[2024-01-24 13:46:03,755] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:03,760] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:03,760] [INFO] DQC Reference Directory: /var/lib/cwl/stg7f10410c-a05c-483d-8197-c0822edac287/dqc_reference
[2024-01-24 13:46:05,146] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:05,147] [INFO] Task started: Prodigal
[2024-01-24 13:46:05,147] [INFO] Running command: gunzip -c /var/lib/cwl/stg0274e1ce-30d8-4fb2-9e4f-add2b8594021/GCF_014283215.1_ASM1428321v1_genomic.fna.gz | prodigal -d GCF_014283215.1_ASM1428321v1_genomic.fna/cds.fna -a GCF_014283215.1_ASM1428321v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:26,515] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:26,515] [INFO] Task started: HMMsearch
[2024-01-24 13:46:26,515] [INFO] Running command: hmmsearch --tblout GCF_014283215.1_ASM1428321v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7f10410c-a05c-483d-8197-c0822edac287/dqc_reference/reference_markers.hmm GCF_014283215.1_ASM1428321v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:26,964] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:26,966] [INFO] Found 6/6 markers.
[2024-01-24 13:46:27,026] [INFO] Query marker FASTA was written to GCF_014283215.1_ASM1428321v1_genomic.fna/markers.fasta
[2024-01-24 13:46:27,027] [INFO] Task started: Blastn
[2024-01-24 13:46:27,027] [INFO] Running command: blastn -query GCF_014283215.1_ASM1428321v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f10410c-a05c-483d-8197-c0822edac287/dqc_reference/reference_markers.fasta -out GCF_014283215.1_ASM1428321v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:27,848] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:27,852] [INFO] Selected 14 target genomes.
[2024-01-24 13:46:27,852] [INFO] Target genome list was writen to GCF_014283215.1_ASM1428321v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:27,863] [INFO] Task started: fastANI
[2024-01-24 13:46:27,863] [INFO] Running command: fastANI --query /var/lib/cwl/stg0274e1ce-30d8-4fb2-9e4f-add2b8594021/GCF_014283215.1_ASM1428321v1_genomic.fna.gz --refList GCF_014283215.1_ASM1428321v1_genomic.fna/target_genomes.txt --output GCF_014283215.1_ASM1428321v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:49,260] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:49,261] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7f10410c-a05c-483d-8197-c0822edac287/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:49,261] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7f10410c-a05c-483d-8197-c0822edac287/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:49,273] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:46:49,273] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:49,273] [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
Siccirubricoccus deserti	strain=SYSU D8009	GCA_014283215.1	2013562	2013562	type	True	100.0	1973	1982	95	conclusive
Siccirubricoccus deserti	strain=CGMCC 1.15936	GCA_014644195.1	2013562	2013562	type	True	99.9775	1899	1982	95	conclusive
Belnapia mucosa	strain=T6	GCA_016775475.1	2804532	2804532	type	True	81.9162	1162	1982	95	below_threshold
Belnapia rosea	strain=CGMCC 1.10758	GCA_900104205.1	938405	938405	type	True	81.7198	1084	1982	95	below_threshold
Belnapia rosea	strain=CPCC 100156	GCA_900101615.1	938405	938405	type	True	81.6525	1097	1982	95	below_threshold
Belnapia arida	strain=T18	GCA_016773205.1	2804533	2804533	type	True	81.2582	1120	1982	95	below_threshold
Belnapia moabensis	strain=DSM 16746	GCA_000745835.1	365533	365533	type	True	81.1852	1074	1982	95	below_threshold
Roseomonas hellenica	strain=LMG 31523	GCA_018129085.1	2687306	2687306	type	True	79.2806	873	1982	95	below_threshold
Falsiroseomonas selenitidurans	strain=BU-1	GCA_012103215.1	2716335	2716335	type	True	79.1852	875	1982	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	78.9129	633	1982	95	below_threshold
Rhodovarius lipocyclicus	strain=CCUG 44693	GCA_009900765.1	268410	268410	type	True	78.6009	668	1982	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	78.3471	662	1982	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	78.3378	675	1982	95	below_threshold
Roseomonas marmotae	strain=1318	GCA_017654485.1	2768161	2768161	type	True	78.3185	634	1982	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:49,275] [INFO] DFAST Taxonomy check result was written to GCF_014283215.1_ASM1428321v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:49,275] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:49,276] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:49,276] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7f10410c-a05c-483d-8197-c0822edac287/dqc_reference/checkm_data
