[2024-01-25 17:41:35,557] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:41:35,558] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:41:35,558] [INFO] DQC Reference Directory: /var/lib/cwl/stgdc1f3db0-c482-4529-8da9-e5eba44613aa/dqc_reference
[2024-01-25 17:41:36,759] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:41:36,759] [INFO] Task started: Prodigal
[2024-01-25 17:41:36,760] [INFO] Running command: gunzip -c /var/lib/cwl/stg86aabf41-3fd9-41c9-80f7-4d84e96dc6c1/GCF_014645495.1_ASM1464549v1_genomic.fna.gz | prodigal -d GCF_014645495.1_ASM1464549v1_genomic.fna/cds.fna -a GCF_014645495.1_ASM1464549v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:41:46,229] [INFO] Task succeeded: Prodigal
[2024-01-25 17:41:46,229] [INFO] Task started: HMMsearch
[2024-01-25 17:41:46,230] [INFO] Running command: hmmsearch --tblout GCF_014645495.1_ASM1464549v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdc1f3db0-c482-4529-8da9-e5eba44613aa/dqc_reference/reference_markers.hmm GCF_014645495.1_ASM1464549v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:41:46,448] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:41:46,449] [INFO] Found 6/6 markers.
[2024-01-25 17:41:46,474] [INFO] Query marker FASTA was written to GCF_014645495.1_ASM1464549v1_genomic.fna/markers.fasta
[2024-01-25 17:41:46,475] [INFO] Task started: Blastn
[2024-01-25 17:41:46,475] [INFO] Running command: blastn -query GCF_014645495.1_ASM1464549v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc1f3db0-c482-4529-8da9-e5eba44613aa/dqc_reference/reference_markers.fasta -out GCF_014645495.1_ASM1464549v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:41:47,107] [INFO] Task succeeded: Blastn
[2024-01-25 17:41:47,109] [INFO] Selected 15 target genomes.
[2024-01-25 17:41:47,110] [INFO] Target genome list was writen to GCF_014645495.1_ASM1464549v1_genomic.fna/target_genomes.txt
[2024-01-25 17:41:47,131] [INFO] Task started: fastANI
[2024-01-25 17:41:47,131] [INFO] Running command: fastANI --query /var/lib/cwl/stg86aabf41-3fd9-41c9-80f7-4d84e96dc6c1/GCF_014645495.1_ASM1464549v1_genomic.fna.gz --refList GCF_014645495.1_ASM1464549v1_genomic.fna/target_genomes.txt --output GCF_014645495.1_ASM1464549v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:41:56,584] [INFO] Task succeeded: fastANI
[2024-01-25 17:41:56,584] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdc1f3db0-c482-4529-8da9-e5eba44613aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:41:56,584] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdc1f3db0-c482-4529-8da9-e5eba44613aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:41:56,594] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:41:56,594] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:41:56,594] [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
Cloacibacterium rupense	strain=CGMCC 1.7656	GCA_014645495.1	517423	517423	type	True	100.0	1048	1049	95	conclusive
Cloacibacterium normanense	strain=DSM 15886	GCA_900104195.1	237258	237258	type	True	82.3975	577	1049	95	below_threshold
Cloacibacterium normanense	strain=NRS-1	GCA_001747495.1	237258	237258	type	True	82.378	577	1049	95	below_threshold
Cloacibacterium normanense	strain=NRS-1	GCA_003860565.1	237258	237258	type	True	82.3385	579	1049	95	below_threshold
Epilithonimonas zeae	strain=DSM 27623	GCA_900141765.1	1416779	1416779	type	True	77.4591	193	1049	95	below_threshold
Soonwooa buanensis	strain=DSM 22323	GCA_900167905.1	619805	619805	type	True	77.4333	171	1049	95	below_threshold
Chryseobacterium schmidteae	strain=Marseille-P9602	GCA_903166575.1	2730404	2730404	type	True	77.3846	198	1049	95	below_threshold
Chryseobacterium formosense	strain=DSM 17452	GCA_900116415.1	236814	236814	type	True	77.3256	207	1049	95	below_threshold
Chryseobacterium tagetis	strain=RG1	GCA_016735585.2	2801334	2801334	type	True	77.1645	194	1049	95	below_threshold
