[2024-01-24 11:02:49,199] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:02:49,201] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:02:49,201] [INFO] DQC Reference Directory: /var/lib/cwl/stg63f70b95-3fd6-43e3-a743-d92703b7384e/dqc_reference
[2024-01-24 11:02:50,407] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:02:50,408] [INFO] Task started: Prodigal
[2024-01-24 11:02:50,408] [INFO] Running command: gunzip -c /var/lib/cwl/stgc10aa7cc-2475-44a6-918d-f5b98d53b302/GCF_016583705.1_ASM1658370v1_genomic.fna.gz | prodigal -d GCF_016583705.1_ASM1658370v1_genomic.fna/cds.fna -a GCF_016583705.1_ASM1658370v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:03:00,236] [INFO] Task succeeded: Prodigal
[2024-01-24 11:03:00,236] [INFO] Task started: HMMsearch
[2024-01-24 11:03:00,237] [INFO] Running command: hmmsearch --tblout GCF_016583705.1_ASM1658370v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg63f70b95-3fd6-43e3-a743-d92703b7384e/dqc_reference/reference_markers.hmm GCF_016583705.1_ASM1658370v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:03:00,508] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:03:00,510] [INFO] Found 6/6 markers.
[2024-01-24 11:03:00,544] [INFO] Query marker FASTA was written to GCF_016583705.1_ASM1658370v1_genomic.fna/markers.fasta
[2024-01-24 11:03:00,544] [INFO] Task started: Blastn
[2024-01-24 11:03:00,544] [INFO] Running command: blastn -query GCF_016583705.1_ASM1658370v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg63f70b95-3fd6-43e3-a743-d92703b7384e/dqc_reference/reference_markers.fasta -out GCF_016583705.1_ASM1658370v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:03:01,488] [INFO] Task succeeded: Blastn
[2024-01-24 11:03:01,492] [INFO] Selected 14 target genomes.
[2024-01-24 11:03:01,493] [INFO] Target genome list was writen to GCF_016583705.1_ASM1658370v1_genomic.fna/target_genomes.txt
[2024-01-24 11:03:01,503] [INFO] Task started: fastANI
[2024-01-24 11:03:01,503] [INFO] Running command: fastANI --query /var/lib/cwl/stgc10aa7cc-2475-44a6-918d-f5b98d53b302/GCF_016583705.1_ASM1658370v1_genomic.fna.gz --refList GCF_016583705.1_ASM1658370v1_genomic.fna/target_genomes.txt --output GCF_016583705.1_ASM1658370v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:03:12,387] [INFO] Task succeeded: fastANI
[2024-01-24 11:03:12,388] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg63f70b95-3fd6-43e3-a743-d92703b7384e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:03:12,389] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg63f70b95-3fd6-43e3-a743-d92703b7384e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:03:12,405] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:03:12,405] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:03:12,405] [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
Rhodovulum adriaticum	strain=DSM 2781	GCA_016583705.1	35804	35804	type	True	100.0	1069	1079	95	conclusive
Rhodovulum adriaticum	strain=DSM 2781	GCA_004345735.1	35804	35804	type	True	99.9859	1063	1079	95	conclusive
Rhodovulum bhavnagarense	strain=DSM 24766	GCA_004343505.1	992286	992286	type	True	83.7754	691	1079	95	below_threshold
Rhodovulum marinum	strain=DSM 18063	GCA_004343075.1	320662	320662	type	True	82.597	720	1079	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	81.7533	684	1079	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	81.6887	633	1079	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	81.6314	647	1079	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	81.5572	654	1079	95	below_threshold
Rhodovulum visakhapatnamense	strain=JA181	GCA_004365965.1	364297	364297	type	True	80.8069	634	1079	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	79.5857	432	1079	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	79.4138	327	1079	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	78.5107	456	1079	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	78.0513	364	1079	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	77.8735	342	1079	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:03:12,407] [INFO] DFAST Taxonomy check result was written to GCF_016583705.1_ASM1658370v1_genomic.fna/tc_result.tsv
[2024-01-24 11:03:12,407] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:03:12,407] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:03:12,408] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg63f70b95-3fd6-43e3-a743-d92703b7384e/dqc_reference/checkm_data
[2024-01-24 11:03:12,408] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:03:12,442] [INFO] Task started: CheckM
[2024-01-24 11:03:12,442] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016583705.1_ASM1658370v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016583705.1_ASM1658370v1_genomic.fna/checkm_input GCF_016583705.1_ASM1658370v1_genomic.fna/checkm_result
[2024-01-24 11:03:45,503] [INFO] Task succeeded: CheckM
[2024-01-24 11:03:45,504] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.56%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:03:45,538] [INFO] ===== Completeness check finished =====
[2024-01-24 11:03:45,538] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:03:45,539] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016583705.1_ASM1658370v1_genomic.fna/markers.fasta)
[2024-01-24 11:03:45,539] [INFO] Task started: Blastn
[2024-01-24 11:03:45,540] [INFO] Running command: blastn -query GCF_016583705.1_ASM1658370v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg63f70b95-3fd6-43e3-a743-d92703b7384e/dqc_reference/reference_markers_gtdb.fasta -out GCF_016583705.1_ASM1658370v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:03:47,171] [INFO] Task succeeded: Blastn
[2024-01-24 11:03:47,174] [INFO] Selected 11 target genomes.
[2024-01-24 11:03:47,174] [INFO] Target genome list was writen to GCF_016583705.1_ASM1658370v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:03:47,186] [INFO] Task started: fastANI
[2024-01-24 11:03:47,187] [INFO] Running command: fastANI --query /var/lib/cwl/stgc10aa7cc-2475-44a6-918d-f5b98d53b302/GCF_016583705.1_ASM1658370v1_genomic.fna.gz --refList GCF_016583705.1_ASM1658370v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016583705.1_ASM1658370v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:03:55,573] [INFO] Task succeeded: fastANI
[2024-01-24 11:03:55,585] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:03:55,585] [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_004345735.1	s__Rhodovulum adriaticum	99.9859	1063	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_004343505.1	s__Rhodovulum bhavnagarense	83.7689	693	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004343075.1	s__Rhodovulum marinum	82.575	723	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016938875.1	s__Rhodovulum sp016938875	82.3713	643	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342445.1	s__Rhodovulum euryhalinum	81.7383	685	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009649175.1	s__Rhodovulum strictum	81.697	631	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339675.1	s__Rhodovulum steppense	81.5936	652	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011048875.1	s__Rhodovulum sp011048875	81.3049	481	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142935.1	s__Rhodovulum sp900142935	81.2956	650	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139985.1	s__JAGSOU01 sp018139985	80.3482	575	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010614805.1	s__Pseudooceanicola sp010614805	79.5979	431	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:03:55,587] [INFO] GTDB search result was written to GCF_016583705.1_ASM1658370v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:03:55,588] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:03:55,591] [INFO] DFAST_QC result json was written to GCF_016583705.1_ASM1658370v1_genomic.fna/dqc_result.json
[2024-01-24 11:03:55,592] [INFO] DFAST_QC completed!
[2024-01-24 11:03:55,592] [INFO] Total running time: 0h1m6s