[2024-01-24 10:57:07,018] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:07,021] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:07,021] [INFO] DQC Reference Directory: /var/lib/cwl/stga317303b-119d-4650-a952-90818f3c7b20/dqc_reference
[2024-01-24 10:57:08,212] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:08,212] [INFO] Task started: Prodigal
[2024-01-24 10:57:08,213] [INFO] Running command: gunzip -c /var/lib/cwl/stg02aa7baa-f30c-44e3-b340-ed60fd35bc3b/GCF_021249345.1_ASM2124934v1_genomic.fna.gz | prodigal -d GCF_021249345.1_ASM2124934v1_genomic.fna/cds.fna -a GCF_021249345.1_ASM2124934v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:23,824] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:23,825] [INFO] Task started: HMMsearch
[2024-01-24 10:57:23,825] [INFO] Running command: hmmsearch --tblout GCF_021249345.1_ASM2124934v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga317303b-119d-4650-a952-90818f3c7b20/dqc_reference/reference_markers.hmm GCF_021249345.1_ASM2124934v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:24,064] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:24,065] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg02aa7baa-f30c-44e3-b340-ed60fd35bc3b/GCF_021249345.1_ASM2124934v1_genomic.fna.gz]
[2024-01-24 10:57:24,093] [INFO] Query marker FASTA was written to GCF_021249345.1_ASM2124934v1_genomic.fna/markers.fasta
[2024-01-24 10:57:24,094] [INFO] Task started: Blastn
[2024-01-24 10:57:24,094] [INFO] Running command: blastn -query GCF_021249345.1_ASM2124934v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga317303b-119d-4650-a952-90818f3c7b20/dqc_reference/reference_markers.fasta -out GCF_021249345.1_ASM2124934v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:24,612] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:24,616] [INFO] Selected 7 target genomes.
[2024-01-24 10:57:24,617] [INFO] Target genome list was writen to GCF_021249345.1_ASM2124934v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:24,620] [INFO] Task started: fastANI
[2024-01-24 10:57:24,620] [INFO] Running command: fastANI --query /var/lib/cwl/stg02aa7baa-f30c-44e3-b340-ed60fd35bc3b/GCF_021249345.1_ASM2124934v1_genomic.fna.gz --refList GCF_021249345.1_ASM2124934v1_genomic.fna/target_genomes.txt --output GCF_021249345.1_ASM2124934v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:29,764] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:29,765] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga317303b-119d-4650-a952-90818f3c7b20/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:29,765] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga317303b-119d-4650-a952-90818f3c7b20/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:29,779] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:57:29,780] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:57:29,780] [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
Halobacterium litoreum	strain=ZS-54-S2	GCA_021233415.1	2039234	2039234	type	True	84.1434	665	1037	95	below_threshold
Halobacterium hubeiense	strain=JI20-1	GCA_001488575.1	1407499	1407499	type	True	83.4922	597	1037	95	below_threshold
Halobacterium noricense	strain=JCM 15102	GCA_021233435.1	223182	223182	type	True	83.0582	596	1037	95	below_threshold
Halobacterium bonnevillei	strain=PCN9	GCA_009831555.1	2692200	2692200	type	True	82.9799	554	1037	95	below_threshold
Halobacterium jilantaiense	strain=CGMCC 1.5337	GCA_900110535.1	355548	355548	type	True	82.3975	631	1037	95	below_threshold
Halobacterium salinarum	strain=91-R6	GCA_004799605.1	2242	2242	type	True	80.5176	443	1037	95	below_threshold
Halarchaeum rubridurum	strain=JCM 16108	GCA_014647115.1	489911	489911	type	True	79.2092	411	1037	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:29,781] [INFO] DFAST Taxonomy check result was written to GCF_021249345.1_ASM2124934v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:29,782] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:29,782] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:29,783] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga317303b-119d-4650-a952-90818f3c7b20/dqc_reference/checkm_data
[2024-01-24 10:57:29,784] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:29,821] [INFO] Task started: CheckM
[2024-01-24 10:57:29,821] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021249345.1_ASM2124934v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021249345.1_ASM2124934v1_genomic.fna/checkm_input GCF_021249345.1_ASM2124934v1_genomic.fna/checkm_result
[2024-01-24 10:58:13,398] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:13,402] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:13,426] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:13,427] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:13,427] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021249345.1_ASM2124934v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:13,428] [INFO] Task started: Blastn
[2024-01-24 10:58:13,428] [INFO] Running command: blastn -query GCF_021249345.1_ASM2124934v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga317303b-119d-4650-a952-90818f3c7b20/dqc_reference/reference_markers_gtdb.fasta -out GCF_021249345.1_ASM2124934v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:13,938] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:13,943] [INFO] Selected 7 target genomes.
[2024-01-24 10:58:13,943] [INFO] Target genome list was writen to GCF_021249345.1_ASM2124934v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:13,946] [INFO] Task started: fastANI
[2024-01-24 10:58:13,946] [INFO] Running command: fastANI --query /var/lib/cwl/stg02aa7baa-f30c-44e3-b340-ed60fd35bc3b/GCF_021249345.1_ASM2124934v1_genomic.fna.gz --refList GCF_021249345.1_ASM2124934v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021249345.1_ASM2124934v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:19,186] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:19,200] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 10:58:19,200] [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_000230955.2	s__Halobacterium sp000230955	89.979	805	1037	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halobacteriaceae;g__Halobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009741975.1	s__Halobacterium sp009741975	84.1474	509	1037	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halobacteriaceae;g__Halobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011734195.1	s__Halobacterium sp011734195	83.6087	640	1037	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halobacteriaceae;g__Halobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001488575.1	s__Halobacterium hubeiense	83.4919	597	1037	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halobacteriaceae;g__Halobacterium	95.0	99.52	99.49	0.94	0.94	8	-
GCF_001485535.1	s__Halobacterium sp001485535	83.1058	601	1037	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halobacteriaceae;g__Halobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009831555.1	s__Halobacterium sp009831555	82.9383	557	1037	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halobacteriaceae;g__Halobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110535.1	s__Halobacterium jilantaiense	82.4053	630	1037	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halobacteriaceae;g__Halobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:19,201] [INFO] GTDB search result was written to GCF_021249345.1_ASM2124934v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:19,202] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:19,204] [INFO] DFAST_QC result json was written to GCF_021249345.1_ASM2124934v1_genomic.fna/dqc_result.json
[2024-01-24 10:58:19,204] [INFO] DFAST_QC completed!
[2024-01-24 10:58:19,205] [INFO] Total running time: 0h1m12s