[2023-06-07 19:51:39,939] [INFO] DFAST_QC pipeline started.
[2023-06-07 19:51:39,941] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 19:51:39,941] [INFO] DQC Reference Directory: /var/lib/cwl/stga5f09a49-b043-4d6d-bf68-d23d83c77642/dqc_reference
[2023-06-07 19:51:41,306] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 19:51:41,307] [INFO] Task started: Prodigal
[2023-06-07 19:51:41,308] [INFO] Running command: gunzip -c /var/lib/cwl/stga961f7aa-15a0-461b-8353-305ec13c072f/GCA_902521905.1_AG-894-P17_genomic.fna.gz | prodigal -d GCA_902521905.1_AG-894-P17_genomic.fna/cds.fna -a GCA_902521905.1_AG-894-P17_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 19:51:44,057] [INFO] Task succeeded: Prodigal
[2023-06-07 19:51:44,058] [INFO] Task started: HMMsearch
[2023-06-07 19:51:44,058] [INFO] Running command: hmmsearch --tblout GCA_902521905.1_AG-894-P17_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga5f09a49-b043-4d6d-bf68-d23d83c77642/dqc_reference/reference_markers.hmm GCA_902521905.1_AG-894-P17_genomic.fna/protein.faa > /dev/null
[2023-06-07 19:51:44,254] [INFO] Task succeeded: HMMsearch
[2023-06-07 19:51:44,256] [WARNING] Found 3/6 markers. [/var/lib/cwl/stga961f7aa-15a0-461b-8353-305ec13c072f/GCA_902521905.1_AG-894-P17_genomic.fna.gz]
[2023-06-07 19:51:44,271] [INFO] Query marker FASTA was written to GCA_902521905.1_AG-894-P17_genomic.fna/markers.fasta
[2023-06-07 19:51:44,271] [INFO] Task started: Blastn
[2023-06-07 19:51:44,272] [INFO] Running command: blastn -query GCA_902521905.1_AG-894-P17_genomic.fna/markers.fasta -db /var/lib/cwl/stga5f09a49-b043-4d6d-bf68-d23d83c77642/dqc_reference/reference_markers.fasta -out GCA_902521905.1_AG-894-P17_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 19:51:45,104] [INFO] Task succeeded: Blastn
[2023-06-07 19:51:45,107] [INFO] Selected 6 target genomes.
[2023-06-07 19:51:45,107] [INFO] Target genome list was writen to GCA_902521905.1_AG-894-P17_genomic.fna/target_genomes.txt
[2023-06-07 19:51:45,111] [INFO] Task started: fastANI
[2023-06-07 19:51:45,112] [INFO] Running command: fastANI --query /var/lib/cwl/stga961f7aa-15a0-461b-8353-305ec13c072f/GCA_902521905.1_AG-894-P17_genomic.fna.gz --refList GCA_902521905.1_AG-894-P17_genomic.fna/target_genomes.txt --output GCA_902521905.1_AG-894-P17_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 19:51:47,019] [INFO] Task succeeded: fastANI
[2023-06-07 19:51:47,020] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga5f09a49-b043-4d6d-bf68-d23d83c77642/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 19:51:47,021] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga5f09a49-b043-4d6d-bf68-d23d83c77642/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 19:51:47,028] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 19:51:47,028] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-07 19:51:47,028] [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
Candidatus Pelagibacter ubique	strain=HTCC1062	GCA_000012345.1	198252	198252	suspected-type	True	77.8337	131	326	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-07 19:51:47,031] [INFO] DFAST Taxonomy check result was written to GCA_902521905.1_AG-894-P17_genomic.fna/tc_result.tsv
[2023-06-07 19:51:47,031] [INFO] ===== Taxonomy check completed =====
[2023-06-07 19:51:47,031] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 19:51:47,032] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga5f09a49-b043-4d6d-bf68-d23d83c77642/dqc_reference/checkm_data
[2023-06-07 19:51:47,033] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 19:51:47,050] [INFO] Task started: CheckM
