[2024-01-24 12:21:57,461] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:57,463] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:57,463] [INFO] DQC Reference Directory: /var/lib/cwl/stgcacb0cdd-78cc-4cba-ba75-842fd9201806/dqc_reference
[2024-01-24 12:21:58,928] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:58,929] [INFO] Task started: Prodigal
[2024-01-24 12:21:58,929] [INFO] Running command: gunzip -c /var/lib/cwl/stg58c35028-09f9-4cda-9688-6064773ee38b/GCF_004342445.1_ASM434244v1_genomic.fna.gz | prodigal -d GCF_004342445.1_ASM434244v1_genomic.fna/cds.fna -a GCF_004342445.1_ASM434244v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:10,467] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:10,467] [INFO] Task started: HMMsearch
[2024-01-24 12:22:10,467] [INFO] Running command: hmmsearch --tblout GCF_004342445.1_ASM434244v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcacb0cdd-78cc-4cba-ba75-842fd9201806/dqc_reference/reference_markers.hmm GCF_004342445.1_ASM434244v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:10,792] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:10,794] [INFO] Found 6/6 markers.
[2024-01-24 12:22:10,829] [INFO] Query marker FASTA was written to GCF_004342445.1_ASM434244v1_genomic.fna/markers.fasta
[2024-01-24 12:22:10,830] [INFO] Task started: Blastn
[2024-01-24 12:22:10,830] [INFO] Running command: blastn -query GCF_004342445.1_ASM434244v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcacb0cdd-78cc-4cba-ba75-842fd9201806/dqc_reference/reference_markers.fasta -out GCF_004342445.1_ASM434244v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:12,008] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:12,012] [INFO] Selected 11 target genomes.
[2024-01-24 12:22:12,012] [INFO] Target genome list was writen to GCF_004342445.1_ASM434244v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:12,016] [INFO] Task started: fastANI
[2024-01-24 12:22:12,017] [INFO] Running command: fastANI --query /var/lib/cwl/stg58c35028-09f9-4cda-9688-6064773ee38b/GCF_004342445.1_ASM434244v1_genomic.fna.gz --refList GCF_004342445.1_ASM434244v1_genomic.fna/target_genomes.txt --output GCF_004342445.1_ASM434244v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:21,356] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:21,357] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcacb0cdd-78cc-4cba-ba75-842fd9201806/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:21,357] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcacb0cdd-78cc-4cba-ba75-842fd9201806/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:21,368] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:22:21,368] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:21,368] [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 euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	100.0	1236	1238	95	conclusive
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	85.9496	869	1238	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	85.7011	886	1238	95	below_threshold
Rhodovulum marinum	strain=DSM 18063	GCA_004343075.1	320662	320662	type	True	85.4973	903	1238	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	85.0988	864	1238	95	below_threshold
Rhodovulum visakhapatnamense	strain=JA181	GCA_004365965.1	364297	364297	type	True	82.0996	793	1238	95	below_threshold
Rhodovulum sulfidophilum	strain=DSM 1374	GCA_001633165.1	35806	35806	type	True	81.7622	740	1238	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.6337	475	1238	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	78.0448	413	1238	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	77.926	395	1238	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.7376	385	1238	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:21,375] [INFO] DFAST Taxonomy check result was written to GCF_004342445.1_ASM434244v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:21,377] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:21,378] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:21,378] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcacb0cdd-78cc-4cba-ba75-842fd9201806/dqc_reference/checkm_data
[2024-01-24 12:22:21,379] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:21,417] [INFO] Task started: CheckM
[2024-01-24 12:22:21,417] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004342445.1_ASM434244v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004342445.1_ASM434244v1_genomic.fna/checkm_input GCF_004342445.1_ASM434244v1_genomic.fna/checkm_result
[2024-01-24 12:23:00,685] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:00,686] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:00,708] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:00,708] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:00,709] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004342445.1_ASM434244v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:00,709] [INFO] Task started: Blastn
[2024-01-24 12:23:00,709] [INFO] Running command: blastn -query GCF_004342445.1_ASM434244v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcacb0cdd-78cc-4cba-ba75-842fd9201806/dqc_reference/reference_markers_gtdb.fasta -out GCF_004342445.1_ASM434244v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:03,007] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:03,010] [INFO] Selected 9 target genomes.
[2024-01-24 12:23:03,010] [INFO] Target genome list was writen to GCF_004342445.1_ASM434244v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:03,017] [INFO] Task started: fastANI
[2024-01-24 12:23:03,017] [INFO] Running command: fastANI --query /var/lib/cwl/stg58c35028-09f9-4cda-9688-6064773ee38b/GCF_004342445.1_ASM434244v1_genomic.fna.gz --refList GCF_004342445.1_ASM434244v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004342445.1_ASM434244v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:10,753] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:10,762] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:10,762] [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_004342445.1	s__Rhodovulum euryhalinum	100.0	1236	1238	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004339675.1	s__Rhodovulum steppense	85.9378	869	1238	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	85.4943	903	1238	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	85.3658	601	1238	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	85.0864	865	1238	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	83.5255	857	1238	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003053725.1	s__Rhodovulum kholense	82.1294	792	1238	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	98.27	98.27	0.96	0.96	2	-
GCF_004343505.1	s__Rhodovulum bhavnagarense	81.2976	601	1238	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	80.6406	645	1238	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:10,764] [INFO] GTDB search result was written to GCF_004342445.1_ASM434244v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:10,764] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:10,768] [INFO] DFAST_QC result json was written to GCF_004342445.1_ASM434244v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:10,768] [INFO] DFAST_QC completed!
[2024-01-24 12:23:10,768] [INFO] Total running time: 0h1m13s