[2024-01-25 18:00:35,333] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:00:35,334] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:00:35,334] [INFO] DQC Reference Directory: /var/lib/cwl/stg66ad7c98-56a4-4bbf-8562-6d9072b94ace/dqc_reference
[2024-01-25 18:00:36,433] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:00:36,434] [INFO] Task started: Prodigal
[2024-01-25 18:00:36,434] [INFO] Running command: gunzip -c /var/lib/cwl/stg1b4f5442-602c-41dc-a746-8e79e88e4b13/GCF_009939225.1_ASM993922v1_genomic.fna.gz | prodigal -d GCF_009939225.1_ASM993922v1_genomic.fna/cds.fna -a GCF_009939225.1_ASM993922v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:00:54,638] [INFO] Task succeeded: Prodigal
[2024-01-25 18:00:54,639] [INFO] Task started: HMMsearch
[2024-01-25 18:00:54,639] [INFO] Running command: hmmsearch --tblout GCF_009939225.1_ASM993922v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg66ad7c98-56a4-4bbf-8562-6d9072b94ace/dqc_reference/reference_markers.hmm GCF_009939225.1_ASM993922v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:00:54,871] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:00:54,872] [INFO] Found 6/6 markers.
[2024-01-25 18:00:54,901] [INFO] Query marker FASTA was written to GCF_009939225.1_ASM993922v1_genomic.fna/markers.fasta
[2024-01-25 18:00:54,901] [INFO] Task started: Blastn
[2024-01-25 18:00:54,902] [INFO] Running command: blastn -query GCF_009939225.1_ASM993922v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg66ad7c98-56a4-4bbf-8562-6d9072b94ace/dqc_reference/reference_markers.fasta -out GCF_009939225.1_ASM993922v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:00:55,438] [INFO] Task succeeded: Blastn
[2024-01-25 18:00:55,440] [INFO] Selected 18 target genomes.
[2024-01-25 18:00:55,441] [INFO] Target genome list was writen to GCF_009939225.1_ASM993922v1_genomic.fna/target_genomes.txt
[2024-01-25 18:00:55,453] [INFO] Task started: fastANI
[2024-01-25 18:00:55,453] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b4f5442-602c-41dc-a746-8e79e88e4b13/GCF_009939225.1_ASM993922v1_genomic.fna.gz --refList GCF_009939225.1_ASM993922v1_genomic.fna/target_genomes.txt --output GCF_009939225.1_ASM993922v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:01:13,202] [INFO] Task succeeded: fastANI
[2024-01-25 18:01:13,202] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg66ad7c98-56a4-4bbf-8562-6d9072b94ace/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:01:13,202] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg66ad7c98-56a4-4bbf-8562-6d9072b94ace/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:01:13,212] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:01:13,212] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:01:13,213] [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 soli	strain=WSJ-3	GCA_009939225.1	2698829	2698829	type	True	100.0	1286	1286	95	conclusive
Sediminibacterium roseum	strain=SYL130	GCA_009939005.1	1978412	1978412	type	True	77.7518	343	1286	95	below_threshold
Sediminibacterium ginsengisoli	strain=DSM 22335	GCA_900167075.1	413434	413434	type	True	77.2416	278	1286	95	below_threshold
Sediminibacterium goheungense	strain=DSM 28323	GCA_004361915.1	1086393	1086393	type	True	77.0811	171	1286	95	below_threshold
Panacibacter microcysteis	strain=DH6	GCA_015831355.1	2793269	2793269	type	True	76.6287	71	1286	95	below_threshold
Deminuibacter soli	strain=K23C18032701	GCA_003412455.1	2291815	2291815	type	True	76.4848	173	1286	95	below_threshold
Parafilimonas terrae	strain=DSM 28286	GCA_900115755.1	1465490	1465490	type	True	76.4038	63	1286	95	below_threshold
Paraflavitalea devenefica	strain=X16	GCA_011759375.1	2716334	2716334	type	True	76.2839	119	1286	95	below_threshold
Filimonas effusa	strain=TTM-71	GCA_004118675.1	2508721	2508721	type	True	76.235	91	1286	95	below_threshold
Niabella pedocola	strain=JCM 31011	GCA_021044425.1	1752077	1752077	type	True	76.1872	75	1286	95	below_threshold
Filimonas lacunae	strain=DSM 21054	GCA_900156765.1	477680	477680	type	True	76.0991	81	1286	95	below_threshold
Flavihumibacter cheonanensis	strain=WS16	GCA_022352215.1	1442385	1442385	type	True	76.0974	74	1286	95	below_threshold
Niabella drilacis	strain=DSM 25811	GCA_900101395.1	1285928	1285928	type	True	76.0288	84	1286	95	below_threshold
Puia dinghuensis	strain=CGMCC 1.15448	GCA_014642875.1	1792502	1792502	type	True	75.9041	72	1286	95	below_threshold
Niastella soli	strain=MAH-29	GCA_017742245.1	2821487	2821487	type	True	75.7984	76	1286	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:01:13,214] [INFO] DFAST Taxonomy check result was written to GCF_009939225.1_ASM993922v1_genomic.fna/tc_result.tsv
