[2024-01-24 15:18:18,187] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:18,190] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:18,190] [INFO] DQC Reference Directory: /var/lib/cwl/stg8f0bb2ce-e042-443e-87d8-030970000a90/dqc_reference
[2024-01-24 15:18:19,458] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:19,459] [INFO] Task started: Prodigal
[2024-01-24 15:18:19,459] [INFO] Running command: gunzip -c /var/lib/cwl/stg96554ac9-8130-45dc-ab98-d45388482839/GCF_014195635.1_ASM1419563v1_genomic.fna.gz | prodigal -d GCF_014195635.1_ASM1419563v1_genomic.fna/cds.fna -a GCF_014195635.1_ASM1419563v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:32,129] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:32,129] [INFO] Task started: HMMsearch
[2024-01-24 15:18:32,129] [INFO] Running command: hmmsearch --tblout GCF_014195635.1_ASM1419563v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8f0bb2ce-e042-443e-87d8-030970000a90/dqc_reference/reference_markers.hmm GCF_014195635.1_ASM1419563v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:32,477] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:32,479] [INFO] Found 6/6 markers.
[2024-01-24 15:18:32,530] [INFO] Query marker FASTA was written to GCF_014195635.1_ASM1419563v1_genomic.fna/markers.fasta
[2024-01-24 15:18:32,531] [INFO] Task started: Blastn
[2024-01-24 15:18:32,531] [INFO] Running command: blastn -query GCF_014195635.1_ASM1419563v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f0bb2ce-e042-443e-87d8-030970000a90/dqc_reference/reference_markers.fasta -out GCF_014195635.1_ASM1419563v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:33,370] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:33,373] [INFO] Selected 18 target genomes.
[2024-01-24 15:18:33,374] [INFO] Target genome list was writen to GCF_014195635.1_ASM1419563v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:33,380] [INFO] Task started: fastANI
[2024-01-24 15:18:33,381] [INFO] Running command: fastANI --query /var/lib/cwl/stg96554ac9-8130-45dc-ab98-d45388482839/GCF_014195635.1_ASM1419563v1_genomic.fna.gz --refList GCF_014195635.1_ASM1419563v1_genomic.fna/target_genomes.txt --output GCF_014195635.1_ASM1419563v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:18:47,518] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:47,519] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8f0bb2ce-e042-443e-87d8-030970000a90/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:18:47,519] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8f0bb2ce-e042-443e-87d8-030970000a90/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:18:47,536] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:18:47,537] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:18:47,537] [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
Pseudochelatococcus contaminans	strain=DSM 28760	GCA_014195635.1	1538103	1538103	type	True	100.0	1345	1346	95	conclusive
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	78.0929	288	1346	95	below_threshold
Chelatococcus sambhunathii	strain=DSM 18167	GCA_001418005.1	363953	363953	type	True	77.7806	229	1346	95	below_threshold
Chelatococcus sambhunathii	strain=DSM 18167	GCA_001517345.1	363953	363953	type	True	77.7521	231	1346	95	below_threshold
Chelatococcus composti	strain=DSM 101465	GCA_018398355.1	1743235	1743235	type	True	77.6203	216	1346	95	below_threshold
Chelatococcus composti	strain=CGMCC 1.15283	GCA_014641535.1	1743235	1743235	type	True	77.5885	216	1346	95	below_threshold
Chelatococcus composti	strain=DSM 101465	GCA_014201415.1	1743235	1743235	type	True	77.5832	215	1346	95	below_threshold
Camelimonas lactis	strain=DSM 22958	GCA_004342915.1	659006	659006	type	True	77.2067	214	1346	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	76.8536	141	1346	95	below_threshold
Methylobacterium adhaesivum	strain=DSM 17169	GCA_022179065.1	333297	333297	type	True	76.8252	144	1346	95	below_threshold
Bosea thiooxidans	strain=DSM 9653	GCA_900168195.1	53254	53254	type	True	76.7717	186	1346	95	below_threshold
Aurantimonas marina	strain=SW136	GCA_017183135.1	2780508	2780508	type	True	76.7129	102	1346	95	below_threshold
Salinarimonas rosea	strain=DSM 21201	GCA_000429045.1	552063	552063	type	True	76.6445	169	1346	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	76.6193	201	1346	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	76.3814	144	1346	95	below_threshold
Gemmobacter aquarius	strain=HYN0069	GCA_003060865.1	2169400	2169400	type	True	76.0092	58	1346	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_004345735.1	35804	35804	type	True	75.9807	60	1346	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_016583705.1	35804	35804	type	True	75.9629	61	1346	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:18:47,538] [INFO] DFAST Taxonomy check result was written to GCF_014195635.1_ASM1419563v1_genomic.fna/tc_result.tsv
