[2023-06-28 04:37:03,565] [INFO] DFAST_QC pipeline started.
[2023-06-28 04:37:03,570] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 04:37:03,570] [INFO] DQC Reference Directory: /var/lib/cwl/stgc7736c63-0029-45ef-85c2-f9345542e4e5/dqc_reference
[2023-06-28 04:37:04,903] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 04:37:04,904] [INFO] Task started: Prodigal
[2023-06-28 04:37:04,904] [INFO] Running command: gunzip -c /var/lib/cwl/stgbc23c167-91f0-4104-b057-9089f4937de5/GCA_944359715.1_BRZ_CE_bin40_genomic.fna.gz | prodigal -d GCA_944359715.1_BRZ_CE_bin40_genomic.fna/cds.fna -a GCA_944359715.1_BRZ_CE_bin40_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 04:37:06,872] [INFO] Task succeeded: Prodigal
[2023-06-28 04:37:06,873] [INFO] Task started: HMMsearch
[2023-06-28 04:37:06,873] [INFO] Running command: hmmsearch --tblout GCA_944359715.1_BRZ_CE_bin40_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc7736c63-0029-45ef-85c2-f9345542e4e5/dqc_reference/reference_markers.hmm GCA_944359715.1_BRZ_CE_bin40_genomic.fna/protein.faa > /dev/null
[2023-06-28 04:37:07,088] [INFO] Task succeeded: HMMsearch
[2023-06-28 04:37:07,090] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgbc23c167-91f0-4104-b057-9089f4937de5/GCA_944359715.1_BRZ_CE_bin40_genomic.fna.gz]
[2023-06-28 04:37:07,132] [INFO] Query marker FASTA was written to GCA_944359715.1_BRZ_CE_bin40_genomic.fna/markers.fasta
[2023-06-28 04:37:07,132] [INFO] Task started: Blastn
[2023-06-28 04:37:07,132] [INFO] Running command: blastn -query GCA_944359715.1_BRZ_CE_bin40_genomic.fna/markers.fasta -db /var/lib/cwl/stgc7736c63-0029-45ef-85c2-f9345542e4e5/dqc_reference/reference_markers.fasta -out GCA_944359715.1_BRZ_CE_bin40_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 04:37:07,751] [INFO] Task succeeded: Blastn
[2023-06-28 04:37:07,755] [INFO] Selected 22 target genomes.
[2023-06-28 04:37:07,755] [INFO] Target genome list was writen to GCA_944359715.1_BRZ_CE_bin40_genomic.fna/target_genomes.txt
[2023-06-28 04:37:07,759] [INFO] Task started: fastANI
[2023-06-28 04:37:07,759] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc23c167-91f0-4104-b057-9089f4937de5/GCA_944359715.1_BRZ_CE_bin40_genomic.fna.gz --refList GCA_944359715.1_BRZ_CE_bin40_genomic.fna/target_genomes.txt --output GCA_944359715.1_BRZ_CE_bin40_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 04:37:19,564] [INFO] Task succeeded: fastANI
[2023-06-28 04:37:19,565] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc7736c63-0029-45ef-85c2-f9345542e4e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 04:37:19,566] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc7736c63-0029-45ef-85c2-f9345542e4e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 04:37:19,567] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 04:37:19,567] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 04:37:19,568] [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
--------------------------------------------------------------------------------
[2023-06-28 04:37:19,570] [INFO] DFAST Taxonomy check result was written to GCA_944359715.1_BRZ_CE_bin40_genomic.fna/tc_result.tsv
[2023-06-28 04:37:19,571] [INFO] ===== Taxonomy check completed =====
[2023-06-28 04:37:19,571] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 04:37:19,571] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc7736c63-0029-45ef-85c2-f9345542e4e5/dqc_reference/checkm_data
[2023-06-28 04:37:19,576] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 04:37:19,594] [INFO] Task started: CheckM
[2023-06-28 04:37:19,594] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944359715.1_BRZ_CE_bin40_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944359715.1_BRZ_CE_bin40_genomic.fna/checkm_input GCA_944359715.1_BRZ_CE_bin40_genomic.fna/checkm_result
[2023-06-28 04:37:34,245] [INFO] Task succeeded: CheckM
[2023-06-28 04:37:34,246] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 04:37:34,266] [INFO] ===== Completeness check finished =====
[2023-06-28 04:37:34,267] [INFO] ===== Start GTDB Search =====
[2023-06-28 04:37:34,267] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944359715.1_BRZ_CE_bin40_genomic.fna/markers.fasta)
[2023-06-28 04:37:34,267] [INFO] Task started: Blastn
[2023-06-28 04:37:34,268] [INFO] Running command: blastn -query GCA_944359715.1_BRZ_CE_bin40_genomic.fna/markers.fasta -db /var/lib/cwl/stgc7736c63-0029-45ef-85c2-f9345542e4e5/dqc_reference/reference_markers_gtdb.fasta -out GCA_944359715.1_BRZ_CE_bin40_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 04:37:35,149] [INFO] Task succeeded: Blastn
[2023-06-28 04:37:35,153] [INFO] Selected 21 target genomes.
[2023-06-28 04:37:35,154] [INFO] Target genome list was writen to GCA_944359715.1_BRZ_CE_bin40_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 04:37:35,200] [INFO] Task started: fastANI
[2023-06-28 04:37:35,200] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc23c167-91f0-4104-b057-9089f4937de5/GCA_944359715.1_BRZ_CE_bin40_genomic.fna.gz --refList GCA_944359715.1_BRZ_CE_bin40_genomic.fna/target_genomes_gtdb.txt --output GCA_944359715.1_BRZ_CE_bin40_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 04:37:40,447] [INFO] Task succeeded: fastANI
[2023-06-28 04:37:40,454] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 04:37:40,455] [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_017887885.1	s__CAG-302 sp017887885	99.5231	326	408	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-302	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900543825.1	s__CAG-302 sp900543825	77.9069	115	408	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-302	95.0	98.18	98.11	0.88	0.87	3	-
GCA_000431795.1	s__CAG-302 sp000431795	77.7883	124	408	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-302	95.0	98.56	98.47	0.90	0.88	5	-
GCA_900549325.1	s__CAG-302 sp900549325	77.4096	117	408	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-302	95.0	97.65	95.34	0.85	0.78	3	-
GCA_017409025.1	s__RUG705 sp017409025	76.2827	52	408	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG705	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905211265.1	s__HGM10818 sp905211265	76.281	58	408	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__HGM10818	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 04:37:40,457] [INFO] GTDB search result was written to GCA_944359715.1_BRZ_CE_bin40_genomic.fna/result_gtdb.tsv
[2023-06-28 04:37:40,458] [INFO] ===== GTDB Search completed =====
[2023-06-28 04:37:40,460] [INFO] DFAST_QC result json was written to GCA_944359715.1_BRZ_CE_bin40_genomic.fna/dqc_result.json
[2023-06-28 04:37:40,461] [INFO] DFAST_QC completed!
[2023-06-28 04:37:40,461] [INFO] Total running time: 0h0m37s