[2024-01-25 20:20:50,871] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:20:50,878] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:20:50,878] [INFO] DQC Reference Directory: /var/lib/cwl/stg2e60e3e7-4be7-4639-9d26-fc4916de3e8a/dqc_reference
[2024-01-25 20:20:52,037] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:20:52,037] [INFO] Task started: Prodigal
[2024-01-25 20:20:52,038] [INFO] Running command: gunzip -c /var/lib/cwl/stg624ff236-9af8-43af-a4fb-6112c1d836b3/GCF_002894645.1_ASM289464v1_genomic.fna.gz | prodigal -d GCF_002894645.1_ASM289464v1_genomic.fna/cds.fna -a GCF_002894645.1_ASM289464v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:21:10,476] [INFO] Task succeeded: Prodigal
[2024-01-25 20:21:10,476] [INFO] Task started: HMMsearch
[2024-01-25 20:21:10,476] [INFO] Running command: hmmsearch --tblout GCF_002894645.1_ASM289464v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2e60e3e7-4be7-4639-9d26-fc4916de3e8a/dqc_reference/reference_markers.hmm GCF_002894645.1_ASM289464v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:21:10,698] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:21:10,699] [INFO] Found 6/6 markers.
[2024-01-25 20:21:10,725] [INFO] Query marker FASTA was written to GCF_002894645.1_ASM289464v1_genomic.fna/markers.fasta
[2024-01-25 20:21:10,725] [INFO] Task started: Blastn
[2024-01-25 20:21:10,725] [INFO] Running command: blastn -query GCF_002894645.1_ASM289464v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e60e3e7-4be7-4639-9d26-fc4916de3e8a/dqc_reference/reference_markers.fasta -out GCF_002894645.1_ASM289464v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:21:11,279] [INFO] Task succeeded: Blastn
[2024-01-25 20:21:11,281] [INFO] Selected 21 target genomes.
[2024-01-25 20:21:11,282] [INFO] Target genome list was writen to GCF_002894645.1_ASM289464v1_genomic.fna/target_genomes.txt
[2024-01-25 20:21:11,303] [INFO] Task started: fastANI
[2024-01-25 20:21:11,303] [INFO] Running command: fastANI --query /var/lib/cwl/stg624ff236-9af8-43af-a4fb-6112c1d836b3/GCF_002894645.1_ASM289464v1_genomic.fna.gz --refList GCF_002894645.1_ASM289464v1_genomic.fna/target_genomes.txt --output GCF_002894645.1_ASM289464v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:21:25,251] [INFO] Task succeeded: fastANI
[2024-01-25 20:21:25,252] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2e60e3e7-4be7-4639-9d26-fc4916de3e8a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:21:25,252] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2e60e3e7-4be7-4639-9d26-fc4916de3e8a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:21:25,258] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:21:25,258] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:21:25,258] [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 altiplanensis	strain=AN15	GCA_002894645.1	1803181	1803181	type	True	100.0	1179	1180	95	conclusive
Salinibacter ruber	strain=DSM 13855; M31	GCA_000013045.1	146919	146919	type	True	85.0634	891	1180	95	below_threshold
Rhodocaloribacter litoris	strain=ISCAR-4553	GCA_011682235.2	2558931	2558931	type	True	76.618	101	1180	95	below_threshold
Longibacter salinarum	strain=KCTC 52045	GCA_002554795.1	1850348	1850348	type	True	76.6086	86	1180	95	below_threshold
Salisaeta longa	strain=DSM 21114	GCA_000419585.1	503170	503170	type	True	76.5313	124	1180	95	below_threshold
Longimonas halophila	strain=KCTC 42399	GCA_002554705.1	1469170	1469170	type	True	76.5236	96	1180	95	below_threshold
Rubrivirga marina	strain=SAORIC-28	GCA_002283365.1	1196024	1196024	type	True	75.7032	94	1180	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:21:25,259] [INFO] DFAST Taxonomy check result was written to GCF_002894645.1_ASM289464v1_genomic.fna/tc_result.tsv
[2024-01-25 20:21:25,260] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:21:25,260] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:21:25,260] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2e60e3e7-4be7-4639-9d26-fc4916de3e8a/dqc_reference/checkm_data
[2024-01-25 20:21:25,261] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:21:25,297] [INFO] Task started: CheckM
[2024-01-25 20:21:25,298] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002894645.1_ASM289464v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002894645.1_ASM289464v1_genomic.fna/checkm_input GCF_002894645.1_ASM289464v1_genomic.fna/checkm_result
[2024-01-25 20:22:14,635] [INFO] Task succeeded: CheckM
[2024-01-25 20:22:14,636] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:22:14,657] [INFO] ===== Completeness check finished =====
[2024-01-25 20:22:14,657] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:22:14,658] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002894645.1_ASM289464v1_genomic.fna/markers.fasta)
[2024-01-25 20:22:14,658] [INFO] Task started: Blastn
[2024-01-25 20:22:14,658] [INFO] Running command: blastn -query GCF_002894645.1_ASM289464v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e60e3e7-4be7-4639-9d26-fc4916de3e8a/dqc_reference/reference_markers_gtdb.fasta -out GCF_002894645.1_ASM289464v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:22:15,586] [INFO] Task succeeded: Blastn
[2024-01-25 20:22:15,589] [INFO] Selected 11 target genomes.
[2024-01-25 20:22:15,589] [INFO] Target genome list was writen to GCF_002894645.1_ASM289464v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:22:15,600] [INFO] Task started: fastANI
[2024-01-25 20:22:15,600] [INFO] Running command: fastANI --query /var/lib/cwl/stg624ff236-9af8-43af-a4fb-6112c1d836b3/GCF_002894645.1_ASM289464v1_genomic.fna.gz --refList GCF_002894645.1_ASM289464v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002894645.1_ASM289464v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:22:21,804] [INFO] Task succeeded: fastANI
[2024-01-25 20:22:21,812] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:22:21,812] [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_002894645.1	s__Salinibacter altiplanensis	100.0	1179	1180	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__Salinibacter	95.0	98.33	98.12	0.91	0.90	3	conclusive
GCF_000013045.1	s__Salinibacter ruber	85.0634	891	1180	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__Salinibacter	95.0	98.51	97.79	0.92	0.85	14	-
GCA_003022565.1	s__Salinibacter sp003022565	80.1868	452	1180	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	79.9038	235	1180	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	79.7404	312	1180	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	79.038	425	1180	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	78.8744	205	1180	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__Salinibacter	95.0	95.78	95.78	0.67	0.67	2	-
GCF_002894665.1	s__Salinibacter iranicus	78.7998	416	1180	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__Salinibacter	96.2585	N/A	N/A	N/A	N/A	1	-
GCA_003022435.1	s__Salinibacter sp003022435	78.2867	285	1180	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	78.1427	171	1180	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__Salinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002283555.1	s__Rubrivirga sp002283555	75.8683	91	1180	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubrivirga	95.0	98.32	98.29	0.93	0.92	3	-
--------------------------------------------------------------------------------
[2024-01-25 20:22:21,813] [INFO] GTDB search result was written to GCF_002894645.1_ASM289464v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:22:21,814] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:22:21,816] [INFO] DFAST_QC result json was written to GCF_002894645.1_ASM289464v1_genomic.fna/dqc_result.json
[2024-01-25 20:22:21,816] [INFO] DFAST_QC completed!
[2024-01-25 20:22:21,817] [INFO] Total running time: 0h1m31s