[2023-06-07 19:51:47,050] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902521905.1_AG-894-P17_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902521905.1_AG-894-P17_genomic.fna/checkm_input GCA_902521905.1_AG-894-P17_genomic.fna/checkm_result
[2023-06-07 19:52:04,241] [INFO] Task succeeded: CheckM
[2023-06-07 19:52:04,243] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 19:52:04,265] [INFO] ===== Completeness check finished =====
[2023-06-07 19:52:04,266] [INFO] ===== Start GTDB Search =====
[2023-06-07 19:52:04,266] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902521905.1_AG-894-P17_genomic.fna/markers.fasta)
[2023-06-07 19:52:04,267] [INFO] Task started: Blastn
[2023-06-07 19:52:04,267] [INFO] Running command: blastn -query GCA_902521905.1_AG-894-P17_genomic.fna/markers.fasta -db /var/lib/cwl/stga5f09a49-b043-4d6d-bf68-d23d83c77642/dqc_reference/reference_markers_gtdb.fasta -out GCA_902521905.1_AG-894-P17_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 19:52:04,946] [INFO] Task succeeded: Blastn
[2023-06-07 19:52:04,950] [INFO] Selected 11 target genomes.
[2023-06-07 19:52:04,951] [INFO] Target genome list was writen to GCA_902521905.1_AG-894-P17_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 19:52:04,958] [INFO] Task started: fastANI
[2023-06-07 19:52:04,958] [INFO] Running command: fastANI --query /var/lib/cwl/stga961f7aa-15a0-461b-8353-305ec13c072f/GCA_902521905.1_AG-894-P17_genomic.fna.gz --refList GCA_902521905.1_AG-894-P17_genomic.fna/target_genomes_gtdb.txt --output GCA_902521905.1_AG-894-P17_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 19:52:07,330] [INFO] Task succeeded: fastANI
[2023-06-07 19:52:07,349] [INFO] Found 11 fastANI hits (2 hits with ANI > circumscription radius)
[2023-06-07 19:52:07,349] [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_902597895.1	s__Pelagibacter sp902597895	97.0099	247	326	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	96.33	95.32	0.80	0.77	6	inconclusive
GCA_902521005.1	s__Pelagibacter sp902521005	95.0641	243	326	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	95.40	95.40	0.75	0.75	2	inconclusive
GCA_902566785.1	s__Pelagibacter sp902566785	85.4946	206	326	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	97.91	97.91	0.63	0.63	2	-
GCA_902551895.1	s__Pelagibacter sp902551895	80.3402	145	326	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902560685.1	s__Pelagibacter sp902560685	79.8647	148	326	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	96.91	96.17	0.76	0.75	4	-
GCA_902569725.1	s__Pelagibacter sp902569725	79.5462	156	326	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902519625.1	s__Pelagibacter sp902519625	79.3681	112	326	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	98.78	98.78	0.51	0.51	2	-
GCA_003212415.1	s__Pelagibacter sp003212415	78.588	144	326	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_902634935.1	s__Pelagibacter sp902634935	78.3128	111	326	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902521075.1	s__Pelagibacter sp902521075	78.2523	116	326	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902519255.1	s__Pelagibacter sp902519255	78.209	121	326	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	99.11	99.05	0.75	0.74	3	-
--------------------------------------------------------------------------------
[2023-06-07 19:52:07,351] [INFO] GTDB search result was written to GCA_902521905.1_AG-894-P17_genomic.fna/result_gtdb.tsv
[2023-06-07 19:52:07,352] [INFO] ===== GTDB Search completed =====
[2023-06-07 19:52:07,356] [INFO] DFAST_QC result json was written to GCA_902521905.1_AG-894-P17_genomic.fna/dqc_result.json
[2023-06-07 19:52:07,357] [INFO] DFAST_QC completed!
[2023-06-07 19:52:07,357] [INFO] Total running time: 0h0m27s