[2023-06-04 19:38:15,806] [INFO] DFAST_QC pipeline started.
[2023-06-04 19:38:15,808] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 19:38:15,808] [INFO] DQC Reference Directory: /var/lib/cwl/stg929cfd11-754e-4227-87d8-aae89e4afc02/dqc_reference
[2023-06-04 19:38:17,028] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 19:38:17,029] [INFO] Task started: Prodigal
[2023-06-04 19:38:17,029] [INFO] Running command: gunzip -c /var/lib/cwl/stg8d96b15f-a4ee-4f3d-9d91-773e65ffcd3d/GCA_902628165.1_AH-321-O19_genomic.fna.gz | prodigal -d GCA_902628165.1_AH-321-O19_genomic.fna/cds.fna -a GCA_902628165.1_AH-321-O19_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 19:38:17,787] [INFO] Task succeeded: Prodigal
[2023-06-04 19:38:17,788] [INFO] Task started: HMMsearch
[2023-06-04 19:38:17,788] [INFO] Running command: hmmsearch --tblout GCA_902628165.1_AH-321-O19_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg929cfd11-754e-4227-87d8-aae89e4afc02/dqc_reference/reference_markers.hmm GCA_902628165.1_AH-321-O19_genomic.fna/protein.faa > /dev/null
[2023-06-04 19:38:17,947] [INFO] Task succeeded: HMMsearch
[2023-06-04 19:38:17,949] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg8d96b15f-a4ee-4f3d-9d91-773e65ffcd3d/GCA_902628165.1_AH-321-O19_genomic.fna.gz]
[2023-06-04 19:38:17,962] [INFO] Query marker FASTA was written to GCA_902628165.1_AH-321-O19_genomic.fna/markers.fasta
[2023-06-04 19:38:17,963] [INFO] Task started: Blastn
[2023-06-04 19:38:17,963] [INFO] Running command: blastn -query GCA_902628165.1_AH-321-O19_genomic.fna/markers.fasta -db /var/lib/cwl/stg929cfd11-754e-4227-87d8-aae89e4afc02/dqc_reference/reference_markers.fasta -out GCA_902628165.1_AH-321-O19_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 19:38:18,469] [INFO] Task succeeded: Blastn
[2023-06-04 19:38:18,474] [INFO] Selected 2 target genomes.
[2023-06-04 19:38:18,475] [INFO] Target genome list was writen to GCA_902628165.1_AH-321-O19_genomic.fna/target_genomes.txt
[2023-06-04 19:38:18,476] [INFO] Task started: fastANI
[2023-06-04 19:38:18,476] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d96b15f-a4ee-4f3d-9d91-773e65ffcd3d/GCA_902628165.1_AH-321-O19_genomic.fna.gz --refList GCA_902628165.1_AH-321-O19_genomic.fna/target_genomes.txt --output GCA_902628165.1_AH-321-O19_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 19:38:19,804] [INFO] Task succeeded: fastANI
[2023-06-04 19:38:19,804] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg929cfd11-754e-4227-87d8-aae89e4afc02/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 19:38:19,805] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg929cfd11-754e-4227-87d8-aae89e4afc02/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 19:38:19,807] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 19:38:19,807] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-04 19:38:19,807] [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
--------------------------------------------------------------------------------
[2023-06-04 19:38:19,809] [INFO] DFAST Taxonomy check result was written to GCA_902628165.1_AH-321-O19_genomic.fna/tc_result.tsv
[2023-06-04 19:38:19,810] [INFO] ===== Taxonomy check completed =====
[2023-06-04 19:38:19,810] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 19:38:19,811] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg929cfd11-754e-4227-87d8-aae89e4afc02/dqc_reference/checkm_data
[2023-06-04 19:38:19,815] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 19:38:19,838] [INFO] Task started: CheckM
[2023-06-04 19:38:19,838] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902628165.1_AH-321-O19_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902628165.1_AH-321-O19_genomic.fna/checkm_input GCA_902628165.1_AH-321-O19_genomic.fna/checkm_result
[2023-06-04 19:38:30,869] [INFO] Task succeeded: CheckM
[2023-06-04 19:38:30,871] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 16.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 19:38:30,890] [INFO] ===== Completeness check finished =====
[2023-06-04 19:38:30,891] [INFO] ===== Start GTDB Search =====
[2023-06-04 19:38:30,891] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902628165.1_AH-321-O19_genomic.fna/markers.fasta)
[2023-06-04 19:38:30,892] [INFO] Task started: Blastn
[2023-06-04 19:38:30,892] [INFO] Running command: blastn -query GCA_902628165.1_AH-321-O19_genomic.fna/markers.fasta -db /var/lib/cwl/stg929cfd11-754e-4227-87d8-aae89e4afc02/dqc_reference/reference_markers_gtdb.fasta -out GCA_902628165.1_AH-321-O19_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 19:38:31,552] [INFO] Task succeeded: Blastn
[2023-06-04 19:38:31,588] [INFO] Selected 9 target genomes.
[2023-06-04 19:38:31,589] [INFO] Target genome list was writen to GCA_902628165.1_AH-321-O19_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 19:38:31,660] [INFO] Task started: fastANI
[2023-06-04 19:38:31,661] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d96b15f-a4ee-4f3d-9d91-773e65ffcd3d/GCA_902628165.1_AH-321-O19_genomic.fna.gz --refList GCA_902628165.1_AH-321-O19_genomic.fna/target_genomes_gtdb.txt --output GCA_902628165.1_AH-321-O19_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 19:38:34,042] [INFO] Task succeeded: fastANI
[2023-06-04 19:38:34,057] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-04 19:38:34,058] [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_902576905.1	s__CACIJG01 sp902576905	92.5526	68	116	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIJG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902596985.1	s__CACIJG01 sp902596985	92.0131	68	116	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIJG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902537215.1	s__CACIJG01 sp902537215	91.8194	93	116	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIJG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902619165.1	s__CACIJG01 sp902619165	91.7969	93	116	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIJG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902530595.1	s__CACIJG01 sp902530595	91.6785	50	116	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIJG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902540655.1	s__CACIJG01 sp902540655	91.3735	67	116	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIJG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902581005.1	s__CACIJG01 sp902581005	91.2459	51	116	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIJG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902574225.1	s__CACIJG01 sp902574225	91.1918	83	116	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIJG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902560505.1	s__CACIJG01 sp902560505	90.2451	51	116	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIJG01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 19:38:34,061] [INFO] GTDB search result was written to GCA_902628165.1_AH-321-O19_genomic.fna/result_gtdb.tsv
[2023-06-04 19:38:34,062] [INFO] ===== GTDB Search completed =====
[2023-06-04 19:38:34,066] [INFO] DFAST_QC result json was written to GCA_902628165.1_AH-321-O19_genomic.fna/dqc_result.json
[2023-06-04 19:38:34,066] [INFO] DFAST_QC completed!
[2023-06-04 19:38:34,066] [INFO] Total running time: 0h0m18s