[2023-06-28 05:38:14,886] [INFO] DFAST_QC pipeline started.
[2023-06-28 05:38:14,890] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 05:38:14,890] [INFO] DQC Reference Directory: /var/lib/cwl/stga4d74149-3c20-4abd-94e7-7c34c4beec8f/dqc_reference
[2023-06-28 05:38:16,784] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 05:38:16,786] [INFO] Task started: Prodigal
[2023-06-28 05:38:16,786] [INFO] Running command: gunzip -c /var/lib/cwl/stgfababb3e-b584-4c44-809b-8b577f81fe1d/GCA_944358355.1_BRZ_NN_bin51_genomic.fna.gz | prodigal -d GCA_944358355.1_BRZ_NN_bin51_genomic.fna/cds.fna -a GCA_944358355.1_BRZ_NN_bin51_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 05:38:18,717] [INFO] Task succeeded: Prodigal
[2023-06-28 05:38:18,717] [INFO] Task started: HMMsearch
[2023-06-28 05:38:18,718] [INFO] Running command: hmmsearch --tblout GCA_944358355.1_BRZ_NN_bin51_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga4d74149-3c20-4abd-94e7-7c34c4beec8f/dqc_reference/reference_markers.hmm GCA_944358355.1_BRZ_NN_bin51_genomic.fna/protein.faa > /dev/null
[2023-06-28 05:38:18,930] [INFO] Task succeeded: HMMsearch
[2023-06-28 05:38:18,931] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgfababb3e-b584-4c44-809b-8b577f81fe1d/GCA_944358355.1_BRZ_NN_bin51_genomic.fna.gz]
[2023-06-28 05:38:18,952] [INFO] Query marker FASTA was written to GCA_944358355.1_BRZ_NN_bin51_genomic.fna/markers.fasta
[2023-06-28 05:38:18,953] [INFO] Task started: Blastn
[2023-06-28 05:38:18,953] [INFO] Running command: blastn -query GCA_944358355.1_BRZ_NN_bin51_genomic.fna/markers.fasta -db /var/lib/cwl/stga4d74149-3c20-4abd-94e7-7c34c4beec8f/dqc_reference/reference_markers.fasta -out GCA_944358355.1_BRZ_NN_bin51_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 05:38:20,837] [INFO] Task succeeded: Blastn
[2023-06-28 05:38:20,843] [INFO] Selected 23 target genomes.
[2023-06-28 05:38:20,843] [INFO] Target genome list was writen to GCA_944358355.1_BRZ_NN_bin51_genomic.fna/target_genomes.txt
[2023-06-28 05:38:20,845] [INFO] Task started: fastANI
[2023-06-28 05:38:20,845] [INFO] Running command: fastANI --query /var/lib/cwl/stgfababb3e-b584-4c44-809b-8b577f81fe1d/GCA_944358355.1_BRZ_NN_bin51_genomic.fna.gz --refList GCA_944358355.1_BRZ_NN_bin51_genomic.fna/target_genomes.txt --output GCA_944358355.1_BRZ_NN_bin51_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 05:38:31,949] [INFO] Task succeeded: fastANI
[2023-06-28 05:38:31,950] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga4d74149-3c20-4abd-94e7-7c34c4beec8f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 05:38:31,950] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga4d74149-3c20-4abd-94e7-7c34c4beec8f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 05:38:31,952] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 05:38:31,952] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 05:38:31,953] [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 05:38:31,955] [INFO] DFAST Taxonomy check result was written to GCA_944358355.1_BRZ_NN_bin51_genomic.fna/tc_result.tsv
[2023-06-28 05:38:31,956] [INFO] ===== Taxonomy check completed =====
[2023-06-28 05:38:31,956] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 05:38:31,956] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga4d74149-3c20-4abd-94e7-7c34c4beec8f/dqc_reference/checkm_data
[2023-06-28 05:38:31,961] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 05:38:31,981] [INFO] Task started: CheckM
[2023-06-28 05:38:31,981] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944358355.1_BRZ_NN_bin51_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944358355.1_BRZ_NN_bin51_genomic.fna/checkm_input GCA_944358355.1_BRZ_NN_bin51_genomic.fna/checkm_result
[2023-06-28 05:38:46,193] [INFO] Task succeeded: CheckM
[2023-06-28 05:38:46,194] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 05:38:46,215] [INFO] ===== Completeness check finished =====
[2023-06-28 05:38:46,215] [INFO] ===== Start GTDB Search =====
[2023-06-28 05:38:46,215] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944358355.1_BRZ_NN_bin51_genomic.fna/markers.fasta)
[2023-06-28 05:38:46,216] [INFO] Task started: Blastn
[2023-06-28 05:38:46,216] [INFO] Running command: blastn -query GCA_944358355.1_BRZ_NN_bin51_genomic.fna/markers.fasta -db /var/lib/cwl/stga4d74149-3c20-4abd-94e7-7c34c4beec8f/dqc_reference/reference_markers_gtdb.fasta -out GCA_944358355.1_BRZ_NN_bin51_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 05:38:47,057] [INFO] Task succeeded: Blastn
[2023-06-28 05:38:47,063] [INFO] Selected 15 target genomes.
[2023-06-28 05:38:47,063] [INFO] Target genome list was writen to GCA_944358355.1_BRZ_NN_bin51_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 05:38:47,069] [INFO] Task started: fastANI
[2023-06-28 05:38:47,070] [INFO] Running command: fastANI --query /var/lib/cwl/stgfababb3e-b584-4c44-809b-8b577f81fe1d/GCA_944358355.1_BRZ_NN_bin51_genomic.fna.gz --refList GCA_944358355.1_BRZ_NN_bin51_genomic.fna/target_genomes_gtdb.txt --output GCA_944358355.1_BRZ_NN_bin51_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 05:38:50,980] [INFO] Task succeeded: fastANI
[2023-06-28 05:38:50,999] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 05:38:50,999] [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_018712385.1	s__Onthousia excrementipullorum	86.7459	289	447	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Onthousia	95.0	97.70	95.09	0.85	0.78	4	-
GCA_018715925.1	s__Onthousia faecipullorum	86.1568	288	447	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Onthousia	95.0	99.48	99.48	0.89	0.89	2	-
GCA_900760545.1	s__Onthousia sp900760545	84.2535	237	447	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Onthousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018711135.1	s__Onthousia faecavium	79.6102	205	447	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Onthousia	95.0	99.89	99.89	0.91	0.91	2	-
GCA_904420615.1	s__Onthousia sp904420615	77.4831	108	447	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Onthousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014846175.1	s__Onthousia sp014846175	77.3216	101	447	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Onthousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900554315.1	s__Faecimonas sp900554315	77.2105	53	447	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Faecimonas	95.0	99.99	99.97	0.89	0.78	3	-
GCA_017886705.1	s__Faecimonas sp017886705	76.9131	72	447	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Faecimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902783435.1	s__UBA3789 sp902783435	76.0538	54	447	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002369415.1	s__UBA3789 sp002369415	76.0217	66	447	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 05:38:51,001] [INFO] GTDB search result was written to GCA_944358355.1_BRZ_NN_bin51_genomic.fna/result_gtdb.tsv
[2023-06-28 05:38:51,002] [INFO] ===== GTDB Search completed =====
[2023-06-28 05:38:51,004] [INFO] DFAST_QC result json was written to GCA_944358355.1_BRZ_NN_bin51_genomic.fna/dqc_result.json
[2023-06-28 05:38:51,004] [INFO] DFAST_QC completed!
[2023-06-28 05:38:51,004] [INFO] Total running time: 0h0m36s