[2023-06-05 09:46:12,177] [INFO] DFAST_QC pipeline started.
[2023-06-05 09:46:12,180] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 09:46:12,180] [INFO] DQC Reference Directory: /var/lib/cwl/stg60ee93c3-c312-4ab9-99e3-f9e68cf2eeef/dqc_reference
[2023-06-05 09:46:13,392] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 09:46:13,393] [INFO] Task started: Prodigal
[2023-06-05 09:46:13,393] [INFO] Running command: gunzip -c /var/lib/cwl/stg25daeb9f-2b49-4e25-a5a0-6ed585ca7b4d/GCA_902628335.1_AH-324-A07_genomic.fna.gz | prodigal -d GCA_902628335.1_AH-324-A07_genomic.fna/cds.fna -a GCA_902628335.1_AH-324-A07_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 09:46:15,090] [INFO] Task succeeded: Prodigal
[2023-06-05 09:46:15,091] [INFO] Task started: HMMsearch
[2023-06-05 09:46:15,091] [INFO] Running command: hmmsearch --tblout GCA_902628335.1_AH-324-A07_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg60ee93c3-c312-4ab9-99e3-f9e68cf2eeef/dqc_reference/reference_markers.hmm GCA_902628335.1_AH-324-A07_genomic.fna/protein.faa > /dev/null
[2023-06-05 09:46:15,336] [INFO] Task succeeded: HMMsearch
[2023-06-05 09:46:15,337] [INFO] Found 6/6 markers.
[2023-06-05 09:46:15,353] [INFO] Query marker FASTA was written to GCA_902628335.1_AH-324-A07_genomic.fna/markers.fasta
[2023-06-05 09:46:15,353] [INFO] Task started: Blastn
[2023-06-05 09:46:15,353] [INFO] Running command: blastn -query GCA_902628335.1_AH-324-A07_genomic.fna/markers.fasta -db /var/lib/cwl/stg60ee93c3-c312-4ab9-99e3-f9e68cf2eeef/dqc_reference/reference_markers.fasta -out GCA_902628335.1_AH-324-A07_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 09:46:15,949] [INFO] Task succeeded: Blastn
[2023-06-05 09:46:15,954] [INFO] Selected 21 target genomes.
[2023-06-05 09:46:15,955] [INFO] Target genome list was writen to GCA_902628335.1_AH-324-A07_genomic.fna/target_genomes.txt
[2023-06-05 09:46:15,958] [INFO] Task started: fastANI
[2023-06-05 09:46:15,958] [INFO] Running command: fastANI --query /var/lib/cwl/stg25daeb9f-2b49-4e25-a5a0-6ed585ca7b4d/GCA_902628335.1_AH-324-A07_genomic.fna.gz --refList GCA_902628335.1_AH-324-A07_genomic.fna/target_genomes.txt --output GCA_902628335.1_AH-324-A07_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 09:46:25,109] [INFO] Task succeeded: fastANI
[2023-06-05 09:46:25,110] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg60ee93c3-c312-4ab9-99e3-f9e68cf2eeef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 09:46:25,110] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg60ee93c3-c312-4ab9-99e3-f9e68cf2eeef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 09:46:25,112] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 09:46:25,113] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 09:46:25,113] [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 09:46:25,115] [INFO] DFAST Taxonomy check result was written to GCA_902628335.1_AH-324-A07_genomic.fna/tc_result.tsv
[2023-06-05 09:46:25,116] [INFO] ===== Taxonomy check completed =====
[2023-06-05 09:46:25,116] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 09:46:25,117] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg60ee93c3-c312-4ab9-99e3-f9e68cf2eeef/dqc_reference/checkm_data
[2023-06-05 09:46:25,121] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 09:46:25,136] [INFO] Task started: CheckM
[2023-06-05 09:46:25,137] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902628335.1_AH-324-A07_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902628335.1_AH-324-A07_genomic.fna/checkm_input GCA_902628335.1_AH-324-A07_genomic.fna/checkm_result
[2023-06-05 09:46:38,799] [INFO] Task succeeded: CheckM
[2023-06-05 09:46:38,800] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 09:46:38,818] [INFO] ===== Completeness check finished =====
[2023-06-05 09:46:38,818] [INFO] ===== Start GTDB Search =====
[2023-06-05 09:46:38,819] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902628335.1_AH-324-A07_genomic.fna/markers.fasta)
[2023-06-05 09:46:38,819] [INFO] Task started: Blastn
[2023-06-05 09:46:38,819] [INFO] Running command: blastn -query GCA_902628335.1_AH-324-A07_genomic.fna/markers.fasta -db /var/lib/cwl/stg60ee93c3-c312-4ab9-99e3-f9e68cf2eeef/dqc_reference/reference_markers_gtdb.fasta -out GCA_902628335.1_AH-324-A07_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 09:46:39,746] [INFO] Task succeeded: Blastn
[2023-06-05 09:46:39,751] [INFO] Selected 22 target genomes.
[2023-06-05 09:46:39,751] [INFO] Target genome list was writen to GCA_902628335.1_AH-324-A07_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 09:46:39,822] [INFO] Task started: fastANI
[2023-06-05 09:46:39,823] [INFO] Running command: fastANI --query /var/lib/cwl/stg25daeb9f-2b49-4e25-a5a0-6ed585ca7b4d/GCA_902628335.1_AH-324-A07_genomic.fna.gz --refList GCA_902628335.1_AH-324-A07_genomic.fna/target_genomes_gtdb.txt --output GCA_902628335.1_AH-324-A07_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 09:46:43,743] [INFO] Task succeeded: fastANI
[2023-06-05 09:46:43,749] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 09:46:43,750] [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_902628335.1	s__GCA-2720195 sp902628335	100.0	293	293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-002705445;f__GCA-002716945;g__GCA-2720195	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902632305.1	s__GCA-2720195 sp902632305	80.1731	77	293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-002705445;f__GCA-002716945;g__GCA-2720195	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 09:46:43,752] [INFO] GTDB search result was written to GCA_902628335.1_AH-324-A07_genomic.fna/result_gtdb.tsv
[2023-06-05 09:46:43,752] [INFO] ===== GTDB Search completed =====
[2023-06-05 09:46:43,755] [INFO] DFAST_QC result json was written to GCA_902628335.1_AH-324-A07_genomic.fna/dqc_result.json
[2023-06-05 09:46:43,755] [INFO] DFAST_QC completed!
[2023-06-05 09:46:43,755] [INFO] Total running time: 0h0m32s