[2023-03-15 18:39:12,255] [INFO] DFAST_QC pipeline started.
[2023-03-15 18:39:12,255] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 18:39:12,256] [INFO] DQC Reference Directory: /var/lib/cwl/stgf867b064-911e-4dc7-b0a4-5fc298a4585a/dqc_reference
[2023-03-15 18:39:13,657] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 18:39:13,657] [INFO] Task started: Prodigal
[2023-03-15 18:39:13,657] [INFO] Running command: cat /var/lib/cwl/stg7140b8a7-0318-4fb5-a48a-f4078d517bb9/OceanDNA-b42090.fa | prodigal -d OceanDNA-b42090/cds.fna -a OceanDNA-b42090/protein.faa -g 11 -q > /dev/null
[2023-03-15 18:39:17,959] [INFO] Task succeeded: Prodigal
[2023-03-15 18:39:17,959] [INFO] Task started: HMMsearch
[2023-03-15 18:39:17,959] [INFO] Running command: hmmsearch --tblout OceanDNA-b42090/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf867b064-911e-4dc7-b0a4-5fc298a4585a/dqc_reference/reference_markers.hmm OceanDNA-b42090/protein.faa > /dev/null
[2023-03-15 18:39:18,132] [INFO] Task succeeded: HMMsearch
[2023-03-15 18:39:18,133] [INFO] Found 6/6 markers.
[2023-03-15 18:39:18,142] [INFO] Query marker FASTA was written to OceanDNA-b42090/markers.fasta
[2023-03-15 18:39:18,143] [INFO] Task started: Blastn
[2023-03-15 18:39:18,143] [INFO] Running command: blastn -query OceanDNA-b42090/markers.fasta -db /var/lib/cwl/stgf867b064-911e-4dc7-b0a4-5fc298a4585a/dqc_reference/reference_markers.fasta -out OceanDNA-b42090/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:39:19,552] [INFO] Task succeeded: Blastn
[2023-03-15 18:39:19,553] [INFO] Selected 19 target genomes.
[2023-03-15 18:39:19,553] [INFO] Target genome list was writen to OceanDNA-b42090/target_genomes.txt
[2023-03-15 18:39:19,564] [INFO] Task started: fastANI
[2023-03-15 18:39:19,564] [INFO] Running command: fastANI --query /var/lib/cwl/stg7140b8a7-0318-4fb5-a48a-f4078d517bb9/OceanDNA-b42090.fa --refList OceanDNA-b42090/target_genomes.txt --output OceanDNA-b42090/fastani_result.tsv --threads 1
[2023-03-15 18:39:27,425] [INFO] Task succeeded: fastANI
[2023-03-15 18:39:27,425] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf867b064-911e-4dc7-b0a4-5fc298a4585a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 18:39:27,425] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf867b064-911e-4dc7-b0a4-5fc298a4585a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 18:39:27,425] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 18:39:27,425] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 18:39:27,426] [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 18:39:27,426] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42090/tc_result.tsv
[2023-03-15 18:39:27,426] [INFO] ===== Taxonomy check completed =====
[2023-03-15 18:39:27,426] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 18:39:27,426] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf867b064-911e-4dc7-b0a4-5fc298a4585a/dqc_reference/checkm_data
[2023-03-15 18:39:27,428] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 18:39:27,431] [INFO] Task started: CheckM
[2023-03-15 18:39:27,431] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42090/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42090/checkm_input OceanDNA-b42090/checkm_result
[2023-03-15 18:39:47,214] [INFO] Task succeeded: CheckM
[2023-03-15 18:39:47,215] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.03%
Contamintation: 1.45%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 18:39:47,216] [INFO] ===== Completeness check finished =====
[2023-03-15 18:39:47,216] [INFO] ===== Start GTDB Search =====
[2023-03-15 18:39:47,216] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42090/markers.fasta)
[2023-03-15 18:39:47,217] [INFO] Task started: Blastn
[2023-03-15 18:39:47,217] [INFO] Running command: blastn -query OceanDNA-b42090/markers.fasta -db /var/lib/cwl/stgf867b064-911e-4dc7-b0a4-5fc298a4585a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42090/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:39:49,886] [INFO] Task succeeded: Blastn
[2023-03-15 18:39:49,887] [INFO] Selected 13 target genomes.
[2023-03-15 18:39:49,887] [INFO] Target genome list was writen to OceanDNA-b42090/target_genomes_gtdb.txt
[2023-03-15 18:39:50,211] [INFO] Task started: fastANI
[2023-03-15 18:39:50,212] [INFO] Running command: fastANI --query /var/lib/cwl/stg7140b8a7-0318-4fb5-a48a-f4078d517bb9/OceanDNA-b42090.fa --refList OceanDNA-b42090/target_genomes_gtdb.txt --output OceanDNA-b42090/fastani_result_gtdb.tsv --threads 1
[2023-03-15 18:39:53,342] [INFO] Task succeeded: fastANI
[2023-03-15 18:39:53,350] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 18:39:53,350] [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_902511425.1	s__D2472 sp902511425	95.3078	159	232	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_000307935.1	s__D2472 sp000307935	88.0757	163	232	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	85.8892	159	232	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	100.00	100.00	0.99	0.99	2	-
GCA_902511575.1	s__D2472 sp902511575	84.8937	186	232	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	84.5174	135	232	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902595065.1	s__D2472 sp902595065	83.8964	204	232	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	98.09	97.88	0.94	0.91	4	-
GCA_902593675.1	s__D2472 sp902593675	83.8732	184	232	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	83.8108	131	232	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003284215.1	s__D2472 sp003284215	83.4737	158	232	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	98.26	97.20	0.81	0.71	5	-
GCA_902596165.1	s__D2472 sp902596165	83.4396	177	232	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	83.0097	143	232	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	82.8852	142	232	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	98.99	98.50	0.76	0.70	3	-
GCA_902602595.1	s__D2472 sp902602595	82.7586	170	232	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 18:39:53,351] [INFO] GTDB search result was written to OceanDNA-b42090/result_gtdb.tsv
[2023-03-15 18:39:53,351] [INFO] ===== GTDB Search completed =====
[2023-03-15 18:39:53,352] [INFO] DFAST_QC result json was written to OceanDNA-b42090/dqc_result.json
[2023-03-15 18:39:53,352] [INFO] DFAST_QC completed!
[2023-03-15 18:39:53,352] [INFO] Total running time: 0h0m41s