[2023-03-15 14:29:42,512] [INFO] DFAST_QC pipeline started.
[2023-03-15 14:29:42,512] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 14:29:42,512] [INFO] DQC Reference Directory: /var/lib/cwl/stg4a18276f-a881-4735-b0f2-4b50926bd7e4/dqc_reference
[2023-03-15 14:29:43,597] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 14:29:43,597] [INFO] Task started: Prodigal
[2023-03-15 14:29:43,597] [INFO] Running command: cat /var/lib/cwl/stg13212765-7478-4d4b-9886-3231ee232c05/OceanDNA-b42120.fa | prodigal -d OceanDNA-b42120/cds.fna -a OceanDNA-b42120/protein.faa -g 11 -q > /dev/null
[2023-03-15 14:29:48,026] [INFO] Task succeeded: Prodigal
[2023-03-15 14:29:48,027] [INFO] Task started: HMMsearch
[2023-03-15 14:29:48,027] [INFO] Running command: hmmsearch --tblout OceanDNA-b42120/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4a18276f-a881-4735-b0f2-4b50926bd7e4/dqc_reference/reference_markers.hmm OceanDNA-b42120/protein.faa > /dev/null
[2023-03-15 14:29:48,168] [INFO] Task succeeded: HMMsearch
[2023-03-15 14:29:48,169] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg13212765-7478-4d4b-9886-3231ee232c05/OceanDNA-b42120.fa]
[2023-03-15 14:29:48,176] [INFO] Query marker FASTA was written to OceanDNA-b42120/markers.fasta
[2023-03-15 14:29:48,176] [INFO] Task started: Blastn
[2023-03-15 14:29:48,176] [INFO] Running command: blastn -query OceanDNA-b42120/markers.fasta -db /var/lib/cwl/stg4a18276f-a881-4735-b0f2-4b50926bd7e4/dqc_reference/reference_markers.fasta -out OceanDNA-b42120/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:29:48,660] [INFO] Task succeeded: Blastn
[2023-03-15 14:29:48,660] [INFO] Selected 9 target genomes.
[2023-03-15 14:29:48,661] [INFO] Target genome list was writen to OceanDNA-b42120/target_genomes.txt
[2023-03-15 14:29:48,664] [INFO] Task started: fastANI
[2023-03-15 14:29:48,664] [INFO] Running command: fastANI --query /var/lib/cwl/stg13212765-7478-4d4b-9886-3231ee232c05/OceanDNA-b42120.fa --refList OceanDNA-b42120/target_genomes.txt --output OceanDNA-b42120/fastani_result.tsv --threads 1
[2023-03-15 14:29:53,475] [INFO] Task succeeded: fastANI
[2023-03-15 14:29:53,475] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4a18276f-a881-4735-b0f2-4b50926bd7e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 14:29:53,475] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4a18276f-a881-4735-b0f2-4b50926bd7e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 14:29:53,475] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 14:29:53,475] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 14:29:53,476] [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
--------------------------------------------------------------------------------
[2023-03-15 14:29:53,476] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42120/tc_result.tsv
[2023-03-15 14:29:53,476] [INFO] ===== Taxonomy check completed =====
[2023-03-15 14:29:53,476] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 14:29:53,476] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4a18276f-a881-4735-b0f2-4b50926bd7e4/dqc_reference/checkm_data
[2023-03-15 14:29:53,479] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 14:29:53,841] [INFO] Task started: CheckM
[2023-03-15 14:29:53,841] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42120/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42120/checkm_input OceanDNA-b42120/checkm_result
[2023-03-15 14:30:10,824] [INFO] Task succeeded: CheckM
[2023-03-15 14:30:10,824] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 29.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 14:30:10,826] [INFO] ===== Completeness check finished =====
[2023-03-15 14:30:10,826] [INFO] ===== Start GTDB Search =====
[2023-03-15 14:30:10,826] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42120/markers.fasta)
[2023-03-15 14:30:10,826] [INFO] Task started: Blastn
[2023-03-15 14:30:10,826] [INFO] Running command: blastn -query OceanDNA-b42120/markers.fasta -db /var/lib/cwl/stg4a18276f-a881-4735-b0f2-4b50926bd7e4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42120/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:30:11,478] [INFO] Task succeeded: Blastn
[2023-03-15 14:30:11,479] [INFO] Selected 12 target genomes.
[2023-03-15 14:30:11,479] [INFO] Target genome list was writen to OceanDNA-b42120/target_genomes_gtdb.txt
[2023-03-15 14:30:11,517] [INFO] Task started: fastANI
[2023-03-15 14:30:11,517] [INFO] Running command: fastANI --query /var/lib/cwl/stg13212765-7478-4d4b-9886-3231ee232c05/OceanDNA-b42120.fa --refList OceanDNA-b42120/target_genomes_gtdb.txt --output OceanDNA-b42120/fastani_result_gtdb.tsv --threads 1
[2023-03-15 14:30:14,185] [INFO] Task succeeded: fastANI
[2023-03-15 14:30:14,192] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 14:30:14,192] [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_902511575.1	s__D2472 sp902511575	87.9674	230	281	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902602595.1	s__D2472 sp902602595	86.4415	222	281	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902509555.1	s__D2472 sp902509555	86.3863	159	281	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003283765.1	s__D2472 sp003283765	86.3437	183	281	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	100.00	100.00	0.99	0.99	2	-
GCA_902593675.1	s__D2472 sp902593675	85.335	237	281	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902596165.1	s__D2472 sp902596165	85.1994	206	281	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902512655.1	s__D2472 sp902512655	83.8413	148	281	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902513515.1	s__D2472 sp902513515	83.7071	172	281	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016779505.1	s__D2472 sp016779505	83.1967	162	281	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	98.99	98.50	0.76	0.70	3	-
GCA_003284215.1	s__D2472 sp003284215	83.1611	183	281	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	98.26	97.20	0.81	0.71	5	-
GCA_000307935.1	s__D2472 sp000307935	80.881	162	281	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 14:30:14,193] [INFO] GTDB search result was written to OceanDNA-b42120/result_gtdb.tsv
[2023-03-15 14:30:14,193] [INFO] ===== GTDB Search completed =====
[2023-03-15 14:30:14,194] [INFO] DFAST_QC result json was written to OceanDNA-b42120/dqc_result.json
[2023-03-15 14:30:14,194] [INFO] DFAST_QC completed!
[2023-03-15 14:30:14,194] [INFO] Total running time: 0h0m32s