[2024-01-24 13:22:01,813] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:01,816] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:01,818] [INFO] DQC Reference Directory: /var/lib/cwl/stg04d62d26-0535-4e28-aa05-886bd4aa74fd/dqc_reference
[2024-01-24 13:22:03,175] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:03,176] [INFO] Task started: Prodigal
[2024-01-24 13:22:03,176] [INFO] Running command: gunzip -c /var/lib/cwl/stgc009e05f-0b4f-49bb-a19f-82f99a2e0652/GCF_007993825.1_ASM799382v1_genomic.fna.gz | prodigal -d GCF_007993825.1_ASM799382v1_genomic.fna/cds.fna -a GCF_007993825.1_ASM799382v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:10,854] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:10,855] [INFO] Task started: HMMsearch
[2024-01-24 13:22:10,855] [INFO] Running command: hmmsearch --tblout GCF_007993825.1_ASM799382v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg04d62d26-0535-4e28-aa05-886bd4aa74fd/dqc_reference/reference_markers.hmm GCF_007993825.1_ASM799382v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:11,147] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:11,148] [INFO] Found 6/6 markers.
[2024-01-24 13:22:11,175] [INFO] Query marker FASTA was written to GCF_007993825.1_ASM799382v1_genomic.fna/markers.fasta
[2024-01-24 13:22:11,175] [INFO] Task started: Blastn
[2024-01-24 13:22:11,175] [INFO] Running command: blastn -query GCF_007993825.1_ASM799382v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg04d62d26-0535-4e28-aa05-886bd4aa74fd/dqc_reference/reference_markers.fasta -out GCF_007993825.1_ASM799382v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:11,906] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:11,909] [INFO] Selected 14 target genomes.
[2024-01-24 13:22:11,910] [INFO] Target genome list was writen to GCF_007993825.1_ASM799382v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:11,919] [INFO] Task started: fastANI
[2024-01-24 13:22:11,919] [INFO] Running command: fastANI --query /var/lib/cwl/stgc009e05f-0b4f-49bb-a19f-82f99a2e0652/GCF_007993825.1_ASM799382v1_genomic.fna.gz --refList GCF_007993825.1_ASM799382v1_genomic.fna/target_genomes.txt --output GCF_007993825.1_ASM799382v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:22,622] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:22,623] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg04d62d26-0535-4e28-aa05-886bd4aa74fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:22,623] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg04d62d26-0535-4e28-aa05-886bd4aa74fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:22,629] [INFO] Found 4 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:22:22,630] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:22:22,630] [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
Salisediminibacterium halotolerans	strain=CGMCC 1.7654	GCA_007993825.1	517425	517425	type	True	100.0	935	937	95	inconclusive
Salisediminibacterium halotolerans	strain=DSM 26530	GCA_003814815.1	517425	517425	type	True	99.9902	933	937	95	inconclusive
Salisediminibacterium halotolerans	strain=NBRC 104935	GCA_007988985.1	517425	517425	type	True	99.9	832	937	95	inconclusive
Salisediminibacterium haloalkalitolerans	strain=10nlg	GCA_900111285.1	1464123	1464123	type	True	97.5718	843	937	95	inconclusive
--------------------------------------------------------------------------------
[2024-01-24 13:22:22,631] [INFO] DFAST Taxonomy check result was written to GCF_007993825.1_ASM799382v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:22,632] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:22,632] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:22,632] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg04d62d26-0535-4e28-aa05-886bd4aa74fd/dqc_reference/checkm_data
[2024-01-24 13:22:22,634] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:22,676] [INFO] Task started: CheckM
[2024-01-24 13:22:22,676] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007993825.1_ASM799382v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007993825.1_ASM799382v1_genomic.fna/checkm_input GCF_007993825.1_ASM799382v1_genomic.fna/checkm_result
[2024-01-24 13:22:51,495] [INFO] Task succeeded: CheckM
[2024-01-24 13:22:51,497] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:22:51,517] [INFO] ===== Completeness check finished =====
[2024-01-24 13:22:51,517] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:22:51,518] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007993825.1_ASM799382v1_genomic.fna/markers.fasta)
[2024-01-24 13:22:51,519] [INFO] Task started: Blastn
[2024-01-24 13:22:51,519] [INFO] Running command: blastn -query GCF_007993825.1_ASM799382v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg04d62d26-0535-4e28-aa05-886bd4aa74fd/dqc_reference/reference_markers_gtdb.fasta -out GCF_007993825.1_ASM799382v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:52,634] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:52,638] [INFO] Selected 26 target genomes.
[2024-01-24 13:22:52,638] [INFO] Target genome list was writen to GCF_007993825.1_ASM799382v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:22:52,693] [INFO] Task started: fastANI
[2024-01-24 13:22:52,693] [INFO] Running command: fastANI --query /var/lib/cwl/stgc009e05f-0b4f-49bb-a19f-82f99a2e0652/GCF_007993825.1_ASM799382v1_genomic.fna.gz --refList GCF_007993825.1_ASM799382v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007993825.1_ASM799382v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:09,380] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:09,383] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:09,383] [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_003814815.1	s__Salisediminibacterium halotolerans	99.9902	933	937	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Salisediminibacterium	95.0	99.40	97.60	0.97	0.91	5	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:23:09,385] [INFO] GTDB search result was written to GCF_007993825.1_ASM799382v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:09,385] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:09,387] [INFO] DFAST_QC result json was written to GCF_007993825.1_ASM799382v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:09,387] [INFO] DFAST_QC completed!
[2024-01-24 13:23:09,387] [INFO] Total running time: 0h1m8s