[2023-06-05 05:03:33,303] [INFO] DFAST_QC pipeline started.
[2023-06-05 05:03:33,305] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 05:03:33,306] [INFO] DQC Reference Directory: /var/lib/cwl/stg2a27a8ff-1014-4d19-a97b-d3b6326c7746/dqc_reference
[2023-06-05 05:03:35,618] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 05:03:35,619] [INFO] Task started: Prodigal
[2023-06-05 05:03:35,619] [INFO] Running command: gunzip -c /var/lib/cwl/stg094ac718-6f4d-493b-bb6c-8751ea59e8b2/GCA_902522815.1_AG-895-D02_genomic.fna.gz | prodigal -d GCA_902522815.1_AG-895-D02_genomic.fna/cds.fna -a GCA_902522815.1_AG-895-D02_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 05:03:36,972] [INFO] Task succeeded: Prodigal
[2023-06-05 05:03:36,972] [INFO] Task started: HMMsearch
[2023-06-05 05:03:36,972] [INFO] Running command: hmmsearch --tblout GCA_902522815.1_AG-895-D02_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2a27a8ff-1014-4d19-a97b-d3b6326c7746/dqc_reference/reference_markers.hmm GCA_902522815.1_AG-895-D02_genomic.fna/protein.faa > /dev/null
[2023-06-05 05:03:37,130] [INFO] Task succeeded: HMMsearch
[2023-06-05 05:03:37,132] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg094ac718-6f4d-493b-bb6c-8751ea59e8b2/GCA_902522815.1_AG-895-D02_genomic.fna.gz]
[2023-06-05 05:03:37,144] [INFO] Query marker FASTA was written to GCA_902522815.1_AG-895-D02_genomic.fna/markers.fasta
[2023-06-05 05:03:37,145] [INFO] Task started: Blastn
[2023-06-05 05:03:37,145] [INFO] Running command: blastn -query GCA_902522815.1_AG-895-D02_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a27a8ff-1014-4d19-a97b-d3b6326c7746/dqc_reference/reference_markers.fasta -out GCA_902522815.1_AG-895-D02_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 05:03:39,050] [INFO] Task succeeded: Blastn
[2023-06-05 05:03:39,054] [INFO] Selected 3 target genomes.
[2023-06-05 05:03:39,055] [INFO] Target genome list was writen to GCA_902522815.1_AG-895-D02_genomic.fna/target_genomes.txt
[2023-06-05 05:03:39,056] [INFO] Task started: fastANI
[2023-06-05 05:03:39,056] [INFO] Running command: fastANI --query /var/lib/cwl/stg094ac718-6f4d-493b-bb6c-8751ea59e8b2/GCA_902522815.1_AG-895-D02_genomic.fna.gz --refList GCA_902522815.1_AG-895-D02_genomic.fna/target_genomes.txt --output GCA_902522815.1_AG-895-D02_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 05:03:39,815] [INFO] Task succeeded: fastANI
[2023-06-05 05:03:39,816] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2a27a8ff-1014-4d19-a97b-d3b6326c7746/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 05:03:39,816] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2a27a8ff-1014-4d19-a97b-d3b6326c7746/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 05:03:39,818] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 05:03:39,818] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 05:03:39,818] [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
--------------------------------------------------------------------------------
[2023-06-05 05:03:39,820] [INFO] DFAST Taxonomy check result was written to GCA_902522815.1_AG-895-D02_genomic.fna/tc_result.tsv
[2023-06-05 05:03:39,821] [INFO] ===== Taxonomy check completed =====
[2023-06-05 05:03:39,822] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 05:03:39,822] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2a27a8ff-1014-4d19-a97b-d3b6326c7746/dqc_reference/checkm_data
[2023-06-05 05:03:39,826] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 05:03:39,838] [INFO] Task started: CheckM
[2023-06-05 05:03:39,839] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902522815.1_AG-895-D02_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902522815.1_AG-895-D02_genomic.fna/checkm_input GCA_902522815.1_AG-895-D02_genomic.fna/checkm_result
[2023-06-05 05:03:53,054] [INFO] Task succeeded: CheckM
[2023-06-05 05:03:53,055] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 38.34%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 05:03:53,074] [INFO] ===== Completeness check finished =====
[2023-06-05 05:03:53,074] [INFO] ===== Start GTDB Search =====
[2023-06-05 05:03:53,074] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902522815.1_AG-895-D02_genomic.fna/markers.fasta)
[2023-06-05 05:03:53,075] [INFO] Task started: Blastn
[2023-06-05 05:03:53,075] [INFO] Running command: blastn -query GCA_902522815.1_AG-895-D02_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a27a8ff-1014-4d19-a97b-d3b6326c7746/dqc_reference/reference_markers_gtdb.fasta -out GCA_902522815.1_AG-895-D02_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 05:03:53,552] [INFO] Task succeeded: Blastn
[2023-06-05 05:03:53,557] [INFO] Selected 5 target genomes.
[2023-06-05 05:03:53,557] [INFO] Target genome list was writen to GCA_902522815.1_AG-895-D02_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 05:03:53,561] [INFO] Task started: fastANI
[2023-06-05 05:03:53,562] [INFO] Running command: fastANI --query /var/lib/cwl/stg094ac718-6f4d-493b-bb6c-8751ea59e8b2/GCA_902522815.1_AG-895-D02_genomic.fna.gz --refList GCA_902522815.1_AG-895-D02_genomic.fna/target_genomes_gtdb.txt --output GCA_902522815.1_AG-895-D02_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 05:03:54,553] [INFO] Task succeeded: fastANI
[2023-06-05 05:03:54,561] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 05:03:54,561] [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_902529785.1	s__Pelagibacter sp902529785	89.0623	87	144	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902537555.1	s__Pelagibacter sp902537555	88.9862	108	144	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902581585.1	s__Pelagibacter sp902581585	87.8937	119	144	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	96.81	96.81	0.86	0.86	2	-
GCA_902577075.1	s__Pelagibacter sp902577075	87.5718	122	144	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	99.76	99.76	0.93	0.93	2	-
GCA_902600205.1	s__Pelagibacter sp902600205	86.7661	94	144	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	97.36	97.36	0.75	0.75	2	-
--------------------------------------------------------------------------------
[2023-06-05 05:03:54,563] [INFO] GTDB search result was written to GCA_902522815.1_AG-895-D02_genomic.fna/result_gtdb.tsv
[2023-06-05 05:03:54,564] [INFO] ===== GTDB Search completed =====
[2023-06-05 05:03:54,567] [INFO] DFAST_QC result json was written to GCA_902522815.1_AG-895-D02_genomic.fna/dqc_result.json
[2023-06-05 05:03:54,567] [INFO] DFAST_QC completed!
[2023-06-05 05:03:54,567] [INFO] Total running time: 0h0m21s