[2023-06-05 08:00:10,804] [INFO] DFAST_QC pipeline started.
[2023-06-05 08:00:10,806] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 08:00:10,807] [INFO] DQC Reference Directory: /var/lib/cwl/stg1aaee854-d57a-4bdb-9e5e-316d1aca6dd3/dqc_reference
[2023-06-05 08:00:13,004] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 08:00:13,005] [INFO] Task started: Prodigal
[2023-06-05 08:00:13,005] [INFO] Running command: gunzip -c /var/lib/cwl/stg7ae5437a-a3c3-48f3-aae2-f1b5e1b0536f/GCA_001785855.1_ASM178585v1_genomic.fna.gz | prodigal -d GCA_001785855.1_ASM178585v1_genomic.fna/cds.fna -a GCA_001785855.1_ASM178585v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 08:00:16,135] [INFO] Task succeeded: Prodigal
[2023-06-05 08:00:16,135] [INFO] Task started: HMMsearch
[2023-06-05 08:00:16,135] [INFO] Running command: hmmsearch --tblout GCA_001785855.1_ASM178585v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1aaee854-d57a-4bdb-9e5e-316d1aca6dd3/dqc_reference/reference_markers.hmm GCA_001785855.1_ASM178585v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 08:00:16,345] [INFO] Task succeeded: HMMsearch
[2023-06-05 08:00:16,346] [INFO] Found 6/6 markers.
[2023-06-05 08:00:16,369] [INFO] Query marker FASTA was written to GCA_001785855.1_ASM178585v1_genomic.fna/markers.fasta
[2023-06-05 08:00:16,370] [INFO] Task started: Blastn
[2023-06-05 08:00:16,370] [INFO] Running command: blastn -query GCA_001785855.1_ASM178585v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1aaee854-d57a-4bdb-9e5e-316d1aca6dd3/dqc_reference/reference_markers.fasta -out GCA_001785855.1_ASM178585v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 08:00:17,422] [INFO] Task succeeded: Blastn
[2023-06-05 08:00:17,427] [INFO] Selected 10 target genomes.
[2023-06-05 08:00:17,428] [INFO] Target genome list was writen to GCA_001785855.1_ASM178585v1_genomic.fna/target_genomes.txt
[2023-06-05 08:00:17,454] [INFO] Task started: fastANI
[2023-06-05 08:00:17,454] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ae5437a-a3c3-48f3-aae2-f1b5e1b0536f/GCA_001785855.1_ASM178585v1_genomic.fna.gz --refList GCA_001785855.1_ASM178585v1_genomic.fna/target_genomes.txt --output GCA_001785855.1_ASM178585v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 08:00:23,092] [INFO] Task succeeded: fastANI
[2023-06-05 08:00:23,093] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1aaee854-d57a-4bdb-9e5e-316d1aca6dd3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 08:00:23,093] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1aaee854-d57a-4bdb-9e5e-316d1aca6dd3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 08:00:23,096] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 08:00:23,096] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 08:00:23,096] [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
--------------------------------------------------------------------------------
[2023-06-05 08:00:23,099] [INFO] DFAST Taxonomy check result was written to GCA_001785855.1_ASM178585v1_genomic.fna/tc_result.tsv
[2023-06-05 08:00:23,100] [INFO] ===== Taxonomy check completed =====
[2023-06-05 08:00:23,100] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 08:00:23,101] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1aaee854-d57a-4bdb-9e5e-316d1aca6dd3/dqc_reference/checkm_data
[2023-06-05 08:00:23,105] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 08:00:23,117] [INFO] Task started: CheckM
[2023-06-05 08:00:23,117] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_001785855.1_ASM178585v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_001785855.1_ASM178585v1_genomic.fna/checkm_input GCA_001785855.1_ASM178585v1_genomic.fna/checkm_result
[2023-06-05 08:00:40,202] [INFO] Task succeeded: CheckM
[2023-06-05 08:00:40,203] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.82%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 08:00:40,221] [INFO] ===== Completeness check finished =====
[2023-06-05 08:00:40,222] [INFO] ===== Start GTDB Search =====
[2023-06-05 08:00:40,222] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_001785855.1_ASM178585v1_genomic.fna/markers.fasta)
[2023-06-05 08:00:40,223] [INFO] Task started: Blastn
[2023-06-05 08:00:40,223] [INFO] Running command: blastn -query GCA_001785855.1_ASM178585v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1aaee854-d57a-4bdb-9e5e-316d1aca6dd3/dqc_reference/reference_markers_gtdb.fasta -out GCA_001785855.1_ASM178585v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 08:00:40,986] [INFO] Task succeeded: Blastn
[2023-06-05 08:00:40,991] [INFO] Selected 17 target genomes.
[2023-06-05 08:00:40,991] [INFO] Target genome list was writen to GCA_001785855.1_ASM178585v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 08:00:41,028] [INFO] Task started: fastANI
[2023-06-05 08:00:41,029] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ae5437a-a3c3-48f3-aae2-f1b5e1b0536f/GCA_001785855.1_ASM178585v1_genomic.fna.gz --refList GCA_001785855.1_ASM178585v1_genomic.fna/target_genomes_gtdb.txt --output GCA_001785855.1_ASM178585v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 08:00:43,850] [INFO] Task succeeded: fastANI
[2023-06-05 08:00:43,858] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 08:00:43,858] [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_001785985.1	s__UBA9973 sp001785985	77.9739	58	215	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__UBA9983_A;f__UBA9973;g__UBA9973	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001786195.1	s__UBA9973 sp001786195	77.6152	78	215	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__UBA9983_A;f__UBA9973;g__UBA9973	95.0	99.98	99.94	0.96	0.94	9	-
GCA_001786365.1	s__UBA9973 sp001786365	76.7198	50	215	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__UBA9983_A;f__UBA9973;g__UBA9973	95.0	99.77	99.69	0.93	0.93	3	-
--------------------------------------------------------------------------------
[2023-06-05 08:00:43,860] [INFO] GTDB search result was written to GCA_001785855.1_ASM178585v1_genomic.fna/result_gtdb.tsv
[2023-06-05 08:00:43,861] [INFO] ===== GTDB Search completed =====
[2023-06-05 08:00:43,863] [INFO] DFAST_QC result json was written to GCA_001785855.1_ASM178585v1_genomic.fna/dqc_result.json
[2023-06-05 08:00:43,864] [INFO] DFAST_QC completed!
[2023-06-05 08:00:43,864] [INFO] Total running time: 0h0m33s