[2023-07-01 02:28:48,568] [INFO] DFAST_QC pipeline started.
[2023-07-01 02:28:48,570] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 02:28:48,571] [INFO] DQC Reference Directory: /var/lib/cwl/stg56706757-468f-45d6-8c86-fbe4d141dc05/dqc_reference
[2023-07-01 02:28:49,795] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 02:28:49,796] [INFO] Task started: Prodigal
[2023-07-01 02:28:49,796] [INFO] Running command: gunzip -c /var/lib/cwl/stg15c470f4-cd1d-4801-8c44-2054fae8b728/GCA_900762765.1_SRS149181_43_genomic.fna.gz | prodigal -d GCA_900762765.1_SRS149181_43_genomic.fna/cds.fna -a GCA_900762765.1_SRS149181_43_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 02:28:53,110] [INFO] Task succeeded: Prodigal
[2023-07-01 02:28:53,110] [INFO] Task started: HMMsearch
[2023-07-01 02:28:53,111] [INFO] Running command: hmmsearch --tblout GCA_900762765.1_SRS149181_43_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg56706757-468f-45d6-8c86-fbe4d141dc05/dqc_reference/reference_markers.hmm GCA_900762765.1_SRS149181_43_genomic.fna/protein.faa > /dev/null
[2023-07-01 02:28:53,346] [INFO] Task succeeded: HMMsearch
[2023-07-01 02:28:53,348] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg15c470f4-cd1d-4801-8c44-2054fae8b728/GCA_900762765.1_SRS149181_43_genomic.fna.gz]
[2023-07-01 02:28:53,371] [INFO] Query marker FASTA was written to GCA_900762765.1_SRS149181_43_genomic.fna/markers.fasta
[2023-07-01 02:28:53,372] [INFO] Task started: Blastn
[2023-07-01 02:28:53,372] [INFO] Running command: blastn -query GCA_900762765.1_SRS149181_43_genomic.fna/markers.fasta -db /var/lib/cwl/stg56706757-468f-45d6-8c86-fbe4d141dc05/dqc_reference/reference_markers.fasta -out GCA_900762765.1_SRS149181_43_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 02:28:54,020] [INFO] Task succeeded: Blastn
[2023-07-01 02:28:54,026] [INFO] Selected 31 target genomes.
[2023-07-01 02:28:54,027] [INFO] Target genome list was writen to GCA_900762765.1_SRS149181_43_genomic.fna/target_genomes.txt
[2023-07-01 02:28:54,049] [INFO] Task started: fastANI
[2023-07-01 02:28:54,050] [INFO] Running command: fastANI --query /var/lib/cwl/stg15c470f4-cd1d-4801-8c44-2054fae8b728/GCA_900762765.1_SRS149181_43_genomic.fna.gz --refList GCA_900762765.1_SRS149181_43_genomic.fna/target_genomes.txt --output GCA_900762765.1_SRS149181_43_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 02:29:12,570] [INFO] Task succeeded: fastANI
[2023-07-01 02:29:12,571] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg56706757-468f-45d6-8c86-fbe4d141dc05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 02:29:12,571] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg56706757-468f-45d6-8c86-fbe4d141dc05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 02:29:12,574] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 02:29:12,574] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-07-01 02:29:12,574] [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
--------------------------------------------------------------------------------
[2023-07-01 02:29:12,577] [INFO] DFAST Taxonomy check result was written to GCA_900762765.1_SRS149181_43_genomic.fna/tc_result.tsv
[2023-07-01 02:29:12,577] [INFO] ===== Taxonomy check completed =====
[2023-07-01 02:29:12,578] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 02:29:12,578] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg56706757-468f-45d6-8c86-fbe4d141dc05/dqc_reference/checkm_data
[2023-07-01 02:29:12,582] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 02:29:12,602] [INFO] Task started: CheckM
[2023-07-01 02:29:12,603] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_900762765.1_SRS149181_43_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_900762765.1_SRS149181_43_genomic.fna/checkm_input GCA_900762765.1_SRS149181_43_genomic.fna/checkm_result
[2023-07-01 02:29:30,694] [INFO] Task succeeded: CheckM
[2023-07-01 02:29:30,695] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.89%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 02:29:30,716] [INFO] ===== Completeness check finished =====
[2023-07-01 02:29:30,717] [INFO] ===== Start GTDB Search =====
[2023-07-01 02:29:30,717] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_900762765.1_SRS149181_43_genomic.fna/markers.fasta)
[2023-07-01 02:29:30,718] [INFO] Task started: Blastn
[2023-07-01 02:29:30,718] [INFO] Running command: blastn -query GCA_900762765.1_SRS149181_43_genomic.fna/markers.fasta -db /var/lib/cwl/stg56706757-468f-45d6-8c86-fbe4d141dc05/dqc_reference/reference_markers_gtdb.fasta -out GCA_900762765.1_SRS149181_43_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 02:29:31,767] [INFO] Task succeeded: Blastn
[2023-07-01 02:29:31,773] [INFO] Selected 19 target genomes.
[2023-07-01 02:29:31,773] [INFO] Target genome list was writen to GCA_900762765.1_SRS149181_43_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 02:29:31,781] [INFO] Task started: fastANI
[2023-07-01 02:29:31,782] [INFO] Running command: fastANI --query /var/lib/cwl/stg15c470f4-cd1d-4801-8c44-2054fae8b728/GCA_900762765.1_SRS149181_43_genomic.fna.gz --refList GCA_900762765.1_SRS149181_43_genomic.fna/target_genomes_gtdb.txt --output GCA_900762765.1_SRS149181_43_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 02:29:36,743] [INFO] Task succeeded: fastANI
[2023-07-01 02:29:36,748] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-07-01 02:29:36,748] [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_900551585.1	s__CAJLXD01 sp900551585	97.4833	170	206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__CAJLXD01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_905210515.1	s__CAJLXD01 sp905210515	78.0965	67	206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__CAJLXD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001917125.1	s__Scatocola faecipullorum	76.9874	57	206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__Scatocola	95.0	98.98	98.59	0.91	0.85	10	-
GCA_910577205.1	s__Scatocola sp910577205	76.8403	56	206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__Scatocola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-07-01 02:29:36,750] [INFO] GTDB search result was written to GCA_900762765.1_SRS149181_43_genomic.fna/result_gtdb.tsv
[2023-07-01 02:29:36,750] [INFO] ===== GTDB Search completed =====
[2023-07-01 02:29:36,752] [INFO] DFAST_QC result json was written to GCA_900762765.1_SRS149181_43_genomic.fna/dqc_result.json
[2023-07-01 02:29:36,753] [INFO] DFAST_QC completed!
[2023-07-01 02:29:36,753] [INFO] Total running time: 0h0m48s