[2024-01-24 12:31:03,239] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:03,240] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:03,241] [INFO] DQC Reference Directory: /var/lib/cwl/stg224dcc46-a1f7-40ec-bd36-4e19b254715a/dqc_reference
[2024-01-24 12:31:04,526] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:04,527] [INFO] Task started: Prodigal
[2024-01-24 12:31:04,527] [INFO] Running command: gunzip -c /var/lib/cwl/stg029b8335-9183-4dc5-ab6b-d9facdaabb9e/GCF_009649175.1_ASM964917v1_genomic.fna.gz | prodigal -d GCF_009649175.1_ASM964917v1_genomic.fna/cds.fna -a GCF_009649175.1_ASM964917v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:14,257] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:14,257] [INFO] Task started: HMMsearch
[2024-01-24 12:31:14,257] [INFO] Running command: hmmsearch --tblout GCF_009649175.1_ASM964917v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg224dcc46-a1f7-40ec-bd36-4e19b254715a/dqc_reference/reference_markers.hmm GCF_009649175.1_ASM964917v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:14,469] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:14,470] [INFO] Found 6/6 markers.
[2024-01-24 12:31:14,498] [INFO] Query marker FASTA was written to GCF_009649175.1_ASM964917v1_genomic.fna/markers.fasta
[2024-01-24 12:31:14,498] [INFO] Task started: Blastn
[2024-01-24 12:31:14,498] [INFO] Running command: blastn -query GCF_009649175.1_ASM964917v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg224dcc46-a1f7-40ec-bd36-4e19b254715a/dqc_reference/reference_markers.fasta -out GCF_009649175.1_ASM964917v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:15,479] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:15,481] [INFO] Selected 13 target genomes.
[2024-01-24 12:31:15,481] [INFO] Target genome list was writen to GCF_009649175.1_ASM964917v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:15,485] [INFO] Task started: fastANI
[2024-01-24 12:31:15,485] [INFO] Running command: fastANI --query /var/lib/cwl/stg029b8335-9183-4dc5-ab6b-d9facdaabb9e/GCF_009649175.1_ASM964917v1_genomic.fna.gz --refList GCF_009649175.1_ASM964917v1_genomic.fna/target_genomes.txt --output GCF_009649175.1_ASM964917v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:26,135] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:26,136] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg224dcc46-a1f7-40ec-bd36-4e19b254715a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:26,136] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg224dcc46-a1f7-40ec-bd36-4e19b254715a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:26,144] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:31:26,144] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:26,145] [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 strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	100.0	1220	1227	95	conclusive
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	91.2019	925	1227	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	90.2192	916	1227	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	85.1046	863	1227	95	below_threshold
Rhodovulum marinum	strain=DSM 18063	GCA_004343075.1	320662	320662	type	True	83.9503	812	1227	95	below_threshold
Rhodovulum visakhapatnamense	strain=JA181	GCA_004365965.1	364297	364297	type	True	82.0844	778	1227	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_004345735.1	35804	35804	type	True	81.6423	654	1227	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_016583705.1	35804	35804	type	True	81.636	642	1227	95	below_threshold
Rhodovulum bhavnagarense	strain=DSM 24766	GCA_004343505.1	992286	992286	type	True	81.3116	593	1227	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	79.44	533	1227	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	79.1734	519	1227	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	78.9598	433	1227	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.605	482	1227	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:26,146] [INFO] DFAST Taxonomy check result was written to GCF_009649175.1_ASM964917v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:26,146] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:26,147] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:26,147] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg224dcc46-a1f7-40ec-bd36-4e19b254715a/dqc_reference/checkm_data
[2024-01-24 12:31:26,147] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:26,187] [INFO] Task started: CheckM
[2024-01-24 12:31:26,187] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009649175.1_ASM964917v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009649175.1_ASM964917v1_genomic.fna/checkm_input GCF_009649175.1_ASM964917v1_genomic.fna/checkm_result
[2024-01-24 12:32:02,047] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:02,048] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:02,063] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:02,063] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:02,064] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009649175.1_ASM964917v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:02,064] [INFO] Task started: Blastn
[2024-01-24 12:32:02,064] [INFO] Running command: blastn -query GCF_009649175.1_ASM964917v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg224dcc46-a1f7-40ec-bd36-4e19b254715a/dqc_reference/reference_markers_gtdb.fasta -out GCF_009649175.1_ASM964917v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:04,014] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:04,018] [INFO] Selected 10 target genomes.
[2024-01-24 12:32:04,018] [INFO] Target genome list was writen to GCF_009649175.1_ASM964917v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:04,022] [INFO] Task started: fastANI
[2024-01-24 12:32:04,023] [INFO] Running command: fastANI --query /var/lib/cwl/stg029b8335-9183-4dc5-ab6b-d9facdaabb9e/GCF_009649175.1_ASM964917v1_genomic.fna.gz --refList GCF_009649175.1_ASM964917v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009649175.1_ASM964917v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:12,886] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:12,893] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:12,893] [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_009649175.1	s__Rhodovulum strictum	100.0	1220	1227	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	91.202	925	1227	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	89.0457	635	1227	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	85.0993	865	1227	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	83.9655	811	1227	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	82.5104	761	1227	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	82.2115	738	1227	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	98.27	98.27	0.96	0.96	2	-
GCF_004365965.1	s__Rhodovulum visakhapatnamense	82.0457	782	1227	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	98.55	98.44	0.90	0.89	5	-
GCA_016938875.1	s__Rhodovulum sp016938875	81.6999	641	1227	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345735.1	s__Rhodovulum adriaticum	81.6609	652	1227	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 12:32:12,895] [INFO] GTDB search result was written to GCF_009649175.1_ASM964917v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:12,899] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:12,904] [INFO] DFAST_QC result json was written to GCF_009649175.1_ASM964917v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:12,904] [INFO] DFAST_QC completed!
[2024-01-24 12:32:12,904] [INFO] Total running time: 0h1m10s