[2024-01-24 14:46:55,037] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:55,040] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:55,041] [INFO] DQC Reference Directory: /var/lib/cwl/stg9ce234f4-be68-4ccd-ad93-c61a04281ce6/dqc_reference
[2024-01-24 14:46:58,015] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:58,016] [INFO] Task started: Prodigal
[2024-01-24 14:46:58,017] [INFO] Running command: gunzip -c /var/lib/cwl/stgb48c31df-9245-4b18-9a2a-20147e1a6414/GCF_007988985.1_ASM798898v1_genomic.fna.gz | prodigal -d GCF_007988985.1_ASM798898v1_genomic.fna/cds.fna -a GCF_007988985.1_ASM798898v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:04,638] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:04,639] [INFO] Task started: HMMsearch
[2024-01-24 14:47:04,639] [INFO] Running command: hmmsearch --tblout GCF_007988985.1_ASM798898v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9ce234f4-be68-4ccd-ad93-c61a04281ce6/dqc_reference/reference_markers.hmm GCF_007988985.1_ASM798898v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:04,921] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:04,922] [INFO] Found 6/6 markers.
[2024-01-24 14:47:04,960] [INFO] Query marker FASTA was written to GCF_007988985.1_ASM798898v1_genomic.fna/markers.fasta
[2024-01-24 14:47:04,961] [INFO] Task started: Blastn
[2024-01-24 14:47:04,961] [INFO] Running command: blastn -query GCF_007988985.1_ASM798898v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ce234f4-be68-4ccd-ad93-c61a04281ce6/dqc_reference/reference_markers.fasta -out GCF_007988985.1_ASM798898v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:05,677] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:05,680] [INFO] Selected 14 target genomes.
[2024-01-24 14:47:05,681] [INFO] Target genome list was writen to GCF_007988985.1_ASM798898v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:05,721] [INFO] Task started: fastANI
[2024-01-24 14:47:05,722] [INFO] Running command: fastANI --query /var/lib/cwl/stgb48c31df-9245-4b18-9a2a-20147e1a6414/GCF_007988985.1_ASM798898v1_genomic.fna.gz --refList GCF_007988985.1_ASM798898v1_genomic.fna/target_genomes.txt --output GCF_007988985.1_ASM798898v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:13,608] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:13,609] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9ce234f4-be68-4ccd-ad93-c61a04281ce6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:13,609] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9ce234f4-be68-4ccd-ad93-c61a04281ce6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:13,615] [INFO] Found 4 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 14:47:13,615] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:47:13,615] [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=NBRC 104935	GCA_007988985.1	517425	517425	type	True	100.0	841	848	95	inconclusive
Salisediminibacterium halotolerans	strain=DSM 26530	GCA_003814815.1	517425	517425	type	True	99.9999	848	848	95	inconclusive
Salisediminibacterium halotolerans	strain=CGMCC 1.7654	GCA_007993825.1	517425	517425	type	True	99.9993	846	848	95	inconclusive
Salisediminibacterium haloalkalitolerans	strain=10nlg	GCA_900111285.1	1464123	1464123	type	True	97.5581	781	848	95	inconclusive
--------------------------------------------------------------------------------
[2024-01-24 14:47:13,617] [INFO] DFAST Taxonomy check result was written to GCF_007988985.1_ASM798898v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:13,617] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:13,618] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:13,618] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9ce234f4-be68-4ccd-ad93-c61a04281ce6/dqc_reference/checkm_data
[2024-01-24 14:47:13,619] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:13,655] [INFO] Task started: CheckM
[2024-01-24 14:47:13,655] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007988985.1_ASM798898v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007988985.1_ASM798898v1_genomic.fna/checkm_input GCF_007988985.1_ASM798898v1_genomic.fna/checkm_result
[2024-01-24 14:47:40,698] [INFO] Task succeeded: CheckM
[2024-01-24 14:47:40,700] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:47:40,721] [INFO] ===== Completeness check finished =====
[2024-01-24 14:47:40,722] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:47:40,722] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007988985.1_ASM798898v1_genomic.fna/markers.fasta)
[2024-01-24 14:47:40,723] [INFO] Task started: Blastn
[2024-01-24 14:47:40,723] [INFO] Running command: blastn -query GCF_007988985.1_ASM798898v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ce234f4-be68-4ccd-ad93-c61a04281ce6/dqc_reference/reference_markers_gtdb.fasta -out GCF_007988985.1_ASM798898v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:41,884] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:41,887] [INFO] Selected 26 target genomes.
[2024-01-24 14:47:41,887] [INFO] Target genome list was writen to GCF_007988985.1_ASM798898v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:47:41,912] [INFO] Task started: fastANI
[2024-01-24 14:47:41,912] [INFO] Running command: fastANI --query /var/lib/cwl/stgb48c31df-9245-4b18-9a2a-20147e1a6414/GCF_007988985.1_ASM798898v1_genomic.fna.gz --refList GCF_007988985.1_ASM798898v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007988985.1_ASM798898v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:47:57,860] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:57,864] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:47:57,864] [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	99.9999	848	848	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 14:47:57,866] [INFO] GTDB search result was written to GCF_007988985.1_ASM798898v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:47:57,867] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:47:57,874] [INFO] DFAST_QC result json was written to GCF_007988985.1_ASM798898v1_genomic.fna/dqc_result.json
[2024-01-24 14:47:57,874] [INFO] DFAST_QC completed!
[2024-01-24 14:47:57,874] [INFO] Total running time: 0h1m3s