[2023-06-19 11:45:58,641] [INFO] DFAST_QC pipeline started.
[2023-06-19 11:45:58,646] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 11:45:58,647] [INFO] DQC Reference Directory: /var/lib/cwl/stg8792e394-3c95-486c-a8bd-69ee0e53f70c/dqc_reference
[2023-06-19 11:46:00,062] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 11:46:00,063] [INFO] Task started: Prodigal
[2023-06-19 11:46:00,063] [INFO] Running command: gunzip -c /var/lib/cwl/stg9f3dd5d9-fb49-4894-a3de-9c212133e146/GCA_013619045.1_ASM1361904v1_genomic.fna.gz | prodigal -d GCA_013619045.1_ASM1361904v1_genomic.fna/cds.fna -a GCA_013619045.1_ASM1361904v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 11:46:05,946] [INFO] Task succeeded: Prodigal
[2023-06-19 11:46:05,946] [INFO] Task started: HMMsearch
[2023-06-19 11:46:05,946] [INFO] Running command: hmmsearch --tblout GCA_013619045.1_ASM1361904v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8792e394-3c95-486c-a8bd-69ee0e53f70c/dqc_reference/reference_markers.hmm GCA_013619045.1_ASM1361904v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 11:46:06,155] [INFO] Task succeeded: HMMsearch
[2023-06-19 11:46:06,156] [INFO] Found 6/6 markers.
[2023-06-19 11:46:06,189] [INFO] Query marker FASTA was written to GCA_013619045.1_ASM1361904v1_genomic.fna/markers.fasta
[2023-06-19 11:46:06,190] [INFO] Task started: Blastn
[2023-06-19 11:46:06,190] [INFO] Running command: blastn -query GCA_013619045.1_ASM1361904v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8792e394-3c95-486c-a8bd-69ee0e53f70c/dqc_reference/reference_markers.fasta -out GCA_013619045.1_ASM1361904v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 11:46:06,761] [INFO] Task succeeded: Blastn
[2023-06-19 11:46:06,764] [INFO] Selected 20 target genomes.
[2023-06-19 11:46:06,765] [INFO] Target genome list was writen to GCA_013619045.1_ASM1361904v1_genomic.fna/target_genomes.txt
[2023-06-19 11:46:06,767] [INFO] Task started: fastANI
[2023-06-19 11:46:06,767] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f3dd5d9-fb49-4894-a3de-9c212133e146/GCA_013619045.1_ASM1361904v1_genomic.fna.gz --refList GCA_013619045.1_ASM1361904v1_genomic.fna/target_genomes.txt --output GCA_013619045.1_ASM1361904v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 11:46:18,523] [INFO] Task succeeded: fastANI
[2023-06-19 11:46:18,523] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8792e394-3c95-486c-a8bd-69ee0e53f70c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 11:46:18,524] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8792e394-3c95-486c-a8bd-69ee0e53f70c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 11:46:18,525] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 11:46:18,525] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 11:46:18,525] [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
--------------------------------------------------------------------------------
[2023-06-19 11:46:18,526] [INFO] DFAST Taxonomy check result was written to GCA_013619045.1_ASM1361904v1_genomic.fna/tc_result.tsv
[2023-06-19 11:46:18,527] [INFO] ===== Taxonomy check completed =====
[2023-06-19 11:46:18,527] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 11:46:18,527] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8792e394-3c95-486c-a8bd-69ee0e53f70c/dqc_reference/checkm_data
[2023-06-19 11:46:18,529] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 11:46:18,561] [INFO] Task started: CheckM
[2023-06-19 11:46:18,561] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013619045.1_ASM1361904v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013619045.1_ASM1361904v1_genomic.fna/checkm_input GCA_013619045.1_ASM1361904v1_genomic.fna/checkm_result
[2023-06-19 11:46:40,962] [INFO] Task succeeded: CheckM
[2023-06-19 11:46:40,963] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.04%
Contamintation: 1.98%
Strain heterogeneity: 40.00%
--------------------------------------------------------------------------------
[2023-06-19 11:46:40,979] [INFO] ===== Completeness check finished =====
[2023-06-19 11:46:40,979] [INFO] ===== Start GTDB Search =====
[2023-06-19 11:46:40,980] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013619045.1_ASM1361904v1_genomic.fna/markers.fasta)
[2023-06-19 11:46:40,981] [INFO] Task started: Blastn
[2023-06-19 11:46:40,981] [INFO] Running command: blastn -query GCA_013619045.1_ASM1361904v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8792e394-3c95-486c-a8bd-69ee0e53f70c/dqc_reference/reference_markers_gtdb.fasta -out GCA_013619045.1_ASM1361904v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 11:46:41,968] [INFO] Task succeeded: Blastn
[2023-06-19 11:46:41,970] [INFO] Selected 14 target genomes.
[2023-06-19 11:46:41,970] [INFO] Target genome list was writen to GCA_013619045.1_ASM1361904v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 11:46:41,975] [INFO] Task started: fastANI
[2023-06-19 11:46:41,975] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f3dd5d9-fb49-4894-a3de-9c212133e146/GCA_013619045.1_ASM1361904v1_genomic.fna.gz --refList GCA_013619045.1_ASM1361904v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013619045.1_ASM1361904v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 11:46:49,913] [INFO] Task succeeded: fastANI
[2023-06-19 11:46:49,919] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 11:46:49,919] [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_012974475.1	s__JAAXQD01 sp012974475	98.7472	443	547	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__UBA11574;g__JAAXQD01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002868985.1	s__UBA11574 sp002868985	79.2983	208	547	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__UBA11574;g__UBA11574	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003486165.1	s__UBA11574 sp003486165	78.9132	164	547	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__UBA11574;g__UBA11574	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004193595.1	s__S5133MH16 sp004193595	77.9922	195	547	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__UBA11574;g__S5133MH16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014383215.1	s__Desulfatibia_A vada	77.4528	94	547	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__UBA11574;g__Desulfatibia_A	95.0	99.39	99.39	0.84	0.84	2	-
GCA_001751005.1	s__S5133MH16 sp001751005	77.4469	142	547	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__UBA11574;g__S5133MH16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013203195.1	s__Desulfatibia_A sp013203195	77.3188	70	547	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__UBA11574;g__Desulfatibia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014382665.1	s__Desulfatibia profunda	76.4595	82	547	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__UBA11574;g__Desulfatibia	95.0	99.67	99.67	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2023-06-19 11:46:49,920] [INFO] GTDB search result was written to GCA_013619045.1_ASM1361904v1_genomic.fna/result_gtdb.tsv
[2023-06-19 11:46:49,921] [INFO] ===== GTDB Search completed =====
[2023-06-19 11:46:49,923] [INFO] DFAST_QC result json was written to GCA_013619045.1_ASM1361904v1_genomic.fna/dqc_result.json
[2023-06-19 11:46:49,923] [INFO] DFAST_QC completed!
[2023-06-19 11:46:49,923] [INFO] Total running time: 0h0m51s