[2024-01-24 15:18:47,539] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:18:47,539] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:18:47,539] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8f0bb2ce-e042-443e-87d8-030970000a90/dqc_reference/checkm_data
[2024-01-24 15:18:47,540] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:18:47,581] [INFO] Task started: CheckM
[2024-01-24 15:18:47,582] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014195635.1_ASM1419563v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014195635.1_ASM1419563v1_genomic.fna/checkm_input GCF_014195635.1_ASM1419563v1_genomic.fna/checkm_result
[2024-01-24 15:19:27,620] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:27,621] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.48%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:27,644] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:27,644] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:27,645] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014195635.1_ASM1419563v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:27,645] [INFO] Task started: Blastn
[2024-01-24 15:19:27,645] [INFO] Running command: blastn -query GCF_014195635.1_ASM1419563v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f0bb2ce-e042-443e-87d8-030970000a90/dqc_reference/reference_markers_gtdb.fasta -out GCF_014195635.1_ASM1419563v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:28,856] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:28,860] [INFO] Selected 12 target genomes.
[2024-01-24 15:19:28,861] [INFO] Target genome list was writen to GCF_014195635.1_ASM1419563v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:28,871] [INFO] Task started: fastANI
[2024-01-24 15:19:28,871] [INFO] Running command: fastANI --query /var/lib/cwl/stg96554ac9-8130-45dc-ab98-d45388482839/GCF_014195635.1_ASM1419563v1_genomic.fna.gz --refList GCF_014195635.1_ASM1419563v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014195635.1_ASM1419563v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:40,918] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:40,934] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:40,934] [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_014195635.1	s__Pseudochelatococcus contaminans	100.0	1345	1346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Pseudochelatococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011762225.1	s__Pseudochelatococcus lubricantis	79.6773	549	1346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Pseudochelatococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196925.1	s__Chelatococcus_A caeni	78.0916	287	1346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Chelatococcus_A	95.0	98.75	98.72	0.96	0.95	3	-
GCF_001418005.1	s__Chelatococcus_A sambhunathii	77.7517	231	1346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Chelatococcus_A	95.0	99.33	99.03	0.97	0.94	5	-
GCF_018398335.1	s__Chelatococcus sp018398335	77.7216	214	1346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Chelatococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201415.1	s__Chelatococcus_A composti	77.5694	216	1346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Chelatococcus_A	95.0	99.84	99.53	0.99	0.98	4	-
GCF_004342915.1	s__Camelimonas lactis	77.1953	215	1346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Camelimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018823835.1	s__RCIZ01 sp018823835	76.8328	122	1346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__RCIZ01	95.0	99.96	99.89	0.99	0.96	11	-
GCF_900168195.1	s__Bosea thiooxidans	76.7844	185	1346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	99.77	99.77	0.94	0.94	2	-
GCA_901457705.2	s__RH-AL1 sp901457705	76.6663	131	1346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__RH-AL1	95.0	99.94	99.94	0.99	0.99	3	-
GCF_000472925.1	s__Bradyrhizobium sp000472925	76.3227	163	1346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345735.1	s__Rhodovulum adriaticum	75.9807	60	1346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:19:40,935] [INFO] GTDB search result was written to GCF_014195635.1_ASM1419563v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:40,936] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:40,940] [INFO] DFAST_QC result json was written to GCF_014195635.1_ASM1419563v1_genomic.fna/dqc_result.json
[2024-01-24 15:19:40,940] [INFO] DFAST_QC completed!
[2024-01-24 15:19:40,940] [INFO] Total running time: 0h1m23s