[2023-06-19 08:39:06,441] [INFO] DFAST_QC pipeline started.
[2023-06-19 08:39:06,443] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 08:39:06,443] [INFO] DQC Reference Directory: /var/lib/cwl/stg08975a02-c97b-4668-bf27-07705f045406/dqc_reference
[2023-06-19 08:39:07,688] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 08:39:07,689] [INFO] Task started: Prodigal
[2023-06-19 08:39:07,690] [INFO] Running command: gunzip -c /var/lib/cwl/stgd3803dea-9354-47fe-8942-e212f4142298/GCA_018780685.1_ASM1878068v1_genomic.fna.gz | prodigal -d GCA_018780685.1_ASM1878068v1_genomic.fna/cds.fna -a GCA_018780685.1_ASM1878068v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 08:39:20,997] [INFO] Task succeeded: Prodigal
[2023-06-19 08:39:20,998] [INFO] Task started: HMMsearch
[2023-06-19 08:39:20,998] [INFO] Running command: hmmsearch --tblout GCA_018780685.1_ASM1878068v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg08975a02-c97b-4668-bf27-07705f045406/dqc_reference/reference_markers.hmm GCA_018780685.1_ASM1878068v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 08:39:21,269] [INFO] Task succeeded: HMMsearch
[2023-06-19 08:39:21,271] [INFO] Found 6/6 markers.
[2023-06-19 08:39:21,310] [INFO] Query marker FASTA was written to GCA_018780685.1_ASM1878068v1_genomic.fna/markers.fasta
[2023-06-19 08:39:21,311] [INFO] Task started: Blastn
[2023-06-19 08:39:21,311] [INFO] Running command: blastn -query GCA_018780685.1_ASM1878068v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg08975a02-c97b-4668-bf27-07705f045406/dqc_reference/reference_markers.fasta -out GCA_018780685.1_ASM1878068v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:39:21,883] [INFO] Task succeeded: Blastn
[2023-06-19 08:39:21,890] [INFO] Selected 22 target genomes.
[2023-06-19 08:39:21,891] [INFO] Target genome list was writen to GCA_018780685.1_ASM1878068v1_genomic.fna/target_genomes.txt
[2023-06-19 08:39:21,897] [INFO] Task started: fastANI
[2023-06-19 08:39:21,898] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3803dea-9354-47fe-8942-e212f4142298/GCA_018780685.1_ASM1878068v1_genomic.fna.gz --refList GCA_018780685.1_ASM1878068v1_genomic.fna/target_genomes.txt --output GCA_018780685.1_ASM1878068v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 08:39:35,215] [INFO] Task succeeded: fastANI
[2023-06-19 08:39:35,216] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg08975a02-c97b-4668-bf27-07705f045406/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 08:39:35,217] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg08975a02-c97b-4668-bf27-07705f045406/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 08:39:35,229] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 08:39:35,229] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 08:39:35,229] [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
Sediminibacterium salmoneum	strain=NBRC 103935	GCA_000511175.1	426421	426421	type	True	79.9436	502	1074	95	below_threshold
Lacibacter cauensis	strain=CGMCC 1.7271	GCA_007830055.1	510947	510947	type	True	77.1166	67	1074	95	below_threshold
Sediminibacterium goheungense	strain=DSM 28323	GCA_004361915.1	1086393	1086393	type	True	76.7737	128	1074	95	below_threshold
Sediminibacterium ginsengisoli	strain=DSM 22335	GCA_900167075.1	413434	413434	type	True	76.6707	61	1074	95	below_threshold
Hydrotalea sandarakina	strain=DSM 23241	GCA_003254115.1	1004304	1004304	type	True	76.3005	93	1074	95	below_threshold
Limnovirga soli	strain=KCS-6	GCA_013106755.1	2656915	2656915	type	True	76.2958	68	1074	95	below_threshold
Hydrotalea flava	strain=CCUG 51397	GCA_001623405.1	714549	714549	suspected-type	True	76.1521	90	1074	95	below_threshold
Hydrotalea lipotrueae	strain=TMF_100	GCA_019249625.1	2803817	2803817	type	True	76.1183	92	1074	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 08:39:35,231] [INFO] DFAST Taxonomy check result was written to GCA_018780685.1_ASM1878068v1_genomic.fna/tc_result.tsv
