[2024-01-24 13:47:10,894] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:47:10,896] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:47:10,896] [INFO] DQC Reference Directory: /var/lib/cwl/stg14c389a9-e077-4b32-ba0a-d7668ce6ecf7/dqc_reference
[2024-01-24 13:47:12,120] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:47:12,121] [INFO] Task started: Prodigal
[2024-01-24 13:47:12,121] [INFO] Running command: gunzip -c /var/lib/cwl/stg3fe1f72e-795f-4bfb-bbea-b07ed6a63061/GCF_000504085.1_ASM50408v1_genomic.fna.gz | prodigal -d GCF_000504085.1_ASM50408v1_genomic.fna/cds.fna -a GCF_000504085.1_ASM50408v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:47:17,308] [INFO] Task succeeded: Prodigal
[2024-01-24 13:47:17,309] [INFO] Task started: HMMsearch
[2024-01-24 13:47:17,309] [INFO] Running command: hmmsearch --tblout GCF_000504085.1_ASM50408v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg14c389a9-e077-4b32-ba0a-d7668ce6ecf7/dqc_reference/reference_markers.hmm GCF_000504085.1_ASM50408v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:47:17,699] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:47:17,701] [INFO] Found 6/6 markers.
[2024-01-24 13:47:17,735] [INFO] Query marker FASTA was written to GCF_000504085.1_ASM50408v1_genomic.fna/markers.fasta
[2024-01-24 13:47:17,736] [INFO] Task started: Blastn
[2024-01-24 13:47:17,736] [INFO] Running command: blastn -query GCF_000504085.1_ASM50408v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg14c389a9-e077-4b32-ba0a-d7668ce6ecf7/dqc_reference/reference_markers.fasta -out GCF_000504085.1_ASM50408v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:18,321] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:18,325] [INFO] Selected 13 target genomes.
[2024-01-24 13:47:18,326] [INFO] Target genome list was writen to GCF_000504085.1_ASM50408v1_genomic.fna/target_genomes.txt
[2024-01-24 13:47:18,336] [INFO] Task started: fastANI
[2024-01-24 13:47:18,337] [INFO] Running command: fastANI --query /var/lib/cwl/stg3fe1f72e-795f-4bfb-bbea-b07ed6a63061/GCF_000504085.1_ASM50408v1_genomic.fna.gz --refList GCF_000504085.1_ASM50408v1_genomic.fna/target_genomes.txt --output GCF_000504085.1_ASM50408v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:24,254] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:24,255] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg14c389a9-e077-4b32-ba0a-d7668ce6ecf7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:24,255] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg14c389a9-e077-4b32-ba0a-d7668ce6ecf7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:24,265] [INFO] Found 3 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:47:24,265] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:47:24,265] [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
Pseudothermotoga elfii	strain=NBRC 107921	GCA_000504085.1	38322	38322	suspected-type	True	100.0	723	723	95	conclusive
Pseudothermotoga elfii	strain=DSM 9442	GCA_000621345.1	38322	38322	suspected-type	True	99.9831	718	723	95	conclusive
Thermotoga profunda	strain=AZM34c06	GCA_000828675.1	1508420	1508420	type	True	78.9028	143	723	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:47:24,267] [INFO] DFAST Taxonomy check result was written to GCF_000504085.1_ASM50408v1_genomic.fna/tc_result.tsv
[2024-01-24 13:47:24,268] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:24,268] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:24,268] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg14c389a9-e077-4b32-ba0a-d7668ce6ecf7/dqc_reference/checkm_data
[2024-01-24 13:47:24,270] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:24,294] [INFO] Task started: CheckM
[2024-01-24 13:47:24,294] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000504085.1_ASM50408v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000504085.1_ASM50408v1_genomic.fna/checkm_input GCF_000504085.1_ASM50408v1_genomic.fna/checkm_result
[2024-01-24 13:47:47,414] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:47,416] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:47,439] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:47,440] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:47,441] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000504085.1_ASM50408v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:47,441] [INFO] Task started: Blastn
[2024-01-24 13:47:47,441] [INFO] Running command: blastn -query GCF_000504085.1_ASM50408v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg14c389a9-e077-4b32-ba0a-d7668ce6ecf7/dqc_reference/reference_markers_gtdb.fasta -out GCF_000504085.1_ASM50408v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:48,329] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:48,334] [INFO] Selected 17 target genomes.
[2024-01-24 13:47:48,335] [INFO] Target genome list was writen to GCF_000504085.1_ASM50408v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:48,352] [INFO] Task started: fastANI
[2024-01-24 13:47:48,352] [INFO] Running command: fastANI --query /var/lib/cwl/stg3fe1f72e-795f-4bfb-bbea-b07ed6a63061/GCF_000504085.1_ASM50408v1_genomic.fna.gz --refList GCF_000504085.1_ASM50408v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000504085.1_ASM50408v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:55,526] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:55,532] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:55,533] [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_000504085.1	s__Pseudothermotoga_B elfii	100.0	723	723	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Thermotogales;f__DSM-5069;g__Pseudothermotoga_B	95.0	99.52	99.34	0.97	0.95	6	conclusive
GCF_000828675.1	s__Pseudothermotoga_B profunda	78.9344	142	723	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Thermotogales;f__DSM-5069;g__Pseudothermotoga_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:55,535] [INFO] GTDB search result was written to GCF_000504085.1_ASM50408v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:55,535] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:55,540] [INFO] DFAST_QC result json was written to GCF_000504085.1_ASM50408v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:55,540] [INFO] DFAST_QC completed!
[2024-01-24 13:47:55,540] [INFO] Total running time: 0h0m45s