[2024-01-25 18:42:20,404] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:42:20,407] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:42:20,407] [INFO] DQC Reference Directory: /var/lib/cwl/stg6c7524c8-15c9-477a-8ce3-fbcdea434488/dqc_reference
[2024-01-25 18:42:21,660] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:42:21,661] [INFO] Task started: Prodigal
[2024-01-25 18:42:21,661] [INFO] Running command: gunzip -c /var/lib/cwl/stgabec9d4f-0fea-4e27-b194-8eb56bac1452/GCF_009939005.1_ASM993900v1_genomic.fna.gz | prodigal -d GCF_009939005.1_ASM993900v1_genomic.fna/cds.fna -a GCF_009939005.1_ASM993900v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:42:44,927] [INFO] Task succeeded: Prodigal
[2024-01-25 18:42:44,927] [INFO] Task started: HMMsearch
[2024-01-25 18:42:44,927] [INFO] Running command: hmmsearch --tblout GCF_009939005.1_ASM993900v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6c7524c8-15c9-477a-8ce3-fbcdea434488/dqc_reference/reference_markers.hmm GCF_009939005.1_ASM993900v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:42:45,169] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:42:45,170] [INFO] Found 6/6 markers.
[2024-01-25 18:42:45,209] [INFO] Query marker FASTA was written to GCF_009939005.1_ASM993900v1_genomic.fna/markers.fasta
[2024-01-25 18:42:45,209] [INFO] Task started: Blastn
[2024-01-25 18:42:45,210] [INFO] Running command: blastn -query GCF_009939005.1_ASM993900v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c7524c8-15c9-477a-8ce3-fbcdea434488/dqc_reference/reference_markers.fasta -out GCF_009939005.1_ASM993900v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:42:45,756] [INFO] Task succeeded: Blastn
[2024-01-25 18:42:45,759] [INFO] Selected 15 target genomes.
[2024-01-25 18:42:45,759] [INFO] Target genome list was writen to GCF_009939005.1_ASM993900v1_genomic.fna/target_genomes.txt
[2024-01-25 18:42:45,769] [INFO] Task started: fastANI
[2024-01-25 18:42:45,770] [INFO] Running command: fastANI --query /var/lib/cwl/stgabec9d4f-0fea-4e27-b194-8eb56bac1452/GCF_009939005.1_ASM993900v1_genomic.fna.gz --refList GCF_009939005.1_ASM993900v1_genomic.fna/target_genomes.txt --output GCF_009939005.1_ASM993900v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:43:00,317] [INFO] Task succeeded: fastANI
[2024-01-25 18:43:00,318] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6c7524c8-15c9-477a-8ce3-fbcdea434488/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:43:00,318] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6c7524c8-15c9-477a-8ce3-fbcdea434488/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:43:00,326] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:43:00,326] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:43:00,327] [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 roseum	strain=SYL130	GCA_009939005.1	1978412	1978412	type	True	100.0	1498	1499	95	conclusive
Sediminibacterium soli	strain=WSJ-3	GCA_009939225.1	2698829	2698829	type	True	77.4842	360	1499	95	below_threshold
Sediminibacterium goheungense	strain=DSM 28323	GCA_004361915.1	1086393	1086393	type	True	77.4691	144	1499	95	below_threshold
Sediminibacterium ginsengisoli	strain=DSM 22335	GCA_900167075.1	413434	413434	type	True	77.4543	272	1499	95	below_threshold
Deminuibacter soli	strain=K23C18032701	GCA_003412455.1	2291815	2291815	type	True	76.4165	135	1499	95	below_threshold
Flavihumibacter rivuli	strain=IMCC34838	GCA_018595685.2	2838156	2838156	type	True	76.3763	67	1499	95	below_threshold
Foetidibacter luteolus	strain=YG09	GCA_009650435.1	2608880	2608880	type	True	76.2108	88	1499	95	below_threshold
Panacibacter microcysteis	strain=DH6	GCA_015831355.1	2793269	2793269	type	True	76.163	77	1499	95	below_threshold
Flavihumibacter cheonanensis	strain=WS16	GCA_022352215.1	1442385	1442385	type	True	76.1573	53	1499	95	below_threshold
Chitinophaga vietnamensis	strain=BD 01	GCA_902167635.1	2593957	2593957	type	True	76.1312	68	1499	95	below_threshold
Niastella koreensis	strain=DSM 17620	GCA_002077985.1	354356	354356	type	True	75.9728	88	1499	95	below_threshold
Niabella beijingensis	strain=3A5MI-3	GCA_020034665.1	2872700	2872700	type	True	75.844	64	1499	95	below_threshold
Paraflavitalea devenefica	strain=X16	GCA_011759375.1	2716334	2716334	type	True	75.706	96	1499	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:43:00,330] [INFO] DFAST Taxonomy check result was written to GCF_009939005.1_ASM993900v1_genomic.fna/tc_result.tsv
