[2024-01-24 14:31:28,851] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:31:28,853] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:31:28,853] [INFO] DQC Reference Directory: /var/lib/cwl/stgfd8850ac-532c-474a-98b7-56b1dc2e37a1/dqc_reference
[2024-01-24 14:31:29,961] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:29,961] [INFO] Task started: Prodigal
[2024-01-24 14:31:29,962] [INFO] Running command: gunzip -c /var/lib/cwl/stg071de29e-d030-4561-8b08-99e0a49b0a11/GCF_013249045.1_ASM1324904v1_genomic.fna.gz | prodigal -d GCF_013249045.1_ASM1324904v1_genomic.fna/cds.fna -a GCF_013249045.1_ASM1324904v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:39,353] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:39,354] [INFO] Task started: HMMsearch
[2024-01-24 14:31:39,354] [INFO] Running command: hmmsearch --tblout GCF_013249045.1_ASM1324904v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfd8850ac-532c-474a-98b7-56b1dc2e37a1/dqc_reference/reference_markers.hmm GCF_013249045.1_ASM1324904v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:39,589] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:39,590] [INFO] Found 6/6 markers.
[2024-01-24 14:31:39,618] [INFO] Query marker FASTA was written to GCF_013249045.1_ASM1324904v1_genomic.fna/markers.fasta
[2024-01-24 14:31:39,619] [INFO] Task started: Blastn
[2024-01-24 14:31:39,619] [INFO] Running command: blastn -query GCF_013249045.1_ASM1324904v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd8850ac-532c-474a-98b7-56b1dc2e37a1/dqc_reference/reference_markers.fasta -out GCF_013249045.1_ASM1324904v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:40,249] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:40,251] [INFO] Selected 17 target genomes.
[2024-01-24 14:31:40,252] [INFO] Target genome list was writen to GCF_013249045.1_ASM1324904v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:40,265] [INFO] Task started: fastANI
[2024-01-24 14:31:40,265] [INFO] Running command: fastANI --query /var/lib/cwl/stg071de29e-d030-4561-8b08-99e0a49b0a11/GCF_013249045.1_ASM1324904v1_genomic.fna.gz --refList GCF_013249045.1_ASM1324904v1_genomic.fna/target_genomes.txt --output GCF_013249045.1_ASM1324904v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:53,558] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:53,558] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfd8850ac-532c-474a-98b7-56b1dc2e37a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:53,558] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfd8850ac-532c-474a-98b7-56b1dc2e37a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:53,568] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:31:53,568] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:53,569] [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 eckloniae	strain=EC29	GCA_013249045.1	1089306	1089306	type	True	100.0	1216	1217	95	conclusive
Winogradskyella endarachnes	strain=HL2-2	GCA_009741275.1	2681965	2681965	type	True	82.8361	789	1217	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	82.0849	788	1217	95	below_threshold
Winogradskyella thalassocola	strain=DSM 15363	GCA_900099995.1	262004	262004	type	True	80.202	658	1217	95	below_threshold
Winogradskyella marina	strain=F6397	GCA_015645385.1	2785530	2785530	type	True	80.1632	607	1217	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	80.129	603	1217	95	below_threshold
Winogradskyella ludwigii	strain=HL116	GCA_013403985.1	2686076	2686076	type	True	80.1131	668	1217	95	below_threshold
Winogradskyella helgolandensis	strain=Z963	GCA_013404085.1	2697010	2697010	type	True	80.0109	668	1217	95	below_threshold
Winogradskyella costae	strain=Z3138	GCA_013403865.1	2697008	2697008	type	True	79.8522	629	1217	95	below_threshold
Winogradskyella vidalii	strain=HL634	GCA_013403955.1	2615024	2615024	type	True	79.5866	609	1217	95	below_threshold
Winogradskyella wichelsiae	strain=Z738	GCA_013403925.1	2697007	2697007	type	True	79.5476	605	1217	95	below_threshold
Winogradskyella schleiferi	strain=Z215	GCA_013394655.1	2686078	2686078	type	True	79.4402	570	1217	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	78.0374	264	1217	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	77.6697	175	1217	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	77.423	193	1217	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.4105	221	1217	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	77.0641	212	1217	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:53,570] [INFO] DFAST Taxonomy check result was written to GCF_013249045.1_ASM1324904v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:53,570] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:53,571] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:53,571] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfd8850ac-532c-474a-98b7-56b1dc2e37a1/dqc_reference/checkm_data
[2024-01-24 14:31:53,571] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:53,608] [INFO] Task started: CheckM
[2024-01-24 14:31:53,608] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013249045.1_ASM1324904v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013249045.1_ASM1324904v1_genomic.fna/checkm_input GCF_013249045.1_ASM1324904v1_genomic.fna/checkm_result
[2024-01-24 14:32:23,123] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:23,124] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:23,139] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:23,139] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:23,139] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013249045.1_ASM1324904v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:23,139] [INFO] Task started: Blastn
[2024-01-24 14:32:23,139] [INFO] Running command: blastn -query GCF_013249045.1_ASM1324904v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd8850ac-532c-474a-98b7-56b1dc2e37a1/dqc_reference/reference_markers_gtdb.fasta -out GCF_013249045.1_ASM1324904v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:24,041] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:24,043] [INFO] Selected 12 target genomes.
[2024-01-24 14:32:24,043] [INFO] Target genome list was writen to GCF_013249045.1_ASM1324904v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:24,049] [INFO] Task started: fastANI
[2024-01-24 14:32:24,049] [INFO] Running command: fastANI --query /var/lib/cwl/stg071de29e-d030-4561-8b08-99e0a49b0a11/GCF_013249045.1_ASM1324904v1_genomic.fna.gz --refList GCF_013249045.1_ASM1324904v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013249045.1_ASM1324904v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:34,279] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:34,287] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:34,287] [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_013249045.1	s__Winogradskyella eckloniae	100.0	1216	1217	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	82.8256	790	1217	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	82.0594	791	1217	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	80.5287	724	1217	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	80.3673	670	1217	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	80.202	658	1217	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	80.1725	606	1217	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	80.1052	671	1217	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	80.0717	655	1217	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	80.0065	669	1217	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	98.14	98.14	0.94	0.94	2	-
GCF_013403865.1	s__Winogradskyella costae	79.8564	629	1217	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016744625.1	s__Winogradskyella sp016744625	79.1451	510	1217	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 14:32:34,288] [INFO] GTDB search result was written to GCF_013249045.1_ASM1324904v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:34,289] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:34,291] [INFO] DFAST_QC result json was written to GCF_013249045.1_ASM1324904v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:34,292] [INFO] DFAST_QC completed!
[2024-01-24 14:32:34,292] [INFO] Total running time: 0h1m5s