[2024-01-24 13:13:39,174] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:39,198] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:39,198] [INFO] DQC Reference Directory: /var/lib/cwl/stg41c541d3-2ac8-4139-b9b1-b7c726a85503/dqc_reference
[2024-01-24 13:13:40,493] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:40,494] [INFO] Task started: Prodigal
[2024-01-24 13:13:40,494] [INFO] Running command: gunzip -c /var/lib/cwl/stg4fed589d-830c-4964-8e6b-8e6c105a6ae0/GCF_001579945.1_ASM157994v1_genomic.fna.gz | prodigal -d GCF_001579945.1_ASM157994v1_genomic.fna/cds.fna -a GCF_001579945.1_ASM157994v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:51,376] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:51,376] [INFO] Task started: HMMsearch
[2024-01-24 13:13:51,376] [INFO] Running command: hmmsearch --tblout GCF_001579945.1_ASM157994v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg41c541d3-2ac8-4139-b9b1-b7c726a85503/dqc_reference/reference_markers.hmm GCF_001579945.1_ASM157994v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:51,631] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:51,632] [INFO] Found 6/6 markers.
[2024-01-24 13:13:51,688] [INFO] Query marker FASTA was written to GCF_001579945.1_ASM157994v1_genomic.fna/markers.fasta
[2024-01-24 13:13:51,688] [INFO] Task started: Blastn
[2024-01-24 13:13:51,689] [INFO] Running command: blastn -query GCF_001579945.1_ASM157994v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg41c541d3-2ac8-4139-b9b1-b7c726a85503/dqc_reference/reference_markers.fasta -out GCF_001579945.1_ASM157994v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:52,624] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:52,628] [INFO] Selected 19 target genomes.
[2024-01-24 13:13:52,629] [INFO] Target genome list was writen to GCF_001579945.1_ASM157994v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:52,636] [INFO] Task started: fastANI
[2024-01-24 13:13:52,637] [INFO] Running command: fastANI --query /var/lib/cwl/stg4fed589d-830c-4964-8e6b-8e6c105a6ae0/GCF_001579945.1_ASM157994v1_genomic.fna.gz --refList GCF_001579945.1_ASM157994v1_genomic.fna/target_genomes.txt --output GCF_001579945.1_ASM157994v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:14:08,197] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:08,198] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg41c541d3-2ac8-4139-b9b1-b7c726a85503/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:14:08,198] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg41c541d3-2ac8-4139-b9b1-b7c726a85503/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:14:08,213] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:14:08,214] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:14:08,214] [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
Steroidobacter denitrificans	strain=DSM 18526	GCA_001579945.1	465721	465721	type	True	100.0	1155	1155	95	conclusive
Pseudomonas yangonensis	strain=MY50	GCA_009932725.1	2579922	2579922	type	True	78.3864	63	1155	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	78.2588	70	1155	95	below_threshold
Steroidobacter gossypii	strain=S1-65	GCA_016801985.1	2805490	2805490	type	True	77.46	263	1155	95	below_threshold
Steroidobacter soli	strain=JW-3	GCA_004138485.1	2497877	2497877	type	True	77.3629	254	1155	95	below_threshold
Steroidobacter agariperforans	strain=KA5-B	GCA_004138335.1	268404	268404	type	True	77.3582	273	1155	95	below_threshold
Steroidobacter cummioxidans	strain=35Y	GCA_003104955.1	1803913	1803913	type	True	77.3014	259	1155	95	below_threshold
Povalibacter uvarum	strain=DSM 26723	GCA_014202975.1	732238	732238	type	True	77.1686	232	1155	95	below_threshold
Methylonatrum kenyense	strain=AMT 1	GCA_023195885.1	455253	455253	type	True	76.5764	53	1155	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	76.351	80	1155	95	below_threshold
Plasticicumulans acidivorans	strain=DSM 23606	GCA_003182095.1	886464	886464	type	True	76.3096	81	1155	95	below_threshold
Pseudomonas guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	76.2155	72	1155	95	below_threshold
Thioalkalivibrio denitrificans	strain=ALJD	GCA_002000365.1	108003	108003	type	True	76.1853	72	1155	95	below_threshold
Arenimonas oryziterrae	strain=YC6267	GCA_000747135.1	498055	498055	type	True	76.0494	60	1155	95	below_threshold
Dokdonella koreensis	strain=DS-123	GCA_001632775.1	323415	323415	type	True	76.033	93	1155	95	below_threshold
Arenimonas oryziterrae	strain=DSM 21050	GCA_000420545.1	498055	498055	type	True	76.0287	61	1155	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	75.9513	107	1155	95	below_threshold
Hydrocarboniphaga effusa	strain=AP103	GCA_000271305.1	243629	243629	type	True	75.7914	86	1155	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:14:08,216] [INFO] DFAST Taxonomy check result was written to GCF_001579945.1_ASM157994v1_genomic.fna/tc_result.tsv
[2024-01-24 13:14:08,217] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:14:08,217] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:14:08,218] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg41c541d3-2ac8-4139-b9b1-b7c726a85503/dqc_reference/checkm_data
