[2023-06-29 04:17:38,831] [INFO] DFAST_QC pipeline started.
[2023-06-29 04:17:38,843] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 04:17:38,844] [INFO] DQC Reference Directory: /var/lib/cwl/stgbcf2e827-e7eb-40d3-8020-4ab05b985fa7/dqc_reference
[2023-06-29 04:17:40,497] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 04:17:40,498] [INFO] Task started: Prodigal
[2023-06-29 04:17:40,498] [INFO] Running command: gunzip -c /var/lib/cwl/stg8e53e830-226d-40de-98fc-80364da2c9ad/GCA_012520855.1_ASM1252085v1_genomic.fna.gz | prodigal -d GCA_012520855.1_ASM1252085v1_genomic.fna/cds.fna -a GCA_012520855.1_ASM1252085v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 04:17:45,025] [INFO] Task succeeded: Prodigal
[2023-06-29 04:17:45,026] [INFO] Task started: HMMsearch
[2023-06-29 04:17:45,026] [INFO] Running command: hmmsearch --tblout GCA_012520855.1_ASM1252085v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbcf2e827-e7eb-40d3-8020-4ab05b985fa7/dqc_reference/reference_markers.hmm GCA_012520855.1_ASM1252085v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 04:17:45,318] [INFO] Task succeeded: HMMsearch
[2023-06-29 04:17:45,319] [INFO] Found 6/6 markers.
[2023-06-29 04:17:45,350] [INFO] Query marker FASTA was written to GCA_012520855.1_ASM1252085v1_genomic.fna/markers.fasta
[2023-06-29 04:17:45,350] [INFO] Task started: Blastn
[2023-06-29 04:17:45,350] [INFO] Running command: blastn -query GCA_012520855.1_ASM1252085v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbcf2e827-e7eb-40d3-8020-4ab05b985fa7/dqc_reference/reference_markers.fasta -out GCA_012520855.1_ASM1252085v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 04:17:45,987] [INFO] Task succeeded: Blastn
[2023-06-29 04:17:45,992] [INFO] Selected 23 target genomes.
[2023-06-29 04:17:45,992] [INFO] Target genome list was writen to GCA_012520855.1_ASM1252085v1_genomic.fna/target_genomes.txt
[2023-06-29 04:17:45,996] [INFO] Task started: fastANI
[2023-06-29 04:17:45,997] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e53e830-226d-40de-98fc-80364da2c9ad/GCA_012520855.1_ASM1252085v1_genomic.fna.gz --refList GCA_012520855.1_ASM1252085v1_genomic.fna/target_genomes.txt --output GCA_012520855.1_ASM1252085v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 04:17:59,014] [INFO] Task succeeded: fastANI
[2023-06-29 04:17:59,015] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbcf2e827-e7eb-40d3-8020-4ab05b985fa7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 04:17:59,015] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbcf2e827-e7eb-40d3-8020-4ab05b985fa7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 04:17:59,017] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 04:17:59,017] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 04:17:59,017] [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
--------------------------------------------------------------------------------
[2023-06-29 04:17:59,024] [INFO] DFAST Taxonomy check result was written to GCA_012520855.1_ASM1252085v1_genomic.fna/tc_result.tsv
[2023-06-29 04:17:59,026] [INFO] ===== Taxonomy check completed =====
[2023-06-29 04:17:59,027] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 04:17:59,027] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbcf2e827-e7eb-40d3-8020-4ab05b985fa7/dqc_reference/checkm_data
[2023-06-29 04:17:59,030] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 04:17:59,062] [INFO] Task started: CheckM
[2023-06-29 04:17:59,062] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_012520855.1_ASM1252085v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_012520855.1_ASM1252085v1_genomic.fna/checkm_input GCA_012520855.1_ASM1252085v1_genomic.fna/checkm_result
[2023-06-29 04:18:20,626] [INFO] Task succeeded: CheckM
[2023-06-29 04:18:20,628] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 04:18:20,653] [INFO] ===== Completeness check finished =====
[2023-06-29 04:18:20,654] [INFO] ===== Start GTDB Search =====
[2023-06-29 04:18:20,654] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_012520855.1_ASM1252085v1_genomic.fna/markers.fasta)
[2023-06-29 04:18:20,654] [INFO] Task started: Blastn
[2023-06-29 04:18:20,655] [INFO] Running command: blastn -query GCA_012520855.1_ASM1252085v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbcf2e827-e7eb-40d3-8020-4ab05b985fa7/dqc_reference/reference_markers_gtdb.fasta -out GCA_012520855.1_ASM1252085v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 04:18:21,629] [INFO] Task succeeded: Blastn
[2023-06-29 04:18:21,634] [INFO] Selected 18 target genomes.
[2023-06-29 04:18:21,634] [INFO] Target genome list was writen to GCA_012520855.1_ASM1252085v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 04:18:21,642] [INFO] Task started: fastANI
[2023-06-29 04:18:21,642] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e53e830-226d-40de-98fc-80364da2c9ad/GCA_012520855.1_ASM1252085v1_genomic.fna.gz --refList GCA_012520855.1_ASM1252085v1_genomic.fna/target_genomes_gtdb.txt --output GCA_012520855.1_ASM1252085v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 04:18:29,716] [INFO] Task succeeded: fastANI
[2023-06-29 04:18:29,726] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 04:18:29,727] [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
GCA_012520855.1	s__DTU059 sp012520855	100.0	625	635	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__DSM-8532;g__DTU059	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_012840245.1	s__DTU059 sp012840245	81.1609	455	635	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__DSM-8532;g__DTU059	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012842645.1	s__DTU059 sp012842645	77.361	111	635	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__DSM-8532;g__DTU059	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003535195.1	s__DTU059 sp003535195	76.8655	52	635	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__DSM-8532;g__DTU059	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012520615.1	s__DTU059 sp012520615	76.8243	134	635	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__DSM-8532;g__DTU059	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002376415.1	s__DTU059 sp002376415	76.4267	54	635	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__DSM-8532;g__DTU059	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 04:18:29,729] [INFO] GTDB search result was written to GCA_012520855.1_ASM1252085v1_genomic.fna/result_gtdb.tsv
[2023-06-29 04:18:29,729] [INFO] ===== GTDB Search completed =====
[2023-06-29 04:18:29,732] [INFO] DFAST_QC result json was written to GCA_012520855.1_ASM1252085v1_genomic.fna/dqc_result.json
[2023-06-29 04:18:29,733] [INFO] DFAST_QC completed!
[2023-06-29 04:18:29,733] [INFO] Total running time: 0h0m51s