[2024-01-24 13:18:26,488] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:26,491] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:26,491] [INFO] DQC Reference Directory: /var/lib/cwl/stg1e351d82-7bd9-41b0-8edb-7192b628ddfc/dqc_reference
[2024-01-24 13:18:27,668] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:27,669] [INFO] Task started: Prodigal
[2024-01-24 13:18:27,669] [INFO] Running command: gunzip -c /var/lib/cwl/stg663c8f93-08b3-4a75-9797-c10d3c6518ca/GCF_000337775.1_ASM33777v1_genomic.fna.gz | prodigal -d GCF_000337775.1_ASM33777v1_genomic.fna/cds.fna -a GCF_000337775.1_ASM33777v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:47,433] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:47,433] [INFO] Task started: HMMsearch
[2024-01-24 13:18:47,434] [INFO] Running command: hmmsearch --tblout GCF_000337775.1_ASM33777v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1e351d82-7bd9-41b0-8edb-7192b628ddfc/dqc_reference/reference_markers.hmm GCF_000337775.1_ASM33777v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:47,735] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:47,736] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg663c8f93-08b3-4a75-9797-c10d3c6518ca/GCF_000337775.1_ASM33777v1_genomic.fna.gz]
[2024-01-24 13:18:47,771] [INFO] Query marker FASTA was written to GCF_000337775.1_ASM33777v1_genomic.fna/markers.fasta
[2024-01-24 13:18:47,772] [INFO] Task started: Blastn
[2024-01-24 13:18:47,772] [INFO] Running command: blastn -query GCF_000337775.1_ASM33777v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e351d82-7bd9-41b0-8edb-7192b628ddfc/dqc_reference/reference_markers.fasta -out GCF_000337775.1_ASM33777v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:48,321] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:48,325] [INFO] Selected 9 target genomes.
[2024-01-24 13:18:48,325] [INFO] Target genome list was writen to GCF_000337775.1_ASM33777v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:48,333] [INFO] Task started: fastANI
[2024-01-24 13:18:48,333] [INFO] Running command: fastANI --query /var/lib/cwl/stg663c8f93-08b3-4a75-9797-c10d3c6518ca/GCF_000337775.1_ASM33777v1_genomic.fna.gz --refList GCF_000337775.1_ASM33777v1_genomic.fna/target_genomes.txt --output GCF_000337775.1_ASM33777v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:57,202] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:57,203] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1e351d82-7bd9-41b0-8edb-7192b628ddfc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:57,203] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1e351d82-7bd9-41b0-8edb-7192b628ddfc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:57,215] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:18:57,216] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:57,216] [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
Haloarcula vallismortis	strain=ATCC 29715	GCA_000337775.1	28442	28442	type	True	100.0	1277	1279	95	conclusive
Haloarcula vallismortis	strain=DSM 3756	GCA_900106715.1	28442	28442	type	True	99.9949	1265	1279	95	conclusive
Haloarcula rubripromontorii	strain=SL3	GCA_001280425.1	1705562	1705562	type	True	90.0323	1073	1279	95	below_threshold
Haloarcula hispanica	strain=CGMCC 1.2049	GCA_000223905.1	51589	51589	type	True	89.3184	1046	1279	95	below_threshold
Haloarcula amylolytica	strain=JCM 13557	GCA_000336615.1	396317	396317	type	True	89.2905	1055	1279	95	below_threshold
Haloarcula salaria	strain=JCM 15759	GCA_014647095.1	575195	575195	type	True	88.9495	965	1279	95	below_threshold
Haloarcula marismortui	strain=ATCC 43049	GCA_000011085.1	2238	2238	suspected-type	True	88.5936	1083	1279	95	below_threshold
Haloarcula marismortui	strain=ATCC 43049	GCA_005310945.1	2238	2238	suspected-type	True	88.5766	1102	1279	95	below_threshold
Haloarcula japonica	strain=DSM 6131	GCA_000336635.1	29282	29282	type	True	88.518	1021	1279	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:57,218] [INFO] DFAST Taxonomy check result was written to GCF_000337775.1_ASM33777v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:57,219] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:57,219] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:57,220] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1e351d82-7bd9-41b0-8edb-7192b628ddfc/dqc_reference/checkm_data
[2024-01-24 13:18:57,221] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:57,259] [INFO] Task started: CheckM
[2024-01-24 13:18:57,260] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000337775.1_ASM33777v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000337775.1_ASM33777v1_genomic.fna/checkm_input GCF_000337775.1_ASM33777v1_genomic.fna/checkm_result
[2024-01-24 13:19:55,070] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:55,072] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:55,094] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:55,095] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:55,095] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000337775.1_ASM33777v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:55,095] [INFO] Task started: Blastn
[2024-01-24 13:19:55,096] [INFO] Running command: blastn -query GCF_000337775.1_ASM33777v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e351d82-7bd9-41b0-8edb-7192b628ddfc/dqc_reference/reference_markers_gtdb.fasta -out GCF_000337775.1_ASM33777v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:55,636] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:55,639] [INFO] Selected 9 target genomes.
[2024-01-24 13:19:55,639] [INFO] Target genome list was writen to GCF_000337775.1_ASM33777v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:55,651] [INFO] Task started: fastANI
[2024-01-24 13:19:55,651] [INFO] Running command: fastANI --query /var/lib/cwl/stg663c8f93-08b3-4a75-9797-c10d3c6518ca/GCF_000337775.1_ASM33777v1_genomic.fna.gz --refList GCF_000337775.1_ASM33777v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000337775.1_ASM33777v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:04,507] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:04,516] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:04,516] [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_000337775.1	s__Haloarcula vallismortis	100.0	1277	1279	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_001280425.1	s__Haloarcula rubripromontorii	90.0216	1074	1279	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.0	99.01	99.01	0.90	0.90	2	-
GCF_002844335.1	s__Haloarcula taiwanensis	89.3663	1057	1279	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.0	99.00	98.44	0.94	0.92	4	-
GCF_000223905.1	s__Haloarcula hispanica	89.3287	1045	1279	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.3005	98.55	97.98	0.94	0.91	11	-
GCF_008729015.1	s__Haloarcula sp008729015	89.3001	1061	1279	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.0	99.99	99.99	0.99	0.99	2	-
GCA_000336895.1	s__Haloarcula argentinensis	88.7257	1060	1279	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.2413	99.05	99.05	0.91	0.91	2	-
GCF_001485575.1	s__Haloarcula sp001485575	88.6547	1061	1279	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000011085.1	s__Haloarcula marismortui	88.5936	1083	1279	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.0	98.41	98.12	0.88	0.85	9	-
GCF_000336635.1	s__Haloarcula japonica	88.518	1021	1279	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:04,518] [INFO] GTDB search result was written to GCF_000337775.1_ASM33777v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:04,518] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:04,521] [INFO] DFAST_QC result json was written to GCF_000337775.1_ASM33777v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:04,521] [INFO] DFAST_QC completed!
[2024-01-24 13:20:04,521] [INFO] Total running time: 0h1m38s