[2024-01-24 13:14:08,219] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:14:08,254] [INFO] Task started: CheckM
[2024-01-24 13:14:08,254] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001579945.1_ASM157994v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001579945.1_ASM157994v1_genomic.fna/checkm_input GCF_001579945.1_ASM157994v1_genomic.fna/checkm_result
[2024-01-24 13:14:44,051] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:44,053] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:44,070] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:44,070] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:44,071] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001579945.1_ASM157994v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:44,071] [INFO] Task started: Blastn
[2024-01-24 13:14:44,071] [INFO] Running command: blastn -query GCF_001579945.1_ASM157994v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg41c541d3-2ac8-4139-b9b1-b7c726a85503/dqc_reference/reference_markers_gtdb.fasta -out GCF_001579945.1_ASM157994v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:45,714] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:45,717] [INFO] Selected 17 target genomes.
[2024-01-24 13:14:45,718] [INFO] Target genome list was writen to GCF_001579945.1_ASM157994v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:45,735] [INFO] Task started: fastANI
[2024-01-24 13:14:45,736] [INFO] Running command: fastANI --query /var/lib/cwl/stg4fed589d-830c-4964-8e6b-8e6c105a6ae0/GCF_001579945.1_ASM157994v1_genomic.fna.gz --refList GCF_001579945.1_ASM157994v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001579945.1_ASM157994v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:58,924] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:58,938] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:58,938] [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_001579945.1	s__Steroidobacter denitrificans	100.0	1155	1155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__Steroidobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016801985.1	s__Steroidobacter_A sp016801985	77.4486	264	1155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__Steroidobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009932555.1	s__Steroidobacter_A agaridevorans	77.4236	283	1155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__Steroidobacter_A	95.0	99.33	99.33	0.96	0.96	2	-
GCF_004138335.1	s__Steroidobacter_A agariperforans	77.3691	272	1155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__Steroidobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004138485.1	s__Steroidobacter_A soli	77.3518	255	1155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__Steroidobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202975.1	s__Povalibacter uvarum	77.1686	232	1155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__Povalibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003242495.1	s__ZC4RG39 sp003242495	77.0115	206	1155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__ZC4RG39	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018059685.1	s__RPQJ01 sp018059685	76.8192	129	1155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__RPQJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000380335.1	s__Azotobacter vinelandii	76.7213	87	1155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Azotobacter	95.0	99.84	99.43	0.98	0.95	5	-
GCA_017577615.1	s__JAAYXG01 sp017577615	76.7033	144	1155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__JAAYXG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019136105.1	s__RPQJ01 sp019136105	76.4701	88	1155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__RPQJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012516015.1	s__JAAYXG01 sp012516015	76.4567	87	1155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__JAAYXG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903898785.1	s__CAIUGU01 sp903898785	76.277	101	1155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__CAIUGU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240265.1	s__TMP-86 sp018240265	75.9729	99	1155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__TMP-86	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003137095.1	s__Bog-1198 sp003137095	75.9607	97	1155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__Bog-1198	95.0	99.69	99.56	0.95	0.94	4	-
GCA_003819815.1	s__RPQJ01 sp003819815	75.7216	80	1155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__RPQJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339665.1	s__Azotobacter chroococcum	75.6922	75	1155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Azotobacter	95.0	97.27	96.18	0.89	0.83	10	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:58,940] [INFO] GTDB search result was written to GCF_001579945.1_ASM157994v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:58,940] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:58,944] [INFO] DFAST_QC result json was written to GCF_001579945.1_ASM157994v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:58,944] [INFO] DFAST_QC completed!
[2024-01-24 13:14:58,944] [INFO] Total running time: 0h1m20s