[2024-01-25 18:01:13,214] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:01:13,214] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:01:13,215] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg66ad7c98-56a4-4bbf-8562-6d9072b94ace/dqc_reference/checkm_data
[2024-01-25 18:01:13,215] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:01:13,257] [INFO] Task started: CheckM
[2024-01-25 18:01:13,258] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009939225.1_ASM993922v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009939225.1_ASM993922v1_genomic.fna/checkm_input GCF_009939225.1_ASM993922v1_genomic.fna/checkm_result
[2024-01-25 18:02:03,845] [INFO] Task succeeded: CheckM
[2024-01-25 18:02:03,846] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:02:03,862] [INFO] ===== Completeness check finished =====
[2024-01-25 18:02:03,862] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:02:03,863] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009939225.1_ASM993922v1_genomic.fna/markers.fasta)
[2024-01-25 18:02:03,863] [INFO] Task started: Blastn
[2024-01-25 18:02:03,863] [INFO] Running command: blastn -query GCF_009939225.1_ASM993922v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg66ad7c98-56a4-4bbf-8562-6d9072b94ace/dqc_reference/reference_markers_gtdb.fasta -out GCF_009939225.1_ASM993922v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:02:04,651] [INFO] Task succeeded: Blastn
[2024-01-25 18:02:04,654] [INFO] Selected 16 target genomes.
[2024-01-25 18:02:04,654] [INFO] Target genome list was writen to GCF_009939225.1_ASM993922v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:02:04,666] [INFO] Task started: fastANI
[2024-01-25 18:02:04,667] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b4f5442-602c-41dc-a746-8e79e88e4b13/GCF_009939225.1_ASM993922v1_genomic.fna.gz --refList GCF_009939225.1_ASM993922v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009939225.1_ASM993922v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:02:17,082] [INFO] Task succeeded: fastANI
[2024-01-25 18:02:17,092] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:02:17,092] [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_009939225.1	s__Sediminibacterium soli	100.0	1286	1286	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_019247775.1	s__Sediminibacterium sp019247775	78.1407	434	1286	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016183765.1	s__Sediminibacterium sp016183765	77.7548	378	1286	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009939005.1	s__Sediminibacterium roseum	77.742	344	1286	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004028765.1	s__Sediminibacterium sp004028765	77.5749	344	1286	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000515315.1	s__Sediminibacterium sp000515315	77.4462	271	1286	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	96.66	96.66	0.84	0.84	2	-
GCA_002973575.1	s__Sediminibacterium magnilacihabitans	77.2704	265	1286	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	99.08	98.17	0.92	0.85	3	-
GCA_009996675.1	s__Sediminibacterium sp009996675	77.1593	220	1286	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004297075.1	s__Sediminibacterium sp004297075	77.0469	244	1286	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	98.05	98.05	0.89	0.89	2	-
GCA_013289065.1	s__Sediminibacterium sp013289065	76.6102	154	1286	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903926855.1	s__Sediminibacterium sp903926855	76.4155	129	1286	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	98.86	97.42	0.87	0.81	7	-
GCF_900115755.1	s__Parafilimonas terrae	76.4038	63	1286	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Parafilimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007970185.1	s__Pseudobacter ginsenosidimutans	76.3077	113	1286	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Pseudobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_012927185.1	s__Pseudobacter sp012927185	76.1558	97	1286	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Pseudobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:02:17,093] [INFO] GTDB search result was written to GCF_009939225.1_ASM993922v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:02:17,096] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:02:17,101] [INFO] DFAST_QC result json was written to GCF_009939225.1_ASM993922v1_genomic.fna/dqc_result.json
[2024-01-25 18:02:17,101] [INFO] DFAST_QC completed!
[2024-01-25 18:02:17,101] [INFO] Total running time: 0h1m42s