[2024-01-24 14:55:50,205] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:50,208] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:50,208] [INFO] DQC Reference Directory: /var/lib/cwl/stge4207ee8-d2c1-47a9-ab21-6f37e295be67/dqc_reference
[2024-01-24 14:55:51,511] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:51,512] [INFO] Task started: Prodigal
[2024-01-24 14:55:51,512] [INFO] Running command: gunzip -c /var/lib/cwl/stg9fba57e2-fa98-4612-8dea-940e292899d3/GCF_003258945.1_ASM325894v1_genomic.fna.gz | prodigal -d GCF_003258945.1_ASM325894v1_genomic.fna/cds.fna -a GCF_003258945.1_ASM325894v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:56:07,443] [INFO] Task succeeded: Prodigal
[2024-01-24 14:56:07,443] [INFO] Task started: HMMsearch
[2024-01-24 14:56:07,444] [INFO] Running command: hmmsearch --tblout GCF_003258945.1_ASM325894v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge4207ee8-d2c1-47a9-ab21-6f37e295be67/dqc_reference/reference_markers.hmm GCF_003258945.1_ASM325894v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:56:07,755] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:56:07,756] [INFO] Found 6/6 markers.
[2024-01-24 14:56:07,809] [INFO] Query marker FASTA was written to GCF_003258945.1_ASM325894v1_genomic.fna/markers.fasta
[2024-01-24 14:56:07,809] [INFO] Task started: Blastn
[2024-01-24 14:56:07,810] [INFO] Running command: blastn -query GCF_003258945.1_ASM325894v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge4207ee8-d2c1-47a9-ab21-6f37e295be67/dqc_reference/reference_markers.fasta -out GCF_003258945.1_ASM325894v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:08,754] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:08,757] [INFO] Selected 12 target genomes.
[2024-01-24 14:56:08,758] [INFO] Target genome list was writen to GCF_003258945.1_ASM325894v1_genomic.fna/target_genomes.txt
[2024-01-24 14:56:08,762] [INFO] Task started: fastANI
[2024-01-24 14:56:08,763] [INFO] Running command: fastANI --query /var/lib/cwl/stg9fba57e2-fa98-4612-8dea-940e292899d3/GCF_003258945.1_ASM325894v1_genomic.fna.gz --refList GCF_003258945.1_ASM325894v1_genomic.fna/target_genomes.txt --output GCF_003258945.1_ASM325894v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:56:26,406] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:26,407] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge4207ee8-d2c1-47a9-ab21-6f37e295be67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:56:26,407] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge4207ee8-d2c1-47a9-ab21-6f37e295be67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:56:26,431] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:56:26,431] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:56:26,431] [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
Belnapia mucosa	strain=T6	GCA_016775475.1	2804532	2804532	type	True	82.5556	1199	1900	95	below_threshold
Belnapia rosea	strain=CGMCC 1.10758	GCA_900104205.1	938405	938405	type	True	82.5228	1146	1900	95	below_threshold
Belnapia rosea	strain=CPCC 100156	GCA_900101615.1	938405	938405	type	True	82.5166	1142	1900	95	below_threshold
Siccirubricoccus deserti	strain=CGMCC 1.15936	GCA_014644195.1	2013562	2013562	type	True	82.501	1152	1900	95	below_threshold
Siccirubricoccus deserti	strain=SYSU D8009	GCA_014283215.1	2013562	2013562	type	True	82.4432	1157	1900	95	below_threshold
Belnapia arida	strain=T18	GCA_016773205.1	2804533	2804533	type	True	82.2006	1135	1900	95	below_threshold
Belnapia moabensis	strain=DSM 16746	GCA_000745835.1	365533	365533	type	True	82.0674	1134	1900	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	79.5123	685	1900	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	78.9423	747	1900	95	below_threshold
Rhodovarius lipocyclicus	strain=CCUG 44693	GCA_009900765.1	268410	268410	type	True	78.827	672	1900	95	below_threshold
Roseomonas marmotae	strain=1318	GCA_017654485.1	2768161	2768161	type	True	78.7917	669	1900	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	78.3157	695	1900	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:56:26,434] [INFO] DFAST Taxonomy check result was written to GCF_003258945.1_ASM325894v1_genomic.fna/tc_result.tsv
[2024-01-24 14:56:26,435] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:56:26,435] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:56:26,436] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge4207ee8-d2c1-47a9-ab21-6f37e295be67/dqc_reference/checkm_data
[2024-01-24 14:56:26,437] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:56:26,491] [INFO] Task started: CheckM
[2024-01-24 14:56:26,492] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003258945.1_ASM325894v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003258945.1_ASM325894v1_genomic.fna/checkm_input GCF_003258945.1_ASM325894v1_genomic.fna/checkm_result
[2024-01-24 14:57:41,080] [INFO] Task succeeded: CheckM
[2024-01-24 14:57:41,082] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:57:41,108] [INFO] ===== Completeness check finished =====
[2024-01-24 14:57:41,109] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:57:41,109] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003258945.1_ASM325894v1_genomic.fna/markers.fasta)
[2024-01-24 14:57:41,110] [INFO] Task started: Blastn
[2024-01-24 14:57:41,110] [INFO] Running command: blastn -query GCF_003258945.1_ASM325894v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge4207ee8-d2c1-47a9-ab21-6f37e295be67/dqc_reference/reference_markers_gtdb.fasta -out GCF_003258945.1_ASM325894v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:57:42,889] [INFO] Task succeeded: Blastn
[2024-01-24 14:57:42,904] [INFO] Selected 9 target genomes.
[2024-01-24 14:57:42,904] [INFO] Target genome list was writen to GCF_003258945.1_ASM325894v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:57:42,915] [INFO] Task started: fastANI
[2024-01-24 14:57:42,915] [INFO] Running command: fastANI --query /var/lib/cwl/stg9fba57e2-fa98-4612-8dea-940e292899d3/GCF_003258945.1_ASM325894v1_genomic.fna.gz --refList GCF_003258945.1_ASM325894v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003258945.1_ASM325894v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:58:01,946] [INFO] Task succeeded: fastANI
[2024-01-24 14:58:01,955] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:58:01,955] [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_003258945.1	s__Paracraurococcus frigidaeris	100.0	1894	1900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Paracraurococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013112485.1	s__Paracraurococcus sp013112485	91.8409	1600	1900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Paracraurococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004343615.1	s__Paracraurococcus sp004343615	85.3063	1323	1900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Paracraurococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004355005.1	s__Paracraurococcus ruber_A	84.5604	1359	1900	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	84.2554	1224	1900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Paracraurococcus	95.0	99.87	99.87	0.95	0.95	2	-
GCF_016775475.1	s__Belnapia sp016775475	82.6019	1193	1900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Belnapia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008360935.1	s__Siccirubricoccus phaeus	82.4355	1216	1900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Siccirubricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019084075.1	s__G192 sp019084075	82.0717	1077	1900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__G192	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004761865.1	s__Crenalkalicoccus roseus	81.7674	980	1900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Crenalkalicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:58:01,959] [INFO] GTDB search result was written to GCF_003258945.1_ASM325894v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:58:01,960] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:58:01,965] [INFO] DFAST_QC result json was written to GCF_003258945.1_ASM325894v1_genomic.fna/dqc_result.json
[2024-01-24 14:58:01,965] [INFO] DFAST_QC completed!
[2024-01-24 14:58:01,965] [INFO] Total running time: 0h2m12s