[2024-01-24 12:13:27,856] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:27,859] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:27,859] [INFO] DQC Reference Directory: /var/lib/cwl/stg42ac45b5-91c1-4619-9eb9-63f0e2564c26/dqc_reference
[2024-01-24 12:13:29,257] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:29,258] [INFO] Task started: Prodigal
[2024-01-24 12:13:29,259] [INFO] Running command: gunzip -c /var/lib/cwl/stg2701c1bf-73d4-4b02-8531-fd1c3e7cc06f/GCF_000296815.2_ASM29681v2_genomic.fna.gz | prodigal -d GCF_000296815.2_ASM29681v2_genomic.fna/cds.fna -a GCF_000296815.2_ASM29681v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:07,049] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:07,049] [INFO] Task started: HMMsearch
[2024-01-24 12:14:07,049] [INFO] Running command: hmmsearch --tblout GCF_000296815.2_ASM29681v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg42ac45b5-91c1-4619-9eb9-63f0e2564c26/dqc_reference/reference_markers.hmm GCF_000296815.2_ASM29681v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:07,395] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:07,396] [INFO] Found 6/6 markers.
[2024-01-24 12:14:07,453] [INFO] Query marker FASTA was written to GCF_000296815.2_ASM29681v2_genomic.fna/markers.fasta
[2024-01-24 12:14:07,453] [INFO] Task started: Blastn
[2024-01-24 12:14:07,453] [INFO] Running command: blastn -query GCF_000296815.2_ASM29681v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg42ac45b5-91c1-4619-9eb9-63f0e2564c26/dqc_reference/reference_markers.fasta -out GCF_000296815.2_ASM29681v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:08,052] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:08,056] [INFO] Selected 19 target genomes.
[2024-01-24 12:14:08,056] [INFO] Target genome list was writen to GCF_000296815.2_ASM29681v2_genomic.fna/target_genomes.txt
[2024-01-24 12:14:08,064] [INFO] Task started: fastANI
[2024-01-24 12:14:08,064] [INFO] Running command: fastANI --query /var/lib/cwl/stg2701c1bf-73d4-4b02-8531-fd1c3e7cc06f/GCF_000296815.2_ASM29681v2_genomic.fna.gz --refList GCF_000296815.2_ASM29681v2_genomic.fna/target_genomes.txt --output GCF_000296815.2_ASM29681v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:29,539] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:29,540] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg42ac45b5-91c1-4619-9eb9-63f0e2564c26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:29,541] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg42ac45b5-91c1-4619-9eb9-63f0e2564c26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:29,559] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:14:29,559] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:29,559] [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
Fibrisoma limi	strain=BUZ 3	GCA_000296815.2	663275	663275	type	True	100.0	2534	2536	95	conclusive
Fibrisoma montanum	strain=HYT19	GCA_003583365.1	2305895	2305895	type	True	85.5917	1968	2536	95	below_threshold
Spirosoma taeanense	strain=TS118	GCA_013127955.1	2735870	2735870	type	True	77.4448	496	2536	95	below_threshold
Spirosoma lacussanchae	strain=CPCC 100624	GCA_005870035.1	1884249	1884249	type	True	77.3283	475	2536	95	below_threshold
Spirosoma sordidisoli	strain=TY50	GCA_004138325.1	2502893	2502893	type	True	77.2309	489	2536	95	below_threshold
Spirosoma rigui	strain=KCTC 12531	GCA_002067135.1	564064	564064	type	True	76.9279	427	2536	95	below_threshold
Spirosoma oryzae	strain=DSM 28354	GCA_003002825.1	1469603	1469603	type	True	76.7983	374	2536	95	below_threshold
Fibrella aestuarina	strain=BUZ 2	GCA_000331105.1	651143	651143	type	True	76.7699	354	2536	95	below_threshold
Rudanella paleaurantiibacter	strain=HX-22-17	GCA_009184635.1	2614655	2614655	type	True	76.7402	315	2536	95	below_threshold
Spirosoma validum	strain=BT704	GCA_014699035.1	2771355	2771355	type	True	76.6417	338	2536	95	below_threshold
Spirosoma panaciterrae	strain=DSM 21099	GCA_000374025.1	496058	496058	type	True	76.5729	347	2536	95	below_threshold
Spirosoma endophyticum	strain=DSM 26130	GCA_900112365.1	662367	662367	type	True	76.4949	325	2536	95	below_threshold
Fibrella aquatilis	strain=HMF5036	GCA_017353255.1	2817059	2817059	type	True	75.962	245	2536	95	below_threshold
Fibrella rubiginis	strain=HMF5335	GCA_017353185.1	2817060	2817060	type	True	75.8736	225	2536	95	below_threshold