[2024-01-25 18:43:00,332] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:43:00,332] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:43:00,332] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6c7524c8-15c9-477a-8ce3-fbcdea434488/dqc_reference/checkm_data
[2024-01-25 18:43:00,333] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:43:00,373] [INFO] Task started: CheckM
[2024-01-25 18:43:00,374] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009939005.1_ASM993900v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009939005.1_ASM993900v1_genomic.fna/checkm_input GCF_009939005.1_ASM993900v1_genomic.fna/checkm_result
[2024-01-25 18:44:05,123] [INFO] Task succeeded: CheckM
[2024-01-25 18:44:05,128] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:44:05,152] [INFO] ===== Completeness check finished =====
[2024-01-25 18:44:05,152] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:44:05,158] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009939005.1_ASM993900v1_genomic.fna/markers.fasta)
[2024-01-25 18:44:05,158] [INFO] Task started: Blastn
[2024-01-25 18:44:05,158] [INFO] Running command: blastn -query GCF_009939005.1_ASM993900v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c7524c8-15c9-477a-8ce3-fbcdea434488/dqc_reference/reference_markers_gtdb.fasta -out GCF_009939005.1_ASM993900v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:44:05,984] [INFO] Task succeeded: Blastn
[2024-01-25 18:44:05,986] [INFO] Selected 17 target genomes.
[2024-01-25 18:44:05,986] [INFO] Target genome list was writen to GCF_009939005.1_ASM993900v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:44:05,999] [INFO] Task started: fastANI
[2024-01-25 18:44:05,999] [INFO] Running command: fastANI --query /var/lib/cwl/stgabec9d4f-0fea-4e27-b194-8eb56bac1452/GCF_009939005.1_ASM993900v1_genomic.fna.gz --refList GCF_009939005.1_ASM993900v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009939005.1_ASM993900v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:44:19,006] [INFO] Task succeeded: fastANI
[2024-01-25 18:44:19,016] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:44:19,017] [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_009939005.1	s__Sediminibacterium roseum	100.0	1498	1499	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_004297075.1	s__Sediminibacterium sp004297075	78.2984	290	1499	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	98.05	98.05	0.89	0.89	2	-
GCA_016183765.1	s__Sediminibacterium sp016183765	77.983	365	1499	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013289065.1	s__Sediminibacterium sp013289065	77.8565	235	1499	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009939225.1	s__Sediminibacterium soli	77.4842	360	1499	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167075.1	s__Sediminibacterium ginsengisoli	77.4657	271	1499	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002973575.1	s__Sediminibacterium magnilacihabitans	77.3437	240	1499	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	99.08	98.17	0.92	0.85	3	-
GCA_004028765.1	s__Sediminibacterium sp004028765	77.3259	333	1499	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019247775.1	s__Sediminibacterium sp019247775	77.2445	290	1499	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903913355.1	s__Sediminibacterium sp903913355	77.1484	143	1499	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017355875.1	s__Segetibacter sp017355875	76.55	68	1499	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Segetibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018595685.1	s__Flavihumibacter sp018595685	76.3568	69	1499	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavihumibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009650435.1	s__Foetidibacter luteolus	76.2108	88	1499	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Foetidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014163555.1	s__Flavisolibacter sp014163555	76.1925	78	1499	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017303855.1	s__JJ008 sp017303855	75.7119	58	1499	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:44:19,018] [INFO] GTDB search result was written to GCF_009939005.1_ASM993900v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:44:19,019] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:44:19,022] [INFO] DFAST_QC result json was written to GCF_009939005.1_ASM993900v1_genomic.fna/dqc_result.json
[2024-01-25 18:44:19,022] [INFO] DFAST_QC completed!
[2024-01-25 18:44:19,022] [INFO] Total running time: 0h1m59s