[2024-01-25 17:40:05,494] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:40:05,495] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:40:05,495] [INFO] DQC Reference Directory: /var/lib/cwl/stgb5fbdd9b-0594-43c7-8a12-922881e4dd44/dqc_reference
[2024-01-25 17:40:06,634] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:40:06,635] [INFO] Task started: Prodigal
[2024-01-25 17:40:06,635] [INFO] Running command: gunzip -c /var/lib/cwl/stg33c00f31-a750-4678-9801-63341a80326e/GCF_014651455.1_ASM1465145v1_genomic.fna.gz | prodigal -d GCF_014651455.1_ASM1465145v1_genomic.fna/cds.fna -a GCF_014651455.1_ASM1465145v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:40:29,305] [INFO] Task succeeded: Prodigal
[2024-01-25 17:40:29,306] [INFO] Task started: HMMsearch
[2024-01-25 17:40:29,306] [INFO] Running command: hmmsearch --tblout GCF_014651455.1_ASM1465145v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb5fbdd9b-0594-43c7-8a12-922881e4dd44/dqc_reference/reference_markers.hmm GCF_014651455.1_ASM1465145v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:40:29,564] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:40:29,565] [INFO] Found 6/6 markers.
[2024-01-25 17:40:29,606] [INFO] Query marker FASTA was written to GCF_014651455.1_ASM1465145v1_genomic.fna/markers.fasta
[2024-01-25 17:40:29,606] [INFO] Task started: Blastn
[2024-01-25 17:40:29,606] [INFO] Running command: blastn -query GCF_014651455.1_ASM1465145v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb5fbdd9b-0594-43c7-8a12-922881e4dd44/dqc_reference/reference_markers.fasta -out GCF_014651455.1_ASM1465145v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:40:30,174] [INFO] Task succeeded: Blastn
[2024-01-25 17:40:30,177] [INFO] Selected 13 target genomes.
[2024-01-25 17:40:30,177] [INFO] Target genome list was writen to GCF_014651455.1_ASM1465145v1_genomic.fna/target_genomes.txt
[2024-01-25 17:40:30,203] [INFO] Task started: fastANI
[2024-01-25 17:40:30,203] [INFO] Running command: fastANI --query /var/lib/cwl/stg33c00f31-a750-4678-9801-63341a80326e/GCF_014651455.1_ASM1465145v1_genomic.fna.gz --refList GCF_014651455.1_ASM1465145v1_genomic.fna/target_genomes.txt --output GCF_014651455.1_ASM1465145v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:40:43,266] [INFO] Task succeeded: fastANI
[2024-01-25 17:40:43,267] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb5fbdd9b-0594-43c7-8a12-922881e4dd44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:40:43,267] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb5fbdd9b-0594-43c7-8a12-922881e4dd44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:40:43,276] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:40:43,276] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:40:43,276] [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
Echinicola pacifica	strain=KCTC 12368	GCA_014651455.1	346377	346377	type	True	100.0	1809	1810	95	conclusive
Echinicola pacifica	strain=DSM 19836	GCA_000373245.1	346377	346377	type	True	99.9821	1800	1810	95	conclusive
Echinicola soli	strain=LN3S3	GCA_006575665.1	2591634	2591634	type	True	78.0176	320	1810	95	below_threshold
Echinicola vietnamensis	strain=DSM 17526	GCA_000325705.1	390884	390884	type	True	77.8961	337	1810	95	below_threshold
Echinicola rosea	strain=JL3085	GCA_005281475.1	1807691	1807691	type	True	77.8738	343	1810	95	below_threshold
Echinicola strongylocentroti	strain=MEBiC08714	GCA_003260975.1	1795355	1795355	type	True	77.7305	373	1810	95	below_threshold
Echinicola arenosa	strain=CAU 1574	GCA_014841125.1	2774144	2774144	type	True	77.6908	297	1810	95	below_threshold
Echinicola salinicaeni	strain=P51	GCA_014280965.1	2762757	2762757	type	True	77.6054	281	1810	95	below_threshold
Echinicola shivajiensis	strain=AK12	GCA_018642165.1	1035916	1035916	type	True	77.5473	279	1810	95	below_threshold
Algoriphagus ratkowskyi	strain=DSM 22686	GCA_002150505.1	57028	57028	type	True	77.4802	72	1810	95	below_threshold
Echinicola marina	strain=SCS 3-6	GCA_020463795.1	2859768	2859768	type	True	77.4708	292	1810	95	below_threshold
Belliella kenyensis	strain=DSM 46651	GCA_022549675.1	1472724	1472724	type	True	76.5816	75	1810	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:40:43,277] [INFO] DFAST Taxonomy check result was written to GCF_014651455.1_ASM1465145v1_genomic.fna/tc_result.tsv
