[2024-01-24 14:12:45,415] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:12:45,425] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:12:45,425] [INFO] DQC Reference Directory: /var/lib/cwl/stge1e7496e-4481-44f0-a3ff-31e5f59b04fc/dqc_reference
[2024-01-24 14:12:46,715] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:12:46,716] [INFO] Task started: Prodigal
[2024-01-24 14:12:46,716] [INFO] Running command: gunzip -c /var/lib/cwl/stgcdcc4b77-15bc-44e2-983d-c9689dc7e65f/GCF_947077765.1_Salinibacter_NZ140_genomic.fna.gz | prodigal -d GCF_947077765.1_Salinibacter_NZ140_genomic.fna/cds.fna -a GCF_947077765.1_Salinibacter_NZ140_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:13:09,252] [INFO] Task succeeded: Prodigal
[2024-01-24 14:13:09,253] [INFO] Task started: HMMsearch
[2024-01-24 14:13:09,253] [INFO] Running command: hmmsearch --tblout GCF_947077765.1_Salinibacter_NZ140_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge1e7496e-4481-44f0-a3ff-31e5f59b04fc/dqc_reference/reference_markers.hmm GCF_947077765.1_Salinibacter_NZ140_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:13:09,565] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:13:09,567] [INFO] Found 6/6 markers.
[2024-01-24 14:13:09,600] [INFO] Query marker FASTA was written to GCF_947077765.1_Salinibacter_NZ140_genomic.fna/markers.fasta
[2024-01-24 14:13:09,601] [INFO] Task started: Blastn
[2024-01-24 14:13:09,601] [INFO] Running command: blastn -query GCF_947077765.1_Salinibacter_NZ140_genomic.fna/markers.fasta -db /var/lib/cwl/stge1e7496e-4481-44f0-a3ff-31e5f59b04fc/dqc_reference/reference_markers.fasta -out GCF_947077765.1_Salinibacter_NZ140_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:10,289] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:10,292] [INFO] Selected 24 target genomes.
[2024-01-24 14:13:10,292] [INFO] Target genome list was writen to GCF_947077765.1_Salinibacter_NZ140_genomic.fna/target_genomes.txt
[2024-01-24 14:13:10,347] [INFO] Task started: fastANI
[2024-01-24 14:13:10,347] [INFO] Running command: fastANI --query /var/lib/cwl/stgcdcc4b77-15bc-44e2-983d-c9689dc7e65f/GCF_947077765.1_Salinibacter_NZ140_genomic.fna.gz --refList GCF_947077765.1_Salinibacter_NZ140_genomic.fna/target_genomes.txt --output GCF_947077765.1_Salinibacter_NZ140_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:13:25,920] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:25,921] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge1e7496e-4481-44f0-a3ff-31e5f59b04fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:13:25,921] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge1e7496e-4481-44f0-a3ff-31e5f59b04fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:13:25,938] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:13:25,938] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:13:25,938] [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
Salinibacter ruber	strain=DSM 13855; M31	GCA_000013045.1	146919	146919	type	True	88.1735	990	1250	95	below_threshold
Salinibacter altiplanensis	strain=AN15	GCA_002894645.1	1803181	1803181	type	True	84.1256	888	1250	95	below_threshold
Rhodocaloribacter litoris	strain=ISCAR-4553	GCA_011682235.2	2558931	2558931	type	True	76.5984	116	1250	95	below_threshold
Salisaeta longa	strain=DSM 21114	GCA_000419585.1	503170	503170	type	True	76.4968	137	1250	95	below_threshold
Longibacter salinarum	strain=KCTC 52045	GCA_002554795.1	1850348	1850348	type	True	76.2727	104	1250	95	below_threshold
Longimonas halophila	strain=KCTC 42399	GCA_002554705.1	1469170	1469170	type	True	76.0859	113	1250	95	below_threshold
Rubricoccus marinus	strain=SG-29	GCA_002257665.1	716817	716817	type	True	75.9043	55	1250	95	below_threshold
Rubrivirga marina	strain=SAORIC-28	GCA_002283365.1	1196024	1196024	type	True	75.6094	105	1250	95	below_threshold
Saccharopolyspora erythraea	strain=DSM 40517	GCA_002564065.1	1836	1836	type	True	74.9309	59	1250	95	below_threshold
Saccharopolyspora erythraea	strain=NRRL 2338	GCA_000062885.1	1836	1836	type	True	74.9262	60	1250	95	below_threshold
Saccharopolyspora erythraea	strain=NRRL 2338	GCA_000171635.1	1836	1836	type	True	74.72	55	1250	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:13:25,940] [INFO] DFAST Taxonomy check result was written to GCF_947077765.1_Salinibacter_NZ140_genomic.fna/tc_result.tsv