[2023-06-19 08:39:35,235] [INFO] ===== Taxonomy check completed =====
[2023-06-19 08:39:35,235] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 08:39:35,235] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg08975a02-c97b-4668-bf27-07705f045406/dqc_reference/checkm_data
[2023-06-19 08:39:35,237] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 08:39:35,279] [INFO] Task started: CheckM
[2023-06-19 08:39:35,279] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018780685.1_ASM1878068v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018780685.1_ASM1878068v1_genomic.fna/checkm_input GCA_018780685.1_ASM1878068v1_genomic.fna/checkm_result
[2023-06-19 08:40:16,690] [INFO] Task succeeded: CheckM
[2023-06-19 08:40:16,691] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 08:40:16,718] [INFO] ===== Completeness check finished =====
[2023-06-19 08:40:16,718] [INFO] ===== Start GTDB Search =====
[2023-06-19 08:40:16,719] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018780685.1_ASM1878068v1_genomic.fna/markers.fasta)
[2023-06-19 08:40:16,719] [INFO] Task started: Blastn
[2023-06-19 08:40:16,719] [INFO] Running command: blastn -query GCA_018780685.1_ASM1878068v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg08975a02-c97b-4668-bf27-07705f045406/dqc_reference/reference_markers_gtdb.fasta -out GCA_018780685.1_ASM1878068v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:40:17,464] [INFO] Task succeeded: Blastn
[2023-06-19 08:40:17,468] [INFO] Selected 8 target genomes.
[2023-06-19 08:40:17,469] [INFO] Target genome list was writen to GCA_018780685.1_ASM1878068v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 08:40:17,477] [INFO] Task started: fastANI
[2023-06-19 08:40:17,477] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3803dea-9354-47fe-8942-e212f4142298/GCA_018780685.1_ASM1878068v1_genomic.fna.gz --refList GCA_018780685.1_ASM1878068v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018780685.1_ASM1878068v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 08:40:23,209] [INFO] Task succeeded: fastANI
[2023-06-19 08:40:23,225] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 08:40:23,225] [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
GCA_001829005.1	s__Sediminibacterium sp001829005	96.1062	932	1074	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	98.07	96.16	0.93	0.87	3	conclusive
GCA_002281875.1	s__Sediminibacterium sp002281875	94.9604	862	1074	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	99.93	99.91	0.97	0.97	3	-
GCA_017996795.1	s__Sediminibacterium sp017996795	89.6114	550	1074	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002281575.1	s__Sediminibacterium sp002281575	86.9078	871	1074	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002786355.1	s__Sediminibacterium sp002786355	84.2047	775	1074	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	98.29	98.29	0.87	0.87	2	-
GCF_000508085.1	s__Sediminibacterium sp000508085	80.1821	540	1074	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000511175.1	s__Sediminibacterium salmoneum	79.9243	505	1074	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018335935.1	s__CAIVPM01 sp018335935	78.8486	106	1074	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__CAIVPM01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 08:40:23,227] [INFO] GTDB search result was written to GCA_018780685.1_ASM1878068v1_genomic.fna/result_gtdb.tsv
[2023-06-19 08:40:23,228] [INFO] ===== GTDB Search completed =====
[2023-06-19 08:40:23,231] [INFO] DFAST_QC result json was written to GCA_018780685.1_ASM1878068v1_genomic.fna/dqc_result.json
[2023-06-19 08:40:23,231] [INFO] DFAST_QC completed!
[2023-06-19 08:40:23,231] [INFO] Total running time: 0h1m17s