[2024-01-25 17:40:43,278] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:40:43,278] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:40:43,278] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb5fbdd9b-0594-43c7-8a12-922881e4dd44/dqc_reference/checkm_data
[2024-01-25 17:40:43,279] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:40:43,332] [INFO] Task started: CheckM
[2024-01-25 17:40:43,332] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014651455.1_ASM1465145v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014651455.1_ASM1465145v1_genomic.fna/checkm_input GCF_014651455.1_ASM1465145v1_genomic.fna/checkm_result
[2024-01-25 17:41:47,001] [INFO] Task succeeded: CheckM
[2024-01-25 17:41:47,002] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:41:47,042] [INFO] ===== Completeness check finished =====
[2024-01-25 17:41:47,042] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:41:47,043] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014651455.1_ASM1465145v1_genomic.fna/markers.fasta)
[2024-01-25 17:41:47,043] [INFO] Task started: Blastn
[2024-01-25 17:41:47,043] [INFO] Running command: blastn -query GCF_014651455.1_ASM1465145v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb5fbdd9b-0594-43c7-8a12-922881e4dd44/dqc_reference/reference_markers_gtdb.fasta -out GCF_014651455.1_ASM1465145v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:41:47,846] [INFO] Task succeeded: Blastn
[2024-01-25 17:41:47,850] [INFO] Selected 17 target genomes.
[2024-01-25 17:41:47,850] [INFO] Target genome list was writen to GCF_014651455.1_ASM1465145v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:41:47,864] [INFO] Task started: fastANI
[2024-01-25 17:41:47,864] [INFO] Running command: fastANI --query /var/lib/cwl/stg33c00f31-a750-4678-9801-63341a80326e/GCF_014651455.1_ASM1465145v1_genomic.fna.gz --refList GCF_014651455.1_ASM1465145v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014651455.1_ASM1465145v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:42:03,515] [INFO] Task succeeded: fastANI
[2024-01-25 17:42:03,525] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:42:03,525] [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_000373245.1	s__Echinicola pacifica	99.9821	1800	1810	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_006575665.1	s__Echinicola sp006575665	78.0255	320	1810	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000325705.1	s__Echinicola vietnamensis	77.8961	337	1810	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005281475.1	s__Echinicola rosea	77.8738	343	1810	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003260975.1	s__Echinicola strongylocentroti	77.7305	373	1810	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014841125.1	s__Echinicola sp014841125	77.6908	297	1810	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015533855.1	s__Echinicola sp015533855	77.6755	311	1810	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014280965.1	s__Echinicola sp014280965	77.6054	281	1810	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018642165.1	s__Echinicola shivajiensis	77.5535	279	1810	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002150505.1	s__Algoriphagus ratkowskyi	77.4802	72	1810	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	100.00	99.99	1.00	1.00	3	-
GCF_018500185.1	s__Litoribacter ruber	77.348	109	1810	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Litoribacter	95.0	98.60	98.60	0.91	0.91	2	-
GCF_000429465.1	s__Algoriphagus vanfongensis	76.7556	80	1810	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015476655.1	s__Aquiflexum lacus	76.3528	78	1810	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Aquiflexum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113375.1	s__Algoriphagus hitonicola	75.9584	74	1810	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:42:03,527] [INFO] GTDB search result was written to GCF_014651455.1_ASM1465145v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:42:03,535] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:42:03,543] [INFO] DFAST_QC result json was written to GCF_014651455.1_ASM1465145v1_genomic.fna/dqc_result.json
[2024-01-25 17:42:03,543] [INFO] DFAST_QC completed!
[2024-01-25 17:42:03,543] [INFO] Total running time: 0h1m58s