[2024-01-24 11:35:11,851] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:11,853] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:11,853] [INFO] DQC Reference Directory: /var/lib/cwl/stgb9c90f39-593c-4bff-b72f-93a477db1746/dqc_reference
[2024-01-24 11:35:13,093] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:13,094] [INFO] Task started: Prodigal
[2024-01-24 11:35:13,094] [INFO] Running command: gunzip -c /var/lib/cwl/stg67c1300f-79c1-433d-af3f-917c90f861b4/GCF_002252985.1_ASM225298v1_genomic.fna.gz | prodigal -d GCF_002252985.1_ASM225298v1_genomic.fna/cds.fna -a GCF_002252985.1_ASM225298v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:27,500] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:27,500] [INFO] Task started: HMMsearch
[2024-01-24 11:35:27,500] [INFO] Running command: hmmsearch --tblout GCF_002252985.1_ASM225298v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb9c90f39-593c-4bff-b72f-93a477db1746/dqc_reference/reference_markers.hmm GCF_002252985.1_ASM225298v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:27,746] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:27,747] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg67c1300f-79c1-433d-af3f-917c90f861b4/GCF_002252985.1_ASM225298v1_genomic.fna.gz]
[2024-01-24 11:35:27,776] [INFO] Query marker FASTA was written to GCF_002252985.1_ASM225298v1_genomic.fna/markers.fasta
[2024-01-24 11:35:27,776] [INFO] Task started: Blastn
[2024-01-24 11:35:27,777] [INFO] Running command: blastn -query GCF_002252985.1_ASM225298v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9c90f39-593c-4bff-b72f-93a477db1746/dqc_reference/reference_markers.fasta -out GCF_002252985.1_ASM225298v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:28,311] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:28,314] [INFO] Selected 6 target genomes.
[2024-01-24 11:35:28,314] [INFO] Target genome list was writen to GCF_002252985.1_ASM225298v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:28,317] [INFO] Task started: fastANI
[2024-01-24 11:35:28,317] [INFO] Running command: fastANI --query /var/lib/cwl/stg67c1300f-79c1-433d-af3f-917c90f861b4/GCF_002252985.1_ASM225298v1_genomic.fna.gz --refList GCF_002252985.1_ASM225298v1_genomic.fna/target_genomes.txt --output GCF_002252985.1_ASM225298v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:34,575] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:34,575] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb9c90f39-593c-4bff-b72f-93a477db1746/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:34,575] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb9c90f39-593c-4bff-b72f-93a477db1746/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:34,585] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:35:34,585] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:34,586] [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
Halorubrum halodurans	strain=Cb34	GCA_002252985.1	1383851	1383851	type	True	100.0	1034	1037	95	conclusive
Halorubrum aethiopicum	strain=SAH-A6	GCA_001542905.1	1758255	1758255	type	True	93.3476	762	1037	95	below_threshold
Halorubrum rubrum	strain=YC87	GCA_024494685.1	1126240	1126240	type	True	90.9401	753	1037	95	below_threshold
Halorubrum cibi	strain=DSM 19504	GCA_900182635.1	413815	413815	type	True	90.8577	727	1037	95	below_threshold
Halorubrum aquaticum	strain=CGMCC 1.6377	GCA_900113615.1	387340	387340	type	True	90.1661	728	1037	95	below_threshold
Halorubrum salipaludis	strain=WN019	GCA_002286985.1	2032630	2032630	type	True	83.7864	641	1037	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:34,587] [INFO] DFAST Taxonomy check result was written to GCF_002252985.1_ASM225298v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:34,588] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:34,589] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:34,589] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb9c90f39-593c-4bff-b72f-93a477db1746/dqc_reference/checkm_data
[2024-01-24 11:35:34,591] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:34,625] [INFO] Task started: CheckM
[2024-01-24 11:35:34,626] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002252985.1_ASM225298v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002252985.1_ASM225298v1_genomic.fna/checkm_input GCF_002252985.1_ASM225298v1_genomic.fna/checkm_result
[2024-01-24 11:36:16,673] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:16,674] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.58%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:16,697] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:16,698] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:16,698] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002252985.1_ASM225298v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:16,699] [INFO] Task started: Blastn
[2024-01-24 11:36:16,699] [INFO] Running command: blastn -query GCF_002252985.1_ASM225298v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9c90f39-593c-4bff-b72f-93a477db1746/dqc_reference/reference_markers_gtdb.fasta -out GCF_002252985.1_ASM225298v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:17,221] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:17,226] [INFO] Selected 6 target genomes.
[2024-01-24 11:36:17,226] [INFO] Target genome list was writen to GCF_002252985.1_ASM225298v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:17,231] [INFO] Task started: fastANI
[2024-01-24 11:36:17,232] [INFO] Running command: fastANI --query /var/lib/cwl/stg67c1300f-79c1-433d-af3f-917c90f861b4/GCF_002252985.1_ASM225298v1_genomic.fna.gz --refList GCF_002252985.1_ASM225298v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002252985.1_ASM225298v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:23,319] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:23,330] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:23,330] [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_002252985.1	s__Halorubrum halodurans	100.0	1034	1037	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001542905.1	s__Halorubrum aethiopicum	93.3366	763	1037	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900182635.1	s__Halorubrum cibi	90.8244	729	1037	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113615.1	s__Halorubrum aquaticum	90.2144	726	1037	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003697845.1	s__Halorubrum sp003697845	88.8488	741	1037	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003287355.1	s__Halorubrum sp003287355	88.169	688	1037	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:23,332] [INFO] GTDB search result was written to GCF_002252985.1_ASM225298v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:23,333] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:23,335] [INFO] DFAST_QC result json was written to GCF_002252985.1_ASM225298v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:23,336] [INFO] DFAST_QC completed!
[2024-01-24 11:36:23,336] [INFO] Total running time: 0h1m11s