[2024-01-24 13:23:11,361] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:23:11,363] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:23:11,363] [INFO] DQC Reference Directory: /var/lib/cwl/stgc92b6c4c-8b2c-4526-bff3-ea7f5a09f48b/dqc_reference
[2024-01-24 13:23:12,668] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:23:12,668] [INFO] Task started: Prodigal
[2024-01-24 13:23:12,669] [INFO] Running command: gunzip -c /var/lib/cwl/stg1b2da008-0e26-4c46-ae91-c8f6651bdb60/GCF_005406125.1_ASM540612v1_genomic.fna.gz | prodigal -d GCF_005406125.1_ASM540612v1_genomic.fna/cds.fna -a GCF_005406125.1_ASM540612v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:23:35,403] [INFO] Task succeeded: Prodigal
[2024-01-24 13:23:35,403] [INFO] Task started: HMMsearch
[2024-01-24 13:23:35,403] [INFO] Running command: hmmsearch --tblout GCF_005406125.1_ASM540612v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc92b6c4c-8b2c-4526-bff3-ea7f5a09f48b/dqc_reference/reference_markers.hmm GCF_005406125.1_ASM540612v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:23:35,660] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:23:35,662] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg1b2da008-0e26-4c46-ae91-c8f6651bdb60/GCF_005406125.1_ASM540612v1_genomic.fna.gz]
[2024-01-24 13:23:35,703] [INFO] Query marker FASTA was written to GCF_005406125.1_ASM540612v1_genomic.fna/markers.fasta
[2024-01-24 13:23:35,704] [INFO] Task started: Blastn
[2024-01-24 13:23:35,704] [INFO] Running command: blastn -query GCF_005406125.1_ASM540612v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc92b6c4c-8b2c-4526-bff3-ea7f5a09f48b/dqc_reference/reference_markers.fasta -out GCF_005406125.1_ASM540612v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:36,227] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:36,230] [INFO] Selected 7 target genomes.
[2024-01-24 13:23:36,231] [INFO] Target genome list was writen to GCF_005406125.1_ASM540612v1_genomic.fna/target_genomes.txt
[2024-01-24 13:23:36,240] [INFO] Task started: fastANI
[2024-01-24 13:23:36,240] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b2da008-0e26-4c46-ae91-c8f6651bdb60/GCF_005406125.1_ASM540612v1_genomic.fna.gz --refList GCF_005406125.1_ASM540612v1_genomic.fna/target_genomes.txt --output GCF_005406125.1_ASM540612v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:23:43,252] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:43,252] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc92b6c4c-8b2c-4526-bff3-ea7f5a09f48b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:23:43,253] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc92b6c4c-8b2c-4526-bff3-ea7f5a09f48b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:23:43,262] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:23:43,263] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:23:43,263] [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 mannanilytica	strain=MD130-1	GCA_005406125.1	2509225	2509225	type	True	100.0	1386	1389	95	conclusive
Haloarcula amylolytica	strain=JCM 13557	GCA_000336615.1	396317	396317	type	True	88.244	949	1389	95	below_threshold
Haloarcula hispanica	strain=CGMCC 1.2049	GCA_000223905.1	51589	51589	type	True	87.988	956	1389	95	below_threshold
Haloarcula japonica	strain=DSM 6131	GCA_000336635.1	29282	29282	type	True	87.6658	1021	1389	95	below_threshold
Haloarcula salaria	strain=JCM 15759	GCA_014647095.1	575195	575195	type	True	87.2786	867	1389	95	below_threshold
Haloarcula vallismortis	strain=DSM 3756	GCA_900106715.1	28442	28442	type	True	87.2112	940	1389	95	below_threshold
Haloarcula rubripromontorii	strain=SL3	GCA_001280425.1	1705562	1705562	type	True	87.0151	950	1389	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:23:43,264] [INFO] DFAST Taxonomy check result was written to GCF_005406125.1_ASM540612v1_genomic.fna/tc_result.tsv
[2024-01-24 13:23:43,265] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:23:43,265] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:23:43,265] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc92b6c4c-8b2c-4526-bff3-ea7f5a09f48b/dqc_reference/checkm_data
[2024-01-24 13:23:43,266] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:23:43,310] [INFO] Task started: CheckM
[2024-01-24 13:23:43,310] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005406125.1_ASM540612v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005406125.1_ASM540612v1_genomic.fna/checkm_input GCF_005406125.1_ASM540612v1_genomic.fna/checkm_result
[2024-01-24 13:24:42,986] [INFO] Task succeeded: CheckM
[2024-01-24 13:24:42,987] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:24:43,009] [INFO] ===== Completeness check finished =====
[2024-01-24 13:24:43,009] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:24:43,009] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005406125.1_ASM540612v1_genomic.fna/markers.fasta)
[2024-01-24 13:24:43,010] [INFO] Task started: Blastn
[2024-01-24 13:24:43,010] [INFO] Running command: blastn -query GCF_005406125.1_ASM540612v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc92b6c4c-8b2c-4526-bff3-ea7f5a09f48b/dqc_reference/reference_markers_gtdb.fasta -out GCF_005406125.1_ASM540612v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:24:43,539] [INFO] Task succeeded: Blastn
[2024-01-24 13:24:43,542] [INFO] Selected 8 target genomes.
[2024-01-24 13:24:43,542] [INFO] Target genome list was writen to GCF_005406125.1_ASM540612v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:24:43,569] [INFO] Task started: fastANI
[2024-01-24 13:24:43,569] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b2da008-0e26-4c46-ae91-c8f6651bdb60/GCF_005406125.1_ASM540612v1_genomic.fna.gz --refList GCF_005406125.1_ASM540612v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005406125.1_ASM540612v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:24:51,391] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:51,402] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:24:51,402] [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_005406125.1	s__Haloarcula sp005406125	100.0	1386	1389	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000336615.1	s__Haloarcula amylolytica	88.2441	949	1389	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.3005	N/A	N/A	N/A	N/A	1	-
GCF_000223905.1	s__Haloarcula hispanica	87.9744	957	1389	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.3005	98.55	97.98	0.94	0.91	11	-
GCF_000336635.1	s__Haloarcula japonica	87.6777	1020	1389	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008729015.1	s__Haloarcula sp008729015	87.3635	984	1389	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000337775.1	s__Haloarcula vallismortis	87.1455	935	1389	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001280425.1	s__Haloarcula rubripromontorii	87.021	949	1389	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.0	99.01	99.01	0.90	0.90	2	-
GCA_000336895.1	s__Haloarcula argentinensis	86.8668	936	1389	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.2413	99.05	99.05	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:24:51,405] [INFO] GTDB search result was written to GCF_005406125.1_ASM540612v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:24:51,405] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:24:51,408] [INFO] DFAST_QC result json was written to GCF_005406125.1_ASM540612v1_genomic.fna/dqc_result.json
[2024-01-24 13:24:51,408] [INFO] DFAST_QC completed!
[2024-01-24 13:24:51,408] [INFO] Total running time: 0h1m40s