[2024-01-24 13:40:55,673] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:55,675] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:55,675] [INFO] DQC Reference Directory: /var/lib/cwl/stg83695ffa-f827-4612-9939-b24905a0c7ff/dqc_reference
[2024-01-24 13:40:56,938] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:56,939] [INFO] Task started: Prodigal
[2024-01-24 13:40:56,939] [INFO] Running command: gunzip -c /var/lib/cwl/stg4542ae26-ad4a-4822-88e4-43a99eabdf9b/GCF_004365965.1_ASM436596v1_genomic.fna.gz | prodigal -d GCF_004365965.1_ASM436596v1_genomic.fna/cds.fna -a GCF_004365965.1_ASM436596v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:07,814] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:07,815] [INFO] Task started: HMMsearch
[2024-01-24 13:41:07,815] [INFO] Running command: hmmsearch --tblout GCF_004365965.1_ASM436596v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg83695ffa-f827-4612-9939-b24905a0c7ff/dqc_reference/reference_markers.hmm GCF_004365965.1_ASM436596v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:08,173] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:08,174] [INFO] Found 6/6 markers.
[2024-01-24 13:41:08,212] [INFO] Query marker FASTA was written to GCF_004365965.1_ASM436596v1_genomic.fna/markers.fasta
[2024-01-24 13:41:08,212] [INFO] Task started: Blastn
[2024-01-24 13:41:08,212] [INFO] Running command: blastn -query GCF_004365965.1_ASM436596v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg83695ffa-f827-4612-9939-b24905a0c7ff/dqc_reference/reference_markers.fasta -out GCF_004365965.1_ASM436596v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:09,210] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:09,213] [INFO] Selected 15 target genomes.
[2024-01-24 13:41:09,213] [INFO] Target genome list was writen to GCF_004365965.1_ASM436596v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:09,217] [INFO] Task started: fastANI
[2024-01-24 13:41:09,217] [INFO] Running command: fastANI --query /var/lib/cwl/stg4542ae26-ad4a-4822-88e4-43a99eabdf9b/GCF_004365965.1_ASM436596v1_genomic.fna.gz --refList GCF_004365965.1_ASM436596v1_genomic.fna/target_genomes.txt --output GCF_004365965.1_ASM436596v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:22,961] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:22,962] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg83695ffa-f827-4612-9939-b24905a0c7ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:22,962] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg83695ffa-f827-4612-9939-b24905a0c7ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:22,972] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:22,972] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:22,972] [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 visakhapatnamense	strain=JA181	GCA_004365965.1	364297	364297	type	True	100.0	1432	1436	95	conclusive
Rhodovulum sulfidophilum	strain=DSM 1374	GCA_001633165.1	35806	35806	type	True	88.7097	1015	1436	95	below_threshold
Rhodovulum sulfidophilum	strain=DSM 1374	GCA_000520135.2	35806	35806	type	True	88.6838	1023	1436	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	82.1777	759	1436	95	below_threshold
Rhodovulum marinum	strain=DSM 18063	GCA_004343075.1	320662	320662	type	True	82.157	799	1436	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	82.1307	756	1436	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	82.0901	769	1436	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	82.0401	823	1436	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_016583705.1	35804	35804	type	True	80.8097	646	1436	95	below_threshold
Cereibacter johrii	strain=JA192	GCA_001720585.1	445629	445629	type	True	79.2458	530	1436	95	below_threshold
Cereibacter johrii	strain=JA192	GCA_003046325.1	445629	445629	type	True	79.0423	579	1436	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	78.774	434	1436	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	78.4975	474	1436	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	77.8752	417	1436	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.8724	405	1436	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:22,973] [INFO] DFAST Taxonomy check result was written to GCF_004365965.1_ASM436596v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:22,974] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:22,974] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:22,974] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg83695ffa-f827-4612-9939-b24905a0c7ff/dqc_reference/checkm_data
[2024-01-24 13:41:22,975] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:23,019] [INFO] Task started: CheckM
[2024-01-24 13:41:23,019] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004365965.1_ASM436596v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004365965.1_ASM436596v1_genomic.fna/checkm_input GCF_004365965.1_ASM436596v1_genomic.fna/checkm_result
[2024-01-24 13:42:01,331] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:01,332] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:01,346] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:01,346] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:01,346] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004365965.1_ASM436596v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:01,346] [INFO] Task started: Blastn
[2024-01-24 13:42:01,346] [INFO] Running command: blastn -query GCF_004365965.1_ASM436596v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg83695ffa-f827-4612-9939-b24905a0c7ff/dqc_reference/reference_markers_gtdb.fasta -out GCF_004365965.1_ASM436596v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:03,283] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:03,286] [INFO] Selected 9 target genomes.
[2024-01-24 13:42:03,286] [INFO] Target genome list was writen to GCF_004365965.1_ASM436596v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:03,291] [INFO] Task started: fastANI
[2024-01-24 13:42:03,291] [INFO] Running command: fastANI --query /var/lib/cwl/stg4542ae26-ad4a-4822-88e4-43a99eabdf9b/GCF_004365965.1_ASM436596v1_genomic.fna.gz --refList GCF_004365965.1_ASM436596v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004365965.1_ASM436596v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:12,245] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:12,251] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:12,251] [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_004365965.1	s__Rhodovulum visakhapatnamense	100.0	1432	1436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	98.55	98.44	0.90	0.89	5	conclusive
GCF_003053725.1	s__Rhodovulum kholense	94.4773	1241	1436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	98.27	98.27	0.96	0.96	2	-
GCF_001633165.1	s__Rhodovulum sulfidophilum	88.7348	1011	1436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	97.78	97.16	0.92	0.88	14	-
GCF_002073975.1	s__Rhodovulum sp002073975	88.1628	1015	1436	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	82.1623	797	1436	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	82.1338	765	1436	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	82.0929	760	1436	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	82.0395	823	1436	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	81.4688	752	1436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:12,253] [INFO] GTDB search result was written to GCF_004365965.1_ASM436596v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:12,253] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:12,256] [INFO] DFAST_QC result json was written to GCF_004365965.1_ASM436596v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:12,256] [INFO] DFAST_QC completed!
[2024-01-24 13:42:12,256] [INFO] Total running time: 0h1m17s