[2024-01-24 14:13:25,940] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:13:25,940] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:13:25,940] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge1e7496e-4481-44f0-a3ff-31e5f59b04fc/dqc_reference/checkm_data
[2024-01-24 14:13:25,941] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:13:25,978] [INFO] Task started: CheckM
[2024-01-24 14:13:25,978] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_947077765.1_Salinibacter_NZ140_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_947077765.1_Salinibacter_NZ140_genomic.fna/checkm_input GCF_947077765.1_Salinibacter_NZ140_genomic.fna/checkm_result
[2024-01-24 14:14:32,590] [INFO] Task succeeded: CheckM
[2024-01-24 14:14:32,591] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:14:32,701] [INFO] ===== Completeness check finished =====
[2024-01-24 14:14:32,702] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:14:32,702] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_947077765.1_Salinibacter_NZ140_genomic.fna/markers.fasta)
[2024-01-24 14:14:32,702] [INFO] Task started: Blastn
[2024-01-24 14:14:32,702] [INFO] Running command: blastn -query GCF_947077765.1_Salinibacter_NZ140_genomic.fna/markers.fasta -db /var/lib/cwl/stge1e7496e-4481-44f0-a3ff-31e5f59b04fc/dqc_reference/reference_markers_gtdb.fasta -out GCF_947077765.1_Salinibacter_NZ140_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:34,760] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:34,765] [INFO] Selected 14 target genomes.
[2024-01-24 14:14:34,765] [INFO] Target genome list was writen to GCF_947077765.1_Salinibacter_NZ140_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:14:34,801] [INFO] Task started: fastANI
[2024-01-24 14:14:34,801] [INFO] Running command: fastANI --query /var/lib/cwl/stgcdcc4b77-15bc-44e2-983d-c9689dc7e65f/GCF_947077765.1_Salinibacter_NZ140_genomic.fna.gz --refList GCF_947077765.1_Salinibacter_NZ140_genomic.fna/target_genomes_gtdb.txt --output GCF_947077765.1_Salinibacter_NZ140_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:14:42,001] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:42,017] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:14:42,018] [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_000013045.1	s__Salinibacter ruber	88.1784	989	1250	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__Salinibacter	95.0	98.51	97.79	0.92	0.85	14	-
GCF_002894645.1	s__Salinibacter altiplanensis	84.1148	889	1250	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__Salinibacter	95.0	98.33	98.12	0.91	0.90	3	-
GCA_003022565.1	s__Salinibacter sp003022565	80.0852	469	1250	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__Salinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003023105.1	s__Salinibacter sp003023105	79.8907	254	1250	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__Salinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003022655.1	s__Salinibacter sp003022655	79.8127	314	1250	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__Salinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002894685.1	s__Salinibacter luteus	79.1189	440	1250	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__Salinibacter	96.2585	N/A	N/A	N/A	N/A	1	-
GCF_002894665.1	s__Salinibacter iranicus	79.0154	420	1250	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__Salinibacter	96.2585	N/A	N/A	N/A	N/A	1	-
GCA_003023125.1	s__Salinibacter sp003023125	78.8903	213	1250	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__Salinibacter	95.0	95.78	95.78	0.67	0.67	2	-
GCA_003022435.1	s__Salinibacter sp003022435	77.958	295	1250	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__Salinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003023365.1	s__Salinibacter sp003023365	77.6863	201	1250	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__Salinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002554705.1	s__Longimonas halophila	76.0859	113	1250	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__Longimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:14:42,019] [INFO] GTDB search result was written to GCF_947077765.1_Salinibacter_NZ140_genomic.fna/result_gtdb.tsv
[2024-01-24 14:14:42,020] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:14:42,025] [INFO] DFAST_QC result json was written to GCF_947077765.1_Salinibacter_NZ140_genomic.fna/dqc_result.json
[2024-01-24 14:14:42,025] [INFO] DFAST_QC completed!
[2024-01-24 14:14:42,025] [INFO] Total running time: 0h1m57s