[2024-01-24 12:45:20,674] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:45:20,675] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:45:20,676] [INFO] DQC Reference Directory: /var/lib/cwl/stgbe647c43-3c91-4a78-8d2e-cb5493c1918f/dqc_reference
[2024-01-24 12:45:22,025] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:45:22,028] [INFO] Task started: Prodigal
[2024-01-24 12:45:22,029] [INFO] Running command: gunzip -c /var/lib/cwl/stg5ace14f6-9914-4161-a3d4-be5944a444dd/GCF_014647155.1_ASM1464715v1_genomic.fna.gz | prodigal -d GCF_014647155.1_ASM1464715v1_genomic.fna/cds.fna -a GCF_014647155.1_ASM1464715v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:36,460] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:36,460] [INFO] Task started: HMMsearch
[2024-01-24 12:45:36,460] [INFO] Running command: hmmsearch --tblout GCF_014647155.1_ASM1464715v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbe647c43-3c91-4a78-8d2e-cb5493c1918f/dqc_reference/reference_markers.hmm GCF_014647155.1_ASM1464715v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:36,702] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:36,703] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg5ace14f6-9914-4161-a3d4-be5944a444dd/GCF_014647155.1_ASM1464715v1_genomic.fna.gz]
[2024-01-24 12:45:36,736] [INFO] Query marker FASTA was written to GCF_014647155.1_ASM1464715v1_genomic.fna/markers.fasta
[2024-01-24 12:45:36,737] [INFO] Task started: Blastn
[2024-01-24 12:45:36,737] [INFO] Running command: blastn -query GCF_014647155.1_ASM1464715v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe647c43-3c91-4a78-8d2e-cb5493c1918f/dqc_reference/reference_markers.fasta -out GCF_014647155.1_ASM1464715v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:37,264] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:37,268] [INFO] Selected 5 target genomes.
[2024-01-24 12:45:37,269] [INFO] Target genome list was writen to GCF_014647155.1_ASM1464715v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:37,273] [INFO] Task started: fastANI
[2024-01-24 12:45:37,273] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ace14f6-9914-4161-a3d4-be5944a444dd/GCF_014647155.1_ASM1464715v1_genomic.fna.gz --refList GCF_014647155.1_ASM1464715v1_genomic.fna/target_genomes.txt --output GCF_014647155.1_ASM1464715v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:41,104] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:41,104] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbe647c43-3c91-4a78-8d2e-cb5493c1918f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:41,105] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbe647c43-3c91-4a78-8d2e-cb5493c1918f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:41,113] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:45:41,113] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:45:41,113] [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
Halarchaeum rubridurum	strain=JCM 16108	GCA_014647115.1	489911	489911	type	True	90.1602	742	1035	95	below_threshold
Halarchaeum rubridurum	strain=DSM 22443	GCA_017873775.1	489911	489911	type	True	90.1423	759	1035	95	below_threshold
Halarchaeum acidiphilum	strain=JCM 16109	GCA_000474235.1	489138	489138	type	True	86.6153	591	1035	95	below_threshold
Halarchaeum acidiphilum	strain=MH1-52-1	GCA_000400975.1	489138	489138	type	True	86.2213	415	1035	95	below_threshold
Halarchaeum grantii	strain=JCM 19585	GCA_014647455.2	1193105	1193105	type	True	85.2878	669	1035	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:41,115] [INFO] DFAST Taxonomy check result was written to GCF_014647155.1_ASM1464715v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:41,118] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:41,118] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:41,119] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbe647c43-3c91-4a78-8d2e-cb5493c1918f/dqc_reference/checkm_data
[2024-01-24 12:45:41,121] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:41,156] [INFO] Task started: CheckM
[2024-01-24 12:45:41,156] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014647155.1_ASM1464715v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014647155.1_ASM1464715v1_genomic.fna/checkm_input GCF_014647155.1_ASM1464715v1_genomic.fna/checkm_result
[2024-01-24 12:46:22,690] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:22,691] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.75%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:22,712] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:22,712] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:22,713] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014647155.1_ASM1464715v1_genomic.fna/markers.fasta)
[2024-01-24 12:46:22,713] [INFO] Task started: Blastn
[2024-01-24 12:46:22,713] [INFO] Running command: blastn -query GCF_014647155.1_ASM1464715v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe647c43-3c91-4a78-8d2e-cb5493c1918f/dqc_reference/reference_markers_gtdb.fasta -out GCF_014647155.1_ASM1464715v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:23,205] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:23,209] [INFO] Selected 6 target genomes.
[2024-01-24 12:46:23,210] [INFO] Target genome list was writen to GCF_014647155.1_ASM1464715v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:23,223] [INFO] Task started: fastANI
[2024-01-24 12:46:23,223] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ace14f6-9914-4161-a3d4-be5944a444dd/GCF_014647155.1_ASM1464715v1_genomic.fna.gz --refList GCF_014647155.1_ASM1464715v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014647155.1_ASM1464715v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:28,445] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:28,454] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:28,454] [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_014647155.1	s__Halarchaeum nitratireducens	100.0	1034	1035	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halobacteriaceae;g__Halarchaeum	95.0	98.88	98.88	0.86	0.86	2	conclusive
GCF_014647115.1	s__Halarchaeum rubridurum	90.1391	743	1035	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halobacteriaceae;g__Halarchaeum	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017874335.1	s__Halarchaeum salinum	87.675	673	1035	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halobacteriaceae;g__Halarchaeum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000474235.1	s__Halarchaeum acidiphilum	86.595	592	1035	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halobacteriaceae;g__Halarchaeum	95.0	99.69	99.69	0.96	0.96	2	-
GCF_014647455.2	s__Halarchaeum grantii	85.2887	670	1035	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halobacteriaceae;g__Halarchaeum	95.0	95.76	95.76	0.83	0.83	2	-
GCF_014647475.1	s__Halocalculus aciditolerans	79.981	517	1035	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halobacteriaceae;g__Halocalculus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:28,459] [INFO] GTDB search result was written to GCF_014647155.1_ASM1464715v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:28,459] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:28,462] [INFO] DFAST_QC result json was written to GCF_014647155.1_ASM1464715v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:28,463] [INFO] DFAST_QC completed!
[2024-01-24 12:46:28,463] [INFO] Total running time: 0h1m8s