[2024-01-24 11:43:52,833] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:52,834] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:52,835] [INFO] DQC Reference Directory: /var/lib/cwl/stg1a3f8572-9474-428e-8d06-0248a21f053b/dqc_reference
[2024-01-24 11:43:54,112] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:54,113] [INFO] Task started: Prodigal
[2024-01-24 11:43:54,113] [INFO] Running command: gunzip -c /var/lib/cwl/stgfbd918d6-ba41-4cd2-a4a6-c34b45e06677/GCF_001547735.1_ASM154773v1_genomic.fna.gz | prodigal -d GCF_001547735.1_ASM154773v1_genomic.fna/cds.fna -a GCF_001547735.1_ASM154773v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:58,358] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:58,358] [INFO] Task started: HMMsearch
[2024-01-24 11:43:58,359] [INFO] Running command: hmmsearch --tblout GCF_001547735.1_ASM154773v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1a3f8572-9474-428e-8d06-0248a21f053b/dqc_reference/reference_markers.hmm GCF_001547735.1_ASM154773v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:58,524] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:58,526] [INFO] Found 6/6 markers.
[2024-01-24 11:43:58,544] [INFO] Query marker FASTA was written to GCF_001547735.1_ASM154773v1_genomic.fna/markers.fasta
[2024-01-24 11:43:58,544] [INFO] Task started: Blastn
[2024-01-24 11:43:58,544] [INFO] Running command: blastn -query GCF_001547735.1_ASM154773v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a3f8572-9474-428e-8d06-0248a21f053b/dqc_reference/reference_markers.fasta -out GCF_001547735.1_ASM154773v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:59,092] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:59,095] [INFO] Selected 16 target genomes.
[2024-01-24 11:43:59,095] [INFO] Target genome list was writen to GCF_001547735.1_ASM154773v1_genomic.fna/target_genomes.txt
[2024-01-24 11:43:59,157] [INFO] Task started: fastANI
[2024-01-24 11:43:59,157] [INFO] Running command: fastANI --query /var/lib/cwl/stgfbd918d6-ba41-4cd2-a4a6-c34b45e06677/GCF_001547735.1_ASM154773v1_genomic.fna.gz --refList GCF_001547735.1_ASM154773v1_genomic.fna/target_genomes.txt --output GCF_001547735.1_ASM154773v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:08,370] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:08,370] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1a3f8572-9474-428e-8d06-0248a21f053b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:08,371] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1a3f8572-9474-428e-8d06-0248a21f053b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:08,375] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:08,375] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:08,375] [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
Thermosulfidibacter takaii	strain=ABI70S6	GCA_001547735.1	412593	412593	type	True	100.0	605	605	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 11:44:08,376] [INFO] DFAST Taxonomy check result was written to GCF_001547735.1_ASM154773v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:08,377] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:08,377] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:08,377] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1a3f8572-9474-428e-8d06-0248a21f053b/dqc_reference/checkm_data
[2024-01-24 11:44:08,379] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:08,400] [INFO] Task started: CheckM
[2024-01-24 11:44:08,400] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001547735.1_ASM154773v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001547735.1_ASM154773v1_genomic.fna/checkm_input GCF_001547735.1_ASM154773v1_genomic.fna/checkm_result
[2024-01-24 11:44:27,337] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:27,339] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:27,355] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:27,355] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:27,355] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001547735.1_ASM154773v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:27,356] [INFO] Task started: Blastn
[2024-01-24 11:44:27,356] [INFO] Running command: blastn -query GCF_001547735.1_ASM154773v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a3f8572-9474-428e-8d06-0248a21f053b/dqc_reference/reference_markers_gtdb.fasta -out GCF_001547735.1_ASM154773v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:28,116] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:28,119] [INFO] Selected 21 target genomes.
[2024-01-24 11:44:28,119] [INFO] Target genome list was writen to GCF_001547735.1_ASM154773v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:28,189] [INFO] Task started: fastANI
[2024-01-24 11:44:28,189] [INFO] Running command: fastANI --query /var/lib/cwl/stgfbd918d6-ba41-4cd2-a4a6-c34b45e06677/GCF_001547735.1_ASM154773v1_genomic.fna.gz --refList GCF_001547735.1_ASM154773v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001547735.1_ASM154773v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:44:35,926] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:35,930] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:44:35,930] [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_001547735.1	s__Thermosulfidibacter takaii	100.0	605	605	d__Bacteria;p__Thermosulfidibacterota;c__Thermosulfidibacteria;o__Thermosulfidibacterales;f__Thermosulfidibacteraceae;g__Thermosulfidibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_015494645.1	s__Thermosulfidibacter sp015494645	77.7769	68	605	d__Bacteria;p__Thermosulfidibacterota;c__Thermosulfidibacteria;o__Thermosulfidibacterales;f__Thermosulfidibacteraceae;g__Thermosulfidibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:44:35,931] [INFO] GTDB search result was written to GCF_001547735.1_ASM154773v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:44:35,932] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:44:35,933] [INFO] DFAST_QC result json was written to GCF_001547735.1_ASM154773v1_genomic.fna/dqc_result.json
[2024-01-24 11:44:35,934] [INFO] DFAST_QC completed!
[2024-01-24 11:44:35,934] [INFO] Total running time: 0h0m43s