[2024-01-24 13:31:57,927] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:57,929] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:57,929] [INFO] DQC Reference Directory: /var/lib/cwl/stg187aa4c0-9f63-4382-8ee8-5553a0452c0a/dqc_reference
[2024-01-24 13:31:59,208] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:59,209] [INFO] Task started: Prodigal
[2024-01-24 13:31:59,209] [INFO] Running command: gunzip -c /var/lib/cwl/stgff3fc099-cda2-490f-9b30-bf7669bb3c95/GCF_003604215.1_ASM360421v1_genomic.fna.gz | prodigal -d GCF_003604215.1_ASM360421v1_genomic.fna/cds.fna -a GCF_003604215.1_ASM360421v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:15,109] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:15,109] [INFO] Task started: HMMsearch
[2024-01-24 13:32:15,109] [INFO] Running command: hmmsearch --tblout GCF_003604215.1_ASM360421v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg187aa4c0-9f63-4382-8ee8-5553a0452c0a/dqc_reference/reference_markers.hmm GCF_003604215.1_ASM360421v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:15,373] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:15,374] [INFO] Found 6/6 markers.
[2024-01-24 13:32:15,416] [INFO] Query marker FASTA was written to GCF_003604215.1_ASM360421v1_genomic.fna/markers.fasta
[2024-01-24 13:32:15,416] [INFO] Task started: Blastn
[2024-01-24 13:32:15,417] [INFO] Running command: blastn -query GCF_003604215.1_ASM360421v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg187aa4c0-9f63-4382-8ee8-5553a0452c0a/dqc_reference/reference_markers.fasta -out GCF_003604215.1_ASM360421v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:16,351] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:16,355] [INFO] Selected 12 target genomes.
[2024-01-24 13:32:16,355] [INFO] Target genome list was writen to GCF_003604215.1_ASM360421v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:16,358] [INFO] Task started: fastANI
[2024-01-24 13:32:16,358] [INFO] Running command: fastANI --query /var/lib/cwl/stgff3fc099-cda2-490f-9b30-bf7669bb3c95/GCF_003604215.1_ASM360421v1_genomic.fna.gz --refList GCF_003604215.1_ASM360421v1_genomic.fna/target_genomes.txt --output GCF_003604215.1_ASM360421v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:29,846] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:29,846] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg187aa4c0-9f63-4382-8ee8-5553a0452c0a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:29,846] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg187aa4c0-9f63-4382-8ee8-5553a0452c0a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:29,857] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:29,858] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:29,858] [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
Roseomonas vastitatis	strain=CPCC 101021	GCA_003604215.1	2307076	2307076	type	True	100.0	1599	1606	95	conclusive
Roseomonas oryzae	strain=KCTC 42542	GCA_008386565.1	1608942	1608942	type	True	86.0422	1123	1606	95	below_threshold
Roseomonas rhizosphaerae	strain=YW11	GCA_002631185.1	1335062	1335062	type	True	82.7335	907	1606	95	below_threshold
Roseomonas cervicalis	strain=ATCC 49957	GCA_000164635.1	204525	204525	type	True	82.6185	844	1606	95	below_threshold
Roseomonas coralli	strain=M0104	GCA_009829925.1	2545983	2545983	type	True	82.4099	951	1606	95	below_threshold
Roseomonas deserti	strain=M3	GCA_001982615.1	1817963	1817963	type	True	81.5848	873	1606	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	81.0431	828	1606	95	below_threshold
Roseomonas ludipueritiae	strain=DSM 14915	GCA_014490445.1	198093	198093	type	True	80.9862	794	1606	95	below_threshold
Roseomonas marmotae	strain=1318	GCA_017654485.1	2768161	2768161	type	True	80.5509	786	1606	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	78.2099	465	1606	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	78.1464	492	1606	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	77.9451	540	1606	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:29,859] [INFO] DFAST Taxonomy check result was written to GCF_003604215.1_ASM360421v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:29,860] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:29,860] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:29,860] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg187aa4c0-9f63-4382-8ee8-5553a0452c0a/dqc_reference/checkm_data
[2024-01-24 13:32:29,862] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:29,912] [INFO] Task started: CheckM
[2024-01-24 13:32:29,912] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003604215.1_ASM360421v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003604215.1_ASM360421v1_genomic.fna/checkm_input GCF_003604215.1_ASM360421v1_genomic.fna/checkm_result
[2024-01-24 13:33:26,068] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:26,069] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:26,084] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:26,084] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:26,084] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003604215.1_ASM360421v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:26,085] [INFO] Task started: Blastn
[2024-01-24 13:33:26,085] [INFO] Running command: blastn -query GCF_003604215.1_ASM360421v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg187aa4c0-9f63-4382-8ee8-5553a0452c0a/dqc_reference/reference_markers_gtdb.fasta -out GCF_003604215.1_ASM360421v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:27,795] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:27,798] [INFO] Selected 8 target genomes.
[2024-01-24 13:33:27,799] [INFO] Target genome list was writen to GCF_003604215.1_ASM360421v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:27,814] [INFO] Task started: fastANI
[2024-01-24 13:33:27,814] [INFO] Running command: fastANI --query /var/lib/cwl/stgff3fc099-cda2-490f-9b30-bf7669bb3c95/GCF_003604215.1_ASM360421v1_genomic.fna.gz --refList GCF_003604215.1_ASM360421v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003604215.1_ASM360421v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:38,103] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:38,111] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:38,111] [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_003604215.1	s__Roseomonas vastitatis	100.0	1599	1606	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_008386565.1	s__Roseomonas oryzae	86.0358	1124	1606	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003116135.1	s__Roseomonas aestuarii	83.0447	978	1606	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002631185.1	s__Roseomonas rhizosphaerae	82.7558	904	1606	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000164635.1	s__Roseomonas cervicalis	82.6115	845	1606	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009829925.1	s__Roseomonas coralli	82.3707	956	1606	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016107285.1	s__Roseomonas sp016107285	82.1415	865	1606	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001982615.1	s__Roseomonas deserti	81.5668	876	1606	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:38,112] [INFO] GTDB search result was written to GCF_003604215.1_ASM360421v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:38,113] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:38,116] [INFO] DFAST_QC result json was written to GCF_003604215.1_ASM360421v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:38,116] [INFO] DFAST_QC completed!
[2024-01-24 13:33:38,116] [INFO] Total running time: 0h1m40s