[2023-06-08 17:47:33,574] [INFO] DFAST_QC pipeline started.
[2023-06-08 17:47:33,581] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 17:47:33,581] [INFO] DQC Reference Directory: /var/lib/cwl/stgdac90ad1-b2ab-4a3c-8732-1247204e2e2c/dqc_reference
[2023-06-08 17:47:35,070] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 17:47:35,071] [INFO] Task started: Prodigal
[2023-06-08 17:47:35,072] [INFO] Running command: gunzip -c /var/lib/cwl/stg2c65d2ad-deb0-45c4-ac1f-3e483aa0278d/GCA_902591485.1_AG-447-A02_genomic.fna.gz | prodigal -d GCA_902591485.1_AG-447-A02_genomic.fna/cds.fna -a GCA_902591485.1_AG-447-A02_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 17:47:37,418] [INFO] Task succeeded: Prodigal
[2023-06-08 17:47:37,419] [INFO] Task started: HMMsearch
[2023-06-08 17:47:37,419] [INFO] Running command: hmmsearch --tblout GCA_902591485.1_AG-447-A02_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdac90ad1-b2ab-4a3c-8732-1247204e2e2c/dqc_reference/reference_markers.hmm GCA_902591485.1_AG-447-A02_genomic.fna/protein.faa > /dev/null
[2023-06-08 17:47:37,677] [INFO] Task succeeded: HMMsearch
[2023-06-08 17:47:37,679] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2c65d2ad-deb0-45c4-ac1f-3e483aa0278d/GCA_902591485.1_AG-447-A02_genomic.fna.gz]
[2023-06-08 17:47:37,699] [INFO] Query marker FASTA was written to GCA_902591485.1_AG-447-A02_genomic.fna/markers.fasta
[2023-06-08 17:47:37,700] [INFO] Task started: Blastn
[2023-06-08 17:47:37,700] [INFO] Running command: blastn -query GCA_902591485.1_AG-447-A02_genomic.fna/markers.fasta -db /var/lib/cwl/stgdac90ad1-b2ab-4a3c-8732-1247204e2e2c/dqc_reference/reference_markers.fasta -out GCA_902591485.1_AG-447-A02_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 17:47:38,318] [INFO] Task succeeded: Blastn
[2023-06-08 17:47:38,322] [INFO] Selected 20 target genomes.
[2023-06-08 17:47:38,322] [INFO] Target genome list was writen to GCA_902591485.1_AG-447-A02_genomic.fna/target_genomes.txt
[2023-06-08 17:47:38,352] [INFO] Task started: fastANI
[2023-06-08 17:47:38,352] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c65d2ad-deb0-45c4-ac1f-3e483aa0278d/GCA_902591485.1_AG-447-A02_genomic.fna.gz --refList GCA_902591485.1_AG-447-A02_genomic.fna/target_genomes.txt --output GCA_902591485.1_AG-447-A02_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 17:47:44,747] [INFO] Task succeeded: fastANI
[2023-06-08 17:47:44,748] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdac90ad1-b2ab-4a3c-8732-1247204e2e2c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 17:47:44,748] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdac90ad1-b2ab-4a3c-8732-1247204e2e2c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 17:47:44,750] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 17:47:44,750] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 17:47:44,750] [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
--------------------------------------------------------------------------------
[2023-06-08 17:47:44,752] [INFO] DFAST Taxonomy check result was written to GCA_902591485.1_AG-447-A02_genomic.fna/tc_result.tsv
[2023-06-08 17:47:44,752] [INFO] ===== Taxonomy check completed =====
[2023-06-08 17:47:44,752] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 17:47:44,753] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdac90ad1-b2ab-4a3c-8732-1247204e2e2c/dqc_reference/checkm_data
[2023-06-08 17:47:44,755] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 17:47:44,782] [INFO] Task started: CheckM
[2023-06-08 17:47:44,783] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902591485.1_AG-447-A02_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902591485.1_AG-447-A02_genomic.fna/checkm_input GCA_902591485.1_AG-447-A02_genomic.fna/checkm_result
[2023-06-08 17:48:01,085] [INFO] Task succeeded: CheckM
[2023-06-08 17:48:01,086] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 17:48:01,107] [INFO] ===== Completeness check finished =====
[2023-06-08 17:48:01,108] [INFO] ===== Start GTDB Search =====
[2023-06-08 17:48:01,108] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902591485.1_AG-447-A02_genomic.fna/markers.fasta)
[2023-06-08 17:48:01,108] [INFO] Task started: Blastn
[2023-06-08 17:48:01,108] [INFO] Running command: blastn -query GCA_902591485.1_AG-447-A02_genomic.fna/markers.fasta -db /var/lib/cwl/stgdac90ad1-b2ab-4a3c-8732-1247204e2e2c/dqc_reference/reference_markers_gtdb.fasta -out GCA_902591485.1_AG-447-A02_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 17:48:02,075] [INFO] Task succeeded: Blastn
[2023-06-08 17:48:02,083] [INFO] Selected 10 target genomes.
[2023-06-08 17:48:02,083] [INFO] Target genome list was writen to GCA_902591485.1_AG-447-A02_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 17:48:02,121] [INFO] Task started: fastANI
[2023-06-08 17:48:02,121] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c65d2ad-deb0-45c4-ac1f-3e483aa0278d/GCA_902591485.1_AG-447-A02_genomic.fna.gz --refList GCA_902591485.1_AG-447-A02_genomic.fna/target_genomes_gtdb.txt --output GCA_902591485.1_AG-447-A02_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 17:48:04,921] [INFO] Task succeeded: fastANI
[2023-06-08 17:48:04,932] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 17:48:04,932] [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_902591485.1	s__AG-337-I02 sp902591485	100.0	443	447	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	97.00	97.00	0.77	0.77	2	conclusive
GCA_902595855.1	s__AG-337-I02 sp902595855	91.016	317	447	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902594815.1	s__AG-337-I02 sp902594815	89.6947	235	447	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902595425.1	s__AG-337-I02 sp902595425	88.9436	299	447	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902589095.1	s__AG-337-I02 sp902589095	88.6871	247	447	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902576125.1	s__AG-337-I02 sp902576125	83.3665	262	447	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902569865.1	s__AG-337-I02 sp902569865	81.773	195	447	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	95.93	95.93	0.69	0.69	2	-
GCA_902512325.1	s__AG-337-I02 sp902512325	81.5156	271	447	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902586695.1	s__AG-337-I02 sp902586695	79.7814	185	447	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 17:48:04,934] [INFO] GTDB search result was written to GCA_902591485.1_AG-447-A02_genomic.fna/result_gtdb.tsv
[2023-06-08 17:48:04,935] [INFO] ===== GTDB Search completed =====
[2023-06-08 17:48:04,939] [INFO] DFAST_QC result json was written to GCA_902591485.1_AG-447-A02_genomic.fna/dqc_result.json
[2023-06-08 17:48:04,939] [INFO] DFAST_QC completed!
[2023-06-08 17:48:04,939] [INFO] Total running time: 0h0m31s