Chryseobacterium balustinum	strain=DSM 16775	GCA_900168205.1	246	246	type	True	77.1529	216	1049	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	77.0864	212	1049	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	76.0113	59	1049	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	75.9158	59	1049	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	75.791	70	1049	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:41:56,596] [INFO] DFAST Taxonomy check result was written to GCF_014645495.1_ASM1464549v1_genomic.fna/tc_result.tsv
[2024-01-25 17:41:56,596] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:41:56,597] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:41:56,597] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdc1f3db0-c482-4529-8da9-e5eba44613aa/dqc_reference/checkm_data
[2024-01-25 17:41:56,598] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:41:56,640] [INFO] Task started: CheckM
[2024-01-25 17:41:56,640] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014645495.1_ASM1464549v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014645495.1_ASM1464549v1_genomic.fna/checkm_input GCF_014645495.1_ASM1464549v1_genomic.fna/checkm_result
[2024-01-25 17:42:27,347] [INFO] Task succeeded: CheckM
[2024-01-25 17:42:27,351] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:42:27,371] [INFO] ===== Completeness check finished =====
[2024-01-25 17:42:27,372] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:42:27,373] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014645495.1_ASM1464549v1_genomic.fna/markers.fasta)
[2024-01-25 17:42:27,373] [INFO] Task started: Blastn
[2024-01-25 17:42:27,373] [INFO] Running command: blastn -query GCF_014645495.1_ASM1464549v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc1f3db0-c482-4529-8da9-e5eba44613aa/dqc_reference/reference_markers_gtdb.fasta -out GCF_014645495.1_ASM1464549v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:42:28,448] [INFO] Task succeeded: Blastn
[2024-01-25 17:42:28,450] [INFO] Selected 6 target genomes.
[2024-01-25 17:42:28,450] [INFO] Target genome list was writen to GCF_014645495.1_ASM1464549v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:42:28,455] [INFO] Task started: fastANI
[2024-01-25 17:42:28,456] [INFO] Running command: fastANI --query /var/lib/cwl/stg86aabf41-3fd9-41c9-80f7-4d84e96dc6c1/GCF_014645495.1_ASM1464549v1_genomic.fna.gz --refList GCF_014645495.1_ASM1464549v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014645495.1_ASM1464549v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:42:32,648] [INFO] Task succeeded: fastANI
[2024-01-25 17:42:32,653] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:42:32,653] [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_014645495.1	s__Cloacibacterium rupense	100.0	1048	1049	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Cloacibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002337005.1	s__Cloacibacterium sp002337005	87.4674	739	1049	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Cloacibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003860565.1	s__Cloacibacterium normanense	82.3385	579	1049	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Cloacibacterium	95.1075	98.41	95.23	0.95	0.87	4	-
GCF_907163125.1	s__Cloacibacterium caeni_B	82.1977	571	1049	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Cloacibacterium	95.1075	N/A	N/A	N/A	N/A	1	-
GCF_002943105.1	s__Cloacibacterium sp002422665	81.969	587	1049	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Cloacibacterium	95.0662	95.27	95.25	0.87	0.85	3	-
GCF_907163105.1	s__Cloacibacterium caeni_A	81.9283	567	1049	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Cloacibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:42:32,655] [INFO] GTDB search result was written to GCF_014645495.1_ASM1464549v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:42:32,655] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:42:32,657] [INFO] DFAST_QC result json was written to GCF_014645495.1_ASM1464549v1_genomic.fna/dqc_result.json
[2024-01-25 17:42:32,657] [INFO] DFAST_QC completed!
[2024-01-25 17:42:32,658] [INFO] Total running time: 0h0m57s