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	75.0591	65	2536	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:29,562] [INFO] DFAST Taxonomy check result was written to GCF_000296815.2_ASM29681v2_genomic.fna/tc_result.tsv
[2024-01-24 12:14:29,562] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:29,562] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:29,563] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg42ac45b5-91c1-4619-9eb9-63f0e2564c26/dqc_reference/checkm_data
[2024-01-24 12:14:29,564] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:29,632] [INFO] Task started: CheckM
[2024-01-24 12:14:29,632] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000296815.2_ASM29681v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000296815.2_ASM29681v2_genomic.fna/checkm_input GCF_000296815.2_ASM29681v2_genomic.fna/checkm_result
[2024-01-24 12:16:08,875] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:08,877] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:08,898] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:08,898] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:08,899] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000296815.2_ASM29681v2_genomic.fna/markers.fasta)
[2024-01-24 12:16:08,899] [INFO] Task started: Blastn
[2024-01-24 12:16:08,899] [INFO] Running command: blastn -query GCF_000296815.2_ASM29681v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg42ac45b5-91c1-4619-9eb9-63f0e2564c26/dqc_reference/reference_markers_gtdb.fasta -out GCF_000296815.2_ASM29681v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:09,706] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:09,711] [INFO] Selected 15 target genomes.
[2024-01-24 12:16:09,711] [INFO] Target genome list was writen to GCF_000296815.2_ASM29681v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:09,722] [INFO] Task started: fastANI
[2024-01-24 12:16:09,722] [INFO] Running command: fastANI --query /var/lib/cwl/stg2701c1bf-73d4-4b02-8531-fd1c3e7cc06f/GCF_000296815.2_ASM29681v2_genomic.fna.gz --refList GCF_000296815.2_ASM29681v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000296815.2_ASM29681v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:28,177] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:28,197] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:28,197] [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_000296815.2	s__Fibrisoma limi	100.0	2534	2536	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Fibrisoma	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003583365.1	s__Fibrisoma montanum	85.5845	1969	2536	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Fibrisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013127955.1	s__Spirosoma taeanense	77.4131	497	2536	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005870035.1	s__Spirosoma lacussanchae	77.3227	476	2536	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004138325.1	s__Spirosoma sordidisoli	77.2256	487	2536	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	98.69	98.69	0.94	0.94	2	-
GCF_012849055.1	s__Spirosoma sp012849055	77.1205	398	2536	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013375035.1	s__Spirosoma sp013375035	77.0649	377	2536	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002067135.1	s__Spirosoma rigui	76.8752	425	2536	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003002825.1	s__Spirosoma oryzae	76.792	375	2536	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000331105.1	s__Fibrella aestuarina	76.7617	354	2536	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Fibrella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009184635.1	s__Rudanella paleaurantiibacter	76.7333	316	2536	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Rudanella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898575.1	s__Spirosoma sp001898575	76.7169	324	2536	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	99.98	99.98	0.99	0.99	2	-
GCF_014699035.1	s__Spirosoma validum	76.6349	339	2536	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374025.1	s__Spirosoma panaciterrae	76.5719	347	2536	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:28,198] [INFO] GTDB search result was written to GCF_000296815.2_ASM29681v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:28,200] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:28,204] [INFO] DFAST_QC result json was written to GCF_000296815.2_ASM29681v2_genomic.fna/dqc_result.json
[2024-01-24 12:16:28,204] [INFO] DFAST_QC completed!
[2024-01-24 12:16:28,204] [INFO] Total running time: 0h3m0s