[2024-01-24 13:46:49,277] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:49,336] [INFO] Task started: CheckM
[2024-01-24 13:46:49,337] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014283215.1_ASM1428321v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014283215.1_ASM1428321v1_genomic.fna/checkm_input GCF_014283215.1_ASM1428321v1_genomic.fna/checkm_result
[2024-01-24 13:47:51,380] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:51,381] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:51,399] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:51,399] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:51,399] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014283215.1_ASM1428321v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:51,399] [INFO] Task started: Blastn
[2024-01-24 13:47:51,399] [INFO] Running command: blastn -query GCF_014283215.1_ASM1428321v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f10410c-a05c-483d-8197-c0822edac287/dqc_reference/reference_markers_gtdb.fasta -out GCF_014283215.1_ASM1428321v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:52,756] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:52,759] [INFO] Selected 13 target genomes.
[2024-01-24 13:47:52,759] [INFO] Target genome list was writen to GCF_014283215.1_ASM1428321v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:52,777] [INFO] Task started: fastANI
[2024-01-24 13:47:52,778] [INFO] Running command: fastANI --query /var/lib/cwl/stg0274e1ce-30d8-4fb2-9e4f-add2b8594021/GCF_014283215.1_ASM1428321v1_genomic.fna.gz --refList GCF_014283215.1_ASM1428321v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014283215.1_ASM1428321v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:48:13,124] [INFO] Task succeeded: fastANI
[2024-01-24 13:48:13,136] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:48:13,136] [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_014283215.1	s__Siccirubricoccus deserti	100.0	1973	1982	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Siccirubricoccus	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_008360935.1	s__Siccirubricoccus phaeus	83.3147	1297	1982	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Siccirubricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004343615.1	s__Paracraurococcus sp004343615	82.4049	1088	1982	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Paracraurococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003258945.1	s__Paracraurococcus frigidaeris	82.3783	1144	1982	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Paracraurococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004353985.1	s__Paracraurococcus ruber	82.1763	1127	1982	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Paracraurococcus	95.0	99.87	99.87	0.95	0.95	2	-
GCF_004355005.1	s__Paracraurococcus ruber_A	82.1523	1206	1982	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Paracraurococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013112485.1	s__Paracraurococcus sp013112485	82.0791	1146	1982	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Paracraurococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019084075.1	s__G192 sp019084075	81.9198	1136	1982	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__G192	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016775475.1	s__Belnapia sp016775475	81.8821	1170	1982	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Belnapia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805545.1	s__Belnapia sp902805545	81.7952	960	1982	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Belnapia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101615.1	s__Belnapia rosea	81.6728	1093	1982	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Belnapia	95.0	98.36	98.36	0.89	0.89	2	-
GCF_000802185.1	s__Belnapia sp000802185	81.2732	1084	1982	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Belnapia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016773205.1	s__Belnapia sp016773205	81.2198	1126	1982	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Belnapia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:48:13,138] [INFO] GTDB search result was written to GCF_014283215.1_ASM1428321v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:48:13,138] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:48:13,142] [INFO] DFAST_QC result json was written to GCF_014283215.1_ASM1428321v1_genomic.fna/dqc_result.json
[2024-01-24 13:48:13,142] [INFO] DFAST_QC completed!
[2024-01-24 13:48:13,142] [INFO] Total running time: 0h2m9s