[2024-01-24 11:59:22,956] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:22,958] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:22,959] [INFO] DQC Reference Directory: /var/lib/cwl/stg1c6df0b7-b2ec-43f6-8540-2588675c5aec/dqc_reference
[2024-01-24 11:59:25,647] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:25,649] [INFO] Task started: Prodigal
[2024-01-24 11:59:25,649] [INFO] Running command: gunzip -c /var/lib/cwl/stg59126672-dc8f-4d67-bc23-755da300c6f8/GCF_021233415.1_ASM2123341v1_genomic.fna.gz | prodigal -d GCF_021233415.1_ASM2123341v1_genomic.fna/cds.fna -a GCF_021233415.1_ASM2123341v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:39,299] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:39,300] [INFO] Task started: HMMsearch
[2024-01-24 11:59:39,300] [INFO] Running command: hmmsearch --tblout GCF_021233415.1_ASM2123341v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1c6df0b7-b2ec-43f6-8540-2588675c5aec/dqc_reference/reference_markers.hmm GCF_021233415.1_ASM2123341v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:39,545] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:39,547] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg59126672-dc8f-4d67-bc23-755da300c6f8/GCF_021233415.1_ASM2123341v1_genomic.fna.gz]
[2024-01-24 11:59:39,582] [INFO] Query marker FASTA was written to GCF_021233415.1_ASM2123341v1_genomic.fna/markers.fasta
[2024-01-24 11:59:39,582] [INFO] Task started: Blastn
[2024-01-24 11:59:39,583] [INFO] Running command: blastn -query GCF_021233415.1_ASM2123341v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c6df0b7-b2ec-43f6-8540-2588675c5aec/dqc_reference/reference_markers.fasta -out GCF_021233415.1_ASM2123341v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:40,106] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:40,110] [INFO] Selected 8 target genomes.
[2024-01-24 11:59:40,110] [INFO] Target genome list was writen to GCF_021233415.1_ASM2123341v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:40,114] [INFO] Task started: fastANI
[2024-01-24 11:59:40,114] [INFO] Running command: fastANI --query /var/lib/cwl/stg59126672-dc8f-4d67-bc23-755da300c6f8/GCF_021233415.1_ASM2123341v1_genomic.fna.gz --refList GCF_021233415.1_ASM2123341v1_genomic.fna/target_genomes.txt --output GCF_021233415.1_ASM2123341v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:46,233] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:46,234] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1c6df0b7-b2ec-43f6-8540-2588675c5aec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:46,234] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1c6df0b7-b2ec-43f6-8540-2588675c5aec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:46,241] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:59:46,241] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:46,242] [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	100.0	901	902	95	conclusive
Halobacterium hubeiense	strain=JI20-1	GCA_001488575.1	1407499	1407499	type	True	84.3187	619	902	95	below_threshold
Halobacterium jilantaiense	strain=CGMCC 1.5337	GCA_900110535.1	355548	355548	type	True	83.7683	691	902	95	below_threshold
Halobacterium noricense	strain=JCM 15102	GCA_021233435.1	223182	223182	type	True	83.7622	613	902	95	below_threshold
Halobacterium bonnevillei	strain=PCN9	GCA_009831555.1	2692200	2692200	type	True	82.9415	579	902	95	below_threshold
Halobacterium salinarum	strain=91-R6	GCA_004799605.1	2242	2242	type	True	81.1189	477	902	95	below_threshold
Haloferax gibbonsii	strain=ATCC 33959	GCA_000336775.1	35746	35746	type	True	78.1345	445	902	95	below_threshold
Haloferax prahovense	strain=DSM 18310	GCA_000336815.1	381852	381852	type	True	77.9268	441	902	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:46,243] [INFO] DFAST Taxonomy check result was written to GCF_021233415.1_ASM2123341v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:46,243] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:46,244] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:46,244] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1c6df0b7-b2ec-43f6-8540-2588675c5aec/dqc_reference/checkm_data
[2024-01-24 11:59:46,245] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:46,272] [INFO] Task started: CheckM
[2024-01-24 11:59:46,272] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021233415.1_ASM2123341v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021233415.1_ASM2123341v1_genomic.fna/checkm_input GCF_021233415.1_ASM2123341v1_genomic.fna/checkm_result
[2024-01-24 12:00:25,440] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:25,441] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:25,466] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:25,467] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:25,467] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021233415.1_ASM2123341v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:25,468] [INFO] Task started: Blastn
[2024-01-24 12:00:25,468] [INFO] Running command: blastn -query GCF_021233415.1_ASM2123341v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c6df0b7-b2ec-43f6-8540-2588675c5aec/dqc_reference/reference_markers_gtdb.fasta -out GCF_021233415.1_ASM2123341v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:26,012] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:26,016] [INFO] Selected 7 target genomes.
[2024-01-24 12:00:26,016] [INFO] Target genome list was writen to GCF_021233415.1_ASM2123341v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:26,026] [INFO] Task started: fastANI
[2024-01-24 12:00:26,027] [INFO] Running command: fastANI --query /var/lib/cwl/stg59126672-dc8f-4d67-bc23-755da300c6f8/GCF_021233415.1_ASM2123341v1_genomic.fna.gz --refList GCF_021233415.1_ASM2123341v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021233415.1_ASM2123341v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:31,413] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:31,423] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:00:31,423] [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_001488575.1	s__Halobacterium hubeiense	84.2757	622	902	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halobacteriaceae;g__Halobacterium	95.0	99.52	99.49	0.94	0.94	8	-
GCF_009741975.1	s__Halobacterium sp009741975	84.1422	531	902	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	83.9886	637	902	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halobacteriaceae;g__Halobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001485535.1	s__Halobacterium sp001485535	83.9616	628	902	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	83.8467	651	902	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	83.7189	695	902	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	82.8534	585	902	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 12:00:31,425] [INFO] GTDB search result was written to GCF_021233415.1_ASM2123341v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:31,425] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:31,429] [INFO] DFAST_QC result json was written to GCF_021233415.1_ASM2123341v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:31,429] [INFO] DFAST_QC completed!
[2024-01-24 12:00:31,429] [INFO] Total running time: 0h1m8s