[2023-06-19 13:34:20,678] [INFO] DFAST_QC pipeline started.
[2023-06-19 13:34:20,680] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 13:34:20,680] [INFO] DQC Reference Directory: /var/lib/cwl/stg43f8bc9f-1fcc-41a9-aee9-ed48e9f3f96e/dqc_reference
[2023-06-19 13:34:21,898] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 13:34:21,899] [INFO] Task started: Prodigal
[2023-06-19 13:34:21,899] [INFO] Running command: gunzip -c /var/lib/cwl/stgb8a58658-d80a-4eb2-9760-885dd1c91c3e/GCA_018433085.1_SV3_genomic.fna.gz | prodigal -d GCA_018433085.1_SV3_genomic.fna/cds.fna -a GCA_018433085.1_SV3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 13:34:33,101] [INFO] Task succeeded: Prodigal
[2023-06-19 13:34:33,102] [INFO] Task started: HMMsearch
[2023-06-19 13:34:33,102] [INFO] Running command: hmmsearch --tblout GCA_018433085.1_SV3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg43f8bc9f-1fcc-41a9-aee9-ed48e9f3f96e/dqc_reference/reference_markers.hmm GCA_018433085.1_SV3_genomic.fna/protein.faa > /dev/null
[2023-06-19 13:34:33,362] [INFO] Task succeeded: HMMsearch
[2023-06-19 13:34:33,364] [INFO] Found 6/6 markers.
[2023-06-19 13:34:33,400] [INFO] Query marker FASTA was written to GCA_018433085.1_SV3_genomic.fna/markers.fasta
[2023-06-19 13:34:33,400] [INFO] Task started: Blastn
[2023-06-19 13:34:33,400] [INFO] Running command: blastn -query GCA_018433085.1_SV3_genomic.fna/markers.fasta -db /var/lib/cwl/stg43f8bc9f-1fcc-41a9-aee9-ed48e9f3f96e/dqc_reference/reference_markers.fasta -out GCA_018433085.1_SV3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 13:34:34,069] [INFO] Task succeeded: Blastn
[2023-06-19 13:34:34,073] [INFO] Selected 24 target genomes.
[2023-06-19 13:34:34,074] [INFO] Target genome list was writen to GCA_018433085.1_SV3_genomic.fna/target_genomes.txt
[2023-06-19 13:34:34,075] [INFO] Task started: fastANI
[2023-06-19 13:34:34,075] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8a58658-d80a-4eb2-9760-885dd1c91c3e/GCA_018433085.1_SV3_genomic.fna.gz --refList GCA_018433085.1_SV3_genomic.fna/target_genomes.txt --output GCA_018433085.1_SV3_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 13:34:51,330] [INFO] Task succeeded: fastANI
[2023-06-19 13:34:51,330] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg43f8bc9f-1fcc-41a9-aee9-ed48e9f3f96e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 13:34:51,331] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg43f8bc9f-1fcc-41a9-aee9-ed48e9f3f96e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 13:34:51,333] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 13:34:51,333] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 13:34:51,333] [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
--------------------------------------------------------------------------------
[2023-06-19 13:34:51,336] [INFO] DFAST Taxonomy check result was written to GCA_018433085.1_SV3_genomic.fna/tc_result.tsv
[2023-06-19 13:34:51,336] [INFO] ===== Taxonomy check completed =====
[2023-06-19 13:34:51,337] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 13:34:51,337] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg43f8bc9f-1fcc-41a9-aee9-ed48e9f3f96e/dqc_reference/checkm_data
[2023-06-19 13:34:51,341] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 13:34:51,381] [INFO] Task started: CheckM
[2023-06-19 13:34:51,381] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018433085.1_SV3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018433085.1_SV3_genomic.fna/checkm_input GCA_018433085.1_SV3_genomic.fna/checkm_result
[2023-06-19 13:35:27,062] [INFO] Task succeeded: CheckM
[2023-06-19 13:35:27,063] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-19 13:35:27,086] [INFO] ===== Completeness check finished =====
[2023-06-19 13:35:27,087] [INFO] ===== Start GTDB Search =====
[2023-06-19 13:35:27,087] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018433085.1_SV3_genomic.fna/markers.fasta)
[2023-06-19 13:35:27,087] [INFO] Task started: Blastn
[2023-06-19 13:35:27,088] [INFO] Running command: blastn -query GCA_018433085.1_SV3_genomic.fna/markers.fasta -db /var/lib/cwl/stg43f8bc9f-1fcc-41a9-aee9-ed48e9f3f96e/dqc_reference/reference_markers_gtdb.fasta -out GCA_018433085.1_SV3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 13:35:28,196] [INFO] Task succeeded: Blastn
[2023-06-19 13:35:28,201] [INFO] Selected 8 target genomes.
[2023-06-19 13:35:28,202] [INFO] Target genome list was writen to GCA_018433085.1_SV3_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 13:35:28,204] [INFO] Task started: fastANI
[2023-06-19 13:35:28,205] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8a58658-d80a-4eb2-9760-885dd1c91c3e/GCA_018433085.1_SV3_genomic.fna.gz --refList GCA_018433085.1_SV3_genomic.fna/target_genomes_gtdb.txt --output GCA_018433085.1_SV3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 13:35:34,504] [INFO] Task succeeded: fastANI
[2023-06-19 13:35:34,513] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 13:35:34,513] [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_018433085.1	s__UBA1062 sp018433085	100.0	1226	1227	d__Bacteria;p__Desulfobacterota;c__Desulfomonilia;o__UBA1062;f__UBA1062;g__UBA1062	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018436855.1	s__UBA1062 sp018436855	90.7847	1010	1227	d__Bacteria;p__Desulfobacterota;c__Desulfomonilia;o__UBA1062;f__UBA1062;g__UBA1062	95.0	99.34	99.34	0.91	0.91	2	-
GCA_018433775.1	s__UBA1062 sp018433775	90.4251	1029	1227	d__Bacteria;p__Desulfobacterota;c__Desulfomonilia;o__UBA1062;f__UBA1062;g__UBA1062	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001896555.1	s__UBA1062 sp001896555	87.1194	862	1227	d__Bacteria;p__Desulfobacterota;c__Desulfomonilia;o__UBA1062;f__UBA1062;g__UBA1062	95.0	99.48	99.38	0.92	0.86	9	-
GCA_002316295.1	s__UBA1062 sp002316295	80.4485	526	1227	d__Bacteria;p__Desulfobacterota;c__Desulfomonilia;o__UBA1062;f__UBA1062;g__UBA1062	95.0	98.80	98.10	0.82	0.79	4	-
GCA_002448235.1	s__UBA1062 sp002448235	78.1478	266	1227	d__Bacteria;p__Desulfobacterota;c__Desulfomonilia;o__UBA1062;f__UBA1062;g__UBA1062	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018434685.1	s__DSAD01 sp018434685	77.1769	240	1227	d__Bacteria;p__Desulfobacterota;c__Desulfomonilia;o__UBA1062;f__UBA1062;g__DSAD01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 13:35:34,515] [INFO] GTDB search result was written to GCA_018433085.1_SV3_genomic.fna/result_gtdb.tsv
[2023-06-19 13:35:34,516] [INFO] ===== GTDB Search completed =====
[2023-06-19 13:35:34,518] [INFO] DFAST_QC result json was written to GCA_018433085.1_SV3_genomic.fna/dqc_result.json
[2023-06-19 13:35:34,519] [INFO] DFAST_QC completed!
[2023-06-19 13:35:34,519] [INFO] Total running time: 0h1m14s