF_013403865.1_ASM1340386v1_genomic.fna/target_genomes.txt --output GCF_013403865.1_ASM1340386v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:42,291] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:42,291] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd70122cd-ae1b-4f81-9954-ba5225d226a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:42,291] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd70122cd-ae1b-4f81-9954-ba5225d226a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:42,304] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:42,304] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:42,304] [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 costae	strain=Z3138	GCA_013403865.1	2697008	2697008	type	True	100.0	1348	1352	95	conclusive
Winogradskyella psychrotolerans	strain=RS-3	GCA_000427335.1	1344585	1344585	type	True	88.3195	1076	1352	95	below_threshold
Winogradskyella helgolandensis	strain=Z963	GCA_013404085.1	2697010	2697010	type	True	86.1791	1049	1352	95	below_threshold
Winogradskyella thalassocola	strain=DSM 15363	GCA_900099995.1	262004	262004	type	True	85.5088	989	1352	95	below_threshold
Winogradskyella ludwigii	strain=HL116	GCA_013403985.1	2686076	2686076	type	True	83.3562	925	1352	95	below_threshold
Winogradskyella wichelsiae	strain=Z738	GCA_013403925.1	2697007	2697007	type	True	83.302	855	1352	95	below_threshold
Winogradskyella marina	strain=F6397	GCA_015645385.1	2785530	2785530	type	True	82.2108	874	1352	95	below_threshold
Winogradskyella undariae	strain=CCUG 63832	GCA_013285155.1	1285465	1285465	type	True	82.1823	822	1352	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	81.7875	812	1352	95	below_threshold
Winogradskyella endarachnes	strain=HL2-2	GCA_009741275.1	2681965	2681965	type	True	80.0542	630	1352	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	77.6231	208	1352	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.3351	213	1352	95	below_threshold
Aestuariivivens insulae	strain=AH-MY3	GCA_022662195.1	1621988	1621988	type	True	76.7532	137	1352	95	below_threshold
Joostella atrarenae	strain=M1-2	GCA_021764745.1	679257	679257	type	True	76.7128	126	1352	95	below_threshold
Abyssalbus ytuae	strain=MT3330	GCA_022807975.1	2926907	2926907	type	True	76.1277	59	1352	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:42,306] [INFO] DFAST Taxonomy check result was written to GCF_013403865.1_ASM1340386v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:42,307] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:42,307] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:42,307] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd70122cd-ae1b-4f81-9954-ba5225d226a4/dqc_reference/checkm_data
[2024-01-24 12:06:42,308] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:42,351] [INFO] Task started: CheckM
[2024-01-24 12:06:42,351] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013403865.1_ASM1340386v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013403865.1_ASM1340386v1_genomic.fna/checkm_input GCF_013403865.1_ASM1340386v1_genomic.fna/checkm_result
[2024-01-24 12:07:22,871] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:22,872] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:22,901] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:22,901] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:22,902] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013403865.1_ASM1340386v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:22,902] [INFO] Task started: Blastn
[2024-01-24 12:07:22,902] [INFO] Running command: blastn -query GCF_013403865.1_ASM1340386v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd70122cd-ae1b-4f81-9954-ba5225d226a4/dqc_reference/reference_markers_gtdb.fasta -out GCF_013403865.1_ASM1340386v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:23,910] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:23,914] [INFO] Selected 9 target genomes.
[2024-01-24 12:07:23,914] [INFO] Target genome list was writen to GCF_013403865.1_ASM1340386v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:23,931] [INFO] Task started: fastANI
[2024-01-24 12:07:23,932] [INFO] Running command: fastANI --query /var/lib/cwl/stg61ac87ae-08f3-432c-91bc-866df74871db/GCF_013403865.1_ASM1340386v1_genomic.fna.gz --refList GCF_013403865.1_ASM1340386v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013403865.1_ASM1340386v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:33,550] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:33,563] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:33,564] [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_013403865.1	s__Winogradskyella costae	100.0	1348	1352	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_000427335.1	s__Winogradskyella psychrotolerans	88.2849	1081	1352	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	87.5843	1062	1352	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	97.90	97.90	0.94	0.94	2	-
GCF_013404085.1	s__Winogradskyella helgolandensis	86.1515	1051	1352	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	98.14	98.14	0.94	0.94	2	-
GCF_900099995.1	s__Winogradskyella thalassocola	85.5032	990	1352	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	83.3513	926	1352	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013403925.1	s__Winogradskyella wichelsiae	83.2941	856	1352	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	82.223	873	1352	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	81.7789	815	1352	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	98.63	98.63	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:33,566] [INFO] GTDB search result was written to GCF_013403865.1_ASM1340386v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:33,566] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:33,570] [INFO] DFAST_QC result json was written to GCF_013403865.1_ASM1340386v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:33,570] [INFO] DFAST_QC completed!
[2024-01-24 12:07:33,570] [INFO] Total running time: 0h1m20s