[2024-01-24 12:22:14,150] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:14,152] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:14,152] [INFO] DQC Reference Directory: /var/lib/cwl/stg2044c1e2-c1c3-499b-b2b5-f337d19d0900/dqc_reference
[2024-01-24 12:22:15,683] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:15,684] [INFO] Task started: Prodigal
[2024-01-24 12:22:15,684] [INFO] Running command: gunzip -c /var/lib/cwl/stg5ab73a2f-e26d-4a0a-b468-baa9d5433f62/GCF_000023945.1_ASM2394v1_genomic.fna.gz | prodigal -d GCF_000023945.1_ASM2394v1_genomic.fna/cds.fna -a GCF_000023945.1_ASM2394v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:32,199] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:32,200] [INFO] Task started: HMMsearch
[2024-01-24 12:22:32,200] [INFO] Running command: hmmsearch --tblout GCF_000023945.1_ASM2394v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2044c1e2-c1c3-499b-b2b5-f337d19d0900/dqc_reference/reference_markers.hmm GCF_000023945.1_ASM2394v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:32,535] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:32,536] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg5ab73a2f-e26d-4a0a-b468-baa9d5433f62/GCF_000023945.1_ASM2394v1_genomic.fna.gz]
[2024-01-24 12:22:32,584] [INFO] Query marker FASTA was written to GCF_000023945.1_ASM2394v1_genomic.fna/markers.fasta
[2024-01-24 12:22:32,585] [INFO] Task started: Blastn
[2024-01-24 12:22:32,585] [INFO] Running command: blastn -query GCF_000023945.1_ASM2394v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2044c1e2-c1c3-499b-b2b5-f337d19d0900/dqc_reference/reference_markers.fasta -out GCF_000023945.1_ASM2394v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:33,154] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:33,158] [INFO] Selected 6 target genomes.
[2024-01-24 12:22:33,159] [INFO] Target genome list was writen to GCF_000023945.1_ASM2394v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:33,163] [INFO] Task started: fastANI
[2024-01-24 12:22:33,163] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ab73a2f-e26d-4a0a-b468-baa9d5433f62/GCF_000023945.1_ASM2394v1_genomic.fna.gz --refList GCF_000023945.1_ASM2394v1_genomic.fna/target_genomes.txt --output GCF_000023945.1_ASM2394v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:37,819] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:37,820] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2044c1e2-c1c3-499b-b2b5-f337d19d0900/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:37,820] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2044c1e2-c1c3-499b-b2b5-f337d19d0900/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:37,827] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:22:37,827] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:37,828] [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
Halorhabdus utahensis	strain=DSM 12940	GCA_000023945.1	146826	146826	type	True	100.0	1038	1038	95	conclusive
Halorhabdus tiamatea	strain=SARL4B	GCA_000215915.3	430914	430914	type	True	86.2331	670	1038	95	below_threshold
Halorhabdus tiamatea	strain=type strain: SARL4B	GCA_000470655.1	430914	430914	type	True	86.1512	704	1038	95	below_threshold
Halorhabdus amylolytica	strain=H27	GCA_004944975.1	2559573	2559573	type	True	81.3796	578	1038	95	below_threshold
Halorhabdus rudnickae		GCA_900880625.1	1775544	1775544	type	True	81.024	528	1038	95	below_threshold
Halorhabdus salina	strain=FL145	GCA_013839425.1	2750670	2750670	type	True	80.2237	474	1038	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:37,829] [INFO] DFAST Taxonomy check result was written to GCF_000023945.1_ASM2394v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:37,830] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:37,830] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:37,831] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2044c1e2-c1c3-499b-b2b5-f337d19d0900/dqc_reference/checkm_data
[2024-01-24 12:22:37,833] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:37,873] [INFO] Task started: CheckM
[2024-01-24 12:22:37,873] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000023945.1_ASM2394v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000023945.1_ASM2394v1_genomic.fna/checkm_input GCF_000023945.1_ASM2394v1_genomic.fna/checkm_result
[2024-01-24 12:23:25,686] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:25,687] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:25,710] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:25,710] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:25,711] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000023945.1_ASM2394v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:25,711] [INFO] Task started: Blastn
[2024-01-24 12:23:25,711] [INFO] Running command: blastn -query GCF_000023945.1_ASM2394v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2044c1e2-c1c3-499b-b2b5-f337d19d0900/dqc_reference/reference_markers_gtdb.fasta -out GCF_000023945.1_ASM2394v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:26,211] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:26,214] [INFO] Selected 5 target genomes.
[2024-01-24 12:23:26,214] [INFO] Target genome list was writen to GCF_000023945.1_ASM2394v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:26,220] [INFO] Task started: fastANI
[2024-01-24 12:23:26,221] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ab73a2f-e26d-4a0a-b468-baa9d5433f62/GCF_000023945.1_ASM2394v1_genomic.fna.gz --refList GCF_000023945.1_ASM2394v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000023945.1_ASM2394v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:30,174] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:30,179] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:30,179] [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_000023945.1	s__Halorhabdus utahensis	100.0	1038	1038	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halorhabdus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000470655.1	s__Halorhabdus tiamatea	86.1422	705	1038	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halorhabdus	95.0	99.99	99.99	0.94	0.94	2	-
GCF_004944975.1	s__Halorhabdus sp004944975	81.3723	578	1038	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900880625.1	s__Halorhabdus rudnickae	81.0273	527	1038	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013839425.1	s__Halorhabdus sp013839425	80.2139	476	1038	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:30,181] [INFO] GTDB search result was written to GCF_000023945.1_ASM2394v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:30,181] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:30,184] [INFO] DFAST_QC result json was written to GCF_000023945.1_ASM2394v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:30,184] [INFO] DFAST_QC completed!
[2024-01-24 12:23:30,184] [INFO] Total running time: 0h1m16s