[2024-01-24 15:18:19,984] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:19,986] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:19,986] [INFO] DQC Reference Directory: /var/lib/cwl/stg7eace9cf-50c9-40ae-b910-4b159432d38c/dqc_reference
[2024-01-24 15:18:21,154] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:21,155] [INFO] Task started: Prodigal
[2024-01-24 15:18:21,155] [INFO] Running command: gunzip -c /var/lib/cwl/stg2f729fbd-94cd-4bee-afae-1b88c144e905/GCF_009831555.1_ASM983155v1_genomic.fna.gz | prodigal -d GCF_009831555.1_ASM983155v1_genomic.fna/cds.fna -a GCF_009831555.1_ASM983155v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:37,624] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:37,624] [INFO] Task started: HMMsearch
[2024-01-24 15:18:37,625] [INFO] Running command: hmmsearch --tblout GCF_009831555.1_ASM983155v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7eace9cf-50c9-40ae-b910-4b159432d38c/dqc_reference/reference_markers.hmm GCF_009831555.1_ASM983155v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:37,859] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:37,860] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg2f729fbd-94cd-4bee-afae-1b88c144e905/GCF_009831555.1_ASM983155v1_genomic.fna.gz]
[2024-01-24 15:18:37,893] [INFO] Query marker FASTA was written to GCF_009831555.1_ASM983155v1_genomic.fna/markers.fasta
[2024-01-24 15:18:37,893] [INFO] Task started: Blastn
[2024-01-24 15:18:37,893] [INFO] Running command: blastn -query GCF_009831555.1_ASM983155v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7eace9cf-50c9-40ae-b910-4b159432d38c/dqc_reference/reference_markers.fasta -out GCF_009831555.1_ASM983155v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:38,428] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:38,432] [INFO] Selected 8 target genomes.
[2024-01-24 15:18:38,433] [INFO] Target genome list was writen to GCF_009831555.1_ASM983155v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:38,437] [INFO] Task started: fastANI
[2024-01-24 15:18:38,438] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f729fbd-94cd-4bee-afae-1b88c144e905/GCF_009831555.1_ASM983155v1_genomic.fna.gz --refList GCF_009831555.1_ASM983155v1_genomic.fna/target_genomes.txt --output GCF_009831555.1_ASM983155v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:18:44,262] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:44,262] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7eace9cf-50c9-40ae-b910-4b159432d38c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:18:44,263] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7eace9cf-50c9-40ae-b910-4b159432d38c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:18:44,273] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:18:44,273] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:18:44,274] [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 bonnevillei	strain=PCN9	GCA_009831555.1	2692200	2692200	type	True	100.0	966	981	95	conclusive
Halobacterium hubeiense	strain=JI20-1	GCA_001488575.1	1407499	1407499	type	True	84.227	574	981	95	below_threshold
Halobacterium noricense	strain=JCM 15102	GCA_021233435.1	223182	223182	type	True	84.0089	572	981	95	below_threshold
Halobacterium litoreum	strain=ZS-54-S2	GCA_021233415.1	2039234	2039234	type	True	82.6787	575	981	95	below_threshold
Halobacterium jilantaiense	strain=CGMCC 1.5337	GCA_900110535.1	355548	355548	type	True	81.9986	533	981	95	below_threshold
Halobacterium salinarum	strain=91-R6	GCA_004799605.1	2242	2242	type	True	80.3515	409	981	95	below_threshold
Halobacterium salinarum	strain=DSM 3754	GCA_008124605.1	2242	2242	type	True	80.2785	400	981	95	below_threshold
Halarchaeum rubridurum	strain=JCM 16108	GCA_014647115.1	489911	489911	type	True	78.5767	337	981	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:18:44,275] [INFO] DFAST Taxonomy check result was written to GCF_009831555.1_ASM983155v1_genomic.fna/tc_result.tsv
[2024-01-24 15:18:44,276] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:18:44,276] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:18:44,276] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7eace9cf-50c9-40ae-b910-4b159432d38c/dqc_reference/checkm_data
[2024-01-24 15:18:44,277] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:18:44,314] [INFO] Task started: CheckM
[2024-01-24 15:18:44,314] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009831555.1_ASM983155v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009831555.1_ASM983155v1_genomic.fna/checkm_input GCF_009831555.1_ASM983155v1_genomic.fna/checkm_result
[2024-01-24 15:19:31,955] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:31,957] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:31,984] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:31,984] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:31,985] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009831555.1_ASM983155v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:31,985] [INFO] Task started: Blastn
[2024-01-24 15:19:31,985] [INFO] Running command: blastn -query GCF_009831555.1_ASM983155v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7eace9cf-50c9-40ae-b910-4b159432d38c/dqc_reference/reference_markers_gtdb.fasta -out GCF_009831555.1_ASM983155v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:32,486] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:32,489] [INFO] Selected 6 target genomes.
[2024-01-24 15:19:32,489] [INFO] Target genome list was writen to GCF_009831555.1_ASM983155v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:32,494] [INFO] Task started: fastANI
[2024-01-24 15:19:32,494] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f729fbd-94cd-4bee-afae-1b88c144e905/GCF_009831555.1_ASM983155v1_genomic.fna.gz --refList GCF_009831555.1_ASM983155v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009831555.1_ASM983155v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:37,244] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:37,250] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:37,250] [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_009831555.1	s__Halobacterium sp009831555	100.0	966	981	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halobacteriaceae;g__Halobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009741975.1	s__Halobacterium sp009741975	84.5638	504	981	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	84.3511	609	981	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	84.2184	575	981	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	83.8942	577	981	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halobacteriaceae;g__Halobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000230955.2	s__Halobacterium sp000230955	82.5835	564	981	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 15:19:37,252] [INFO] GTDB search result was written to GCF_009831555.1_ASM983155v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:37,258] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:37,262] [INFO] DFAST_QC result json was written to GCF_009831555.1_ASM983155v1_genomic.fna/dqc_result.json
[2024-01-24 15:19:37,262] [INFO] DFAST_QC completed!
[2024-01-24 15:19:37,262] [INFO] Total running time: 0h1m17s