[2024-01-24 13:25:46,468] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:46,469] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:46,470] [INFO] DQC Reference Directory: /var/lib/cwl/stg63cea75c-36b1-4f3c-b15f-a81aa03d3141/dqc_reference
[2024-01-24 13:25:47,895] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:47,896] [INFO] Task started: Prodigal
[2024-01-24 13:25:47,897] [INFO] Running command: gunzip -c /var/lib/cwl/stg73f4ff76-5342-49f8-aca4-eeee7d374e4b/GCF_009792295.1_ASM979229v1_genomic.fna.gz | prodigal -d GCF_009792295.1_ASM979229v1_genomic.fna/cds.fna -a GCF_009792295.1_ASM979229v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:26:02,775] [INFO] Task succeeded: Prodigal
[2024-01-24 13:26:02,776] [INFO] Task started: HMMsearch
[2024-01-24 13:26:02,776] [INFO] Running command: hmmsearch --tblout GCF_009792295.1_ASM979229v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg63cea75c-36b1-4f3c-b15f-a81aa03d3141/dqc_reference/reference_markers.hmm GCF_009792295.1_ASM979229v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:26:03,066] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:26:03,068] [INFO] Found 6/6 markers.
[2024-01-24 13:26:03,101] [INFO] Query marker FASTA was written to GCF_009792295.1_ASM979229v1_genomic.fna/markers.fasta
[2024-01-24 13:26:03,102] [INFO] Task started: Blastn
[2024-01-24 13:26:03,102] [INFO] Running command: blastn -query GCF_009792295.1_ASM979229v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg63cea75c-36b1-4f3c-b15f-a81aa03d3141/dqc_reference/reference_markers.fasta -out GCF_009792295.1_ASM979229v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:03,785] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:03,789] [INFO] Selected 18 target genomes.
[2024-01-24 13:26:03,790] [INFO] Target genome list was writen to GCF_009792295.1_ASM979229v1_genomic.fna/target_genomes.txt
[2024-01-24 13:26:03,797] [INFO] Task started: fastANI
[2024-01-24 13:26:03,798] [INFO] Running command: fastANI --query /var/lib/cwl/stg73f4ff76-5342-49f8-aca4-eeee7d374e4b/GCF_009792295.1_ASM979229v1_genomic.fna.gz --refList GCF_009792295.1_ASM979229v1_genomic.fna/target_genomes.txt --output GCF_009792295.1_ASM979229v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:14,258] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:14,259] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg63cea75c-36b1-4f3c-b15f-a81aa03d3141/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:14,259] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg63cea75c-36b1-4f3c-b15f-a81aa03d3141/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:14,270] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:26:14,271] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:26:14,271] [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
Myroides fluvii	strain=CJ210	GCA_009792295.1	2572594	2572594	type	True	100.0	1251	1255	95	conclusive
Myroides odoratus	strain=NCTC11036	GCA_900453865.1	256	256	type	True	85.0089	908	1255	95	below_threshold
Myroides odoratus	strain=FDAARGOS_1131	GCA_016726985.1	256	256	type	True	84.9351	926	1255	95	below_threshold
Myroides odoratus	strain=DSM 2801	GCA_000243275.1	256	256	type	True	84.8727	918	1255	95	below_threshold
Myroides albus	strain=BIT-d1	GCA_009711045.1	2562892	2562892	type	True	78.7171	255	1255	95	below_threshold
Myroides phaeus	strain=DSM 23313	GCA_900099675.1	702745	702745	type	True	78.6204	288	1255	95	below_threshold
Myroides marinus	strain=DSM 23048	GCA_900109075.1	703342	703342	type	True	78.5372	279	1255	95	below_threshold
Flavobacterium sangjuense	strain=GS03	GCA_004797125.1	2518177	2518177	type	True	78.1101	82	1255	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	78.0879	107	1255	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	77.0522	62	1255	95	below_threshold
Tenacibaculum haliotis	strain=KCTC 52419	GCA_025215075.1	1888914	1888914	type	True	76.4764	55	1255	95	below_threshold
Joostella atrarenae	strain=M1-2	GCA_021764745.1	679257	679257	type	True	76.2519	61	1255	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:14,273] [INFO] DFAST Taxonomy check result was written to GCF_009792295.1_ASM979229v1_genomic.fna/tc_result.tsv
[2024-01-24 13:26:14,274] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:14,274] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:14,275] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg63cea75c-36b1-4f3c-b15f-a81aa03d3141/dqc_reference/checkm_data
[2024-01-24 13:26:14,277] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:14,321] [INFO] Task started: CheckM
[2024-01-24 13:26:14,322] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009792295.1_ASM979229v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009792295.1_ASM979229v1_genomic.fna/checkm_input GCF_009792295.1_ASM979229v1_genomic.fna/checkm_result
[2024-01-24 13:26:58,753] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:58,754] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:26:58,771] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:58,772] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:58,772] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009792295.1_ASM979229v1_genomic.fna/markers.fasta)
[2024-01-24 13:26:58,772] [INFO] Task started: Blastn
[2024-01-24 13:26:58,773] [INFO] Running command: blastn -query GCF_009792295.1_ASM979229v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg63cea75c-36b1-4f3c-b15f-a81aa03d3141/dqc_reference/reference_markers_gtdb.fasta -out GCF_009792295.1_ASM979229v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:59,680] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:59,684] [INFO] Selected 8 target genomes.
[2024-01-24 13:26:59,684] [INFO] Target genome list was writen to GCF_009792295.1_ASM979229v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:59,691] [INFO] Task started: fastANI
[2024-01-24 13:26:59,691] [INFO] Running command: fastANI --query /var/lib/cwl/stg73f4ff76-5342-49f8-aca4-eeee7d374e4b/GCF_009792295.1_ASM979229v1_genomic.fna.gz --refList GCF_009792295.1_ASM979229v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009792295.1_ASM979229v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:27:05,568] [INFO] Task succeeded: fastANI
[2024-01-24 13:27:05,580] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:27:05,580] [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_009792295.1	s__Flavobacterium sp009792295	100.0	1253	1255	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000243275.1	s__Flavobacterium odoratum	84.8763	918	1255	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.25	95.68	0.94	0.87	6	-
GCF_001549985.1	s__Flavobacterium odoratum_A	84.5636	913	1255	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014145635.1	s__Flavobacterium sp014145635	83.1876	799	1255	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014145665.1	s__Flavobacterium sp014145665	82.4023	715	1255	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018384465.1	s__Flavobacterium sp018384465	77.2686	61	1255	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:27:05,581] [INFO] GTDB search result was written to GCF_009792295.1_ASM979229v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:27:05,582] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:27:05,584] [INFO] DFAST_QC result json was written to GCF_009792295.1_ASM979229v1_genomic.fna/dqc_result.json
[2024-01-24 13:27:05,584] [INFO] DFAST_QC completed!
[2024-01-24 13:27:05,584] [INFO] Total running time: 0h1m19s