[2023-06-27 11:50:41,791] [INFO] DFAST_QC pipeline started.
[2023-06-27 11:50:41,792] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 11:50:41,793] [INFO] DQC Reference Directory: /var/lib/cwl/stg8695dfb5-5f88-4c9b-a01d-770503595557/dqc_reference
[2023-06-27 11:50:42,891] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 11:50:42,892] [INFO] Task started: Prodigal
[2023-06-27 11:50:42,892] [INFO] Running command: gunzip -c /var/lib/cwl/stg9a4b73a9-bd02-4c50-a8d3-9e2b7824ba01/GCA_002786355.1_ASM278635v1_genomic.fna.gz | prodigal -d GCA_002786355.1_ASM278635v1_genomic.fna/cds.fna -a GCA_002786355.1_ASM278635v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 11:50:53,501] [INFO] Task succeeded: Prodigal
[2023-06-27 11:50:53,502] [INFO] Task started: HMMsearch
[2023-06-27 11:50:53,502] [INFO] Running command: hmmsearch --tblout GCA_002786355.1_ASM278635v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8695dfb5-5f88-4c9b-a01d-770503595557/dqc_reference/reference_markers.hmm GCA_002786355.1_ASM278635v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 11:50:53,747] [INFO] Task succeeded: HMMsearch
[2023-06-27 11:50:53,748] [INFO] Found 6/6 markers.
[2023-06-27 11:50:53,777] [INFO] Query marker FASTA was written to GCA_002786355.1_ASM278635v1_genomic.fna/markers.fasta
[2023-06-27 11:50:53,777] [INFO] Task started: Blastn
[2023-06-27 11:50:53,777] [INFO] Running command: blastn -query GCA_002786355.1_ASM278635v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8695dfb5-5f88-4c9b-a01d-770503595557/dqc_reference/reference_markers.fasta -out GCA_002786355.1_ASM278635v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 11:50:54,322] [INFO] Task succeeded: Blastn
[2023-06-27 11:50:54,328] [INFO] Selected 24 target genomes.
[2023-06-27 11:50:54,328] [INFO] Target genome list was writen to GCA_002786355.1_ASM278635v1_genomic.fna/target_genomes.txt
[2023-06-27 11:50:54,333] [INFO] Task started: fastANI
[2023-06-27 11:50:54,333] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a4b73a9-bd02-4c50-a8d3-9e2b7824ba01/GCA_002786355.1_ASM278635v1_genomic.fna.gz --refList GCA_002786355.1_ASM278635v1_genomic.fna/target_genomes.txt --output GCA_002786355.1_ASM278635v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 11:51:10,266] [INFO] Task succeeded: fastANI
[2023-06-27 11:51:10,266] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8695dfb5-5f88-4c9b-a01d-770503595557/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 11:51:10,267] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8695dfb5-5f88-4c9b-a01d-770503595557/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 11:51:10,272] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 11:51:10,272] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 11:51:10,272] [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	79.4781	491	1067	95	below_threshold
Sediminibacterium ginsengisoli	strain=DSM 22335	GCA_900167075.1	413434	413434	type	True	76.9092	50	1067	95	below_threshold
Sediminibacterium goheungense	strain=DSM 28323	GCA_004361915.1	1086393	1086393	type	True	76.6973	120	1067	95	below_threshold
Limnovirga soli	strain=KCS-6	GCA_013106755.1	2656915	2656915	type	True	75.9435	73	1067	95	below_threshold
Hydrotalea sandarakina	strain=DSM 23241	GCA_003254115.1	1004304	1004304	type	True	75.9328	82	1067	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 11:51:10,275] [INFO] DFAST Taxonomy check result was written to GCA_002786355.1_ASM278635v1_genomic.fna/tc_result.tsv
[2023-06-27 11:51:10,275] [INFO] ===== Taxonomy check completed =====
[2023-06-27 11:51:10,275] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 11:51:10,276] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8695dfb5-5f88-4c9b-a01d-770503595557/dqc_reference/checkm_data
[2023-06-27 11:51:10,276] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 11:51:10,309] [INFO] Task started: CheckM
[2023-06-27 11:51:10,309] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002786355.1_ASM278635v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002786355.1_ASM278635v1_genomic.fna/checkm_input GCA_002786355.1_ASM278635v1_genomic.fna/checkm_result
[2023-06-27 11:51:43,213] [INFO] Task succeeded: CheckM
[2023-06-27 11:51:43,214] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 11:51:43,228] [INFO] ===== Completeness check finished =====
[2023-06-27 11:51:43,229] [INFO] ===== Start GTDB Search =====
[2023-06-27 11:51:43,229] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002786355.1_ASM278635v1_genomic.fna/markers.fasta)
[2023-06-27 11:51:43,230] [INFO] Task started: Blastn
[2023-06-27 11:51:43,230] [INFO] Running command: blastn -query GCA_002786355.1_ASM278635v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8695dfb5-5f88-4c9b-a01d-770503595557/dqc_reference/reference_markers_gtdb.fasta -out GCA_002786355.1_ASM278635v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 11:51:43,956] [INFO] Task succeeded: Blastn
[2023-06-27 11:51:43,958] [INFO] Selected 11 target genomes.
[2023-06-27 11:51:43,958] [INFO] Target genome list was writen to GCA_002786355.1_ASM278635v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 11:51:43,965] [INFO] Task started: fastANI
[2023-06-27 11:51:43,965] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a4b73a9-bd02-4c50-a8d3-9e2b7824ba01/GCA_002786355.1_ASM278635v1_genomic.fna.gz --refList GCA_002786355.1_ASM278635v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002786355.1_ASM278635v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 11:51:50,894] [INFO] Task succeeded: fastANI
[2023-06-27 11:51:50,902] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 11:51:50,902] [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_002786355.1	s__Sediminibacterium sp002786355	100.0	1067	1067	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	98.29	98.29	0.87	0.87	2	conclusive
GCA_002281575.1	s__Sediminibacterium sp002281575	84.2242	772	1067	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001829005.1	s__Sediminibacterium sp001829005	84.0985	805	1067	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	98.07	96.16	0.93	0.87	3	-
GCA_002281875.1	s__Sediminibacterium sp002281875	84.0745	744	1067	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	83.8287	502	1067	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000508085.1	s__Sediminibacterium sp000508085	79.4865	515	1067	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008080615.1	s__Sediminibacterium sp008080615	77.9424	206	1067	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	99.13	99.13	0.64	0.64	2	-
GCA_018335935.1	s__CAIVPM01 sp018335935	77.5962	98	1067	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__CAIVPM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015999745.1	s__Sediminibacterium sp015999745	77.5798	159	1067	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004294135.1	s__Sediminibacterium sp004294135	77.4538	247	1067	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	99.62	99.37	0.87	0.86	3	-
GCF_004361915.1	s__Sediminibacterium goheungense	76.6793	121	1067	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 11:51:50,904] [INFO] GTDB search result was written to GCA_002786355.1_ASM278635v1_genomic.fna/result_gtdb.tsv
[2023-06-27 11:51:50,905] [INFO] ===== GTDB Search completed =====
[2023-06-27 11:51:50,908] [INFO] DFAST_QC result json was written to GCA_002786355.1_ASM278635v1_genomic.fna/dqc_result.json
[2023-06-27 11:51:50,908] [INFO] DFAST_QC completed!
[2023-06-27 11:51:50,908] [INFO] Total running time: 0h1m9s