[2023-03-17 11:29:30,415] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:29:30,416] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:29:30,416] [INFO] DQC Reference Directory: /var/lib/cwl/stg01eb73b3-8c24-425e-b6e5-a14a8e9f1b4a/dqc_reference
[2023-03-17 11:29:31,509] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:29:31,510] [INFO] Task started: Prodigal
[2023-03-17 11:29:31,510] [INFO] Running command: cat /var/lib/cwl/stg72ebdbe7-33d6-4d00-8883-f4488dcfc6c5/OceanDNA-b41859.fa | prodigal -d OceanDNA-b41859/cds.fna -a OceanDNA-b41859/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:29:36,279] [INFO] Task succeeded: Prodigal
[2023-03-17 11:29:36,279] [INFO] Task started: HMMsearch
[2023-03-17 11:29:36,279] [INFO] Running command: hmmsearch --tblout OceanDNA-b41859/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg01eb73b3-8c24-425e-b6e5-a14a8e9f1b4a/dqc_reference/reference_markers.hmm OceanDNA-b41859/protein.faa > /dev/null
[2023-03-17 11:29:36,438] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:29:36,439] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg72ebdbe7-33d6-4d00-8883-f4488dcfc6c5/OceanDNA-b41859.fa]
[2023-03-17 11:29:36,447] [INFO] Query marker FASTA was written to OceanDNA-b41859/markers.fasta
[2023-03-17 11:29:36,448] [INFO] Task started: Blastn
[2023-03-17 11:29:36,448] [INFO] Running command: blastn -query OceanDNA-b41859/markers.fasta -db /var/lib/cwl/stg01eb73b3-8c24-425e-b6e5-a14a8e9f1b4a/dqc_reference/reference_markers.fasta -out OceanDNA-b41859/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:29:36,977] [INFO] Task succeeded: Blastn
[2023-03-17 11:29:36,978] [INFO] Selected 12 target genomes.
[2023-03-17 11:29:36,978] [INFO] Target genome list was writen to OceanDNA-b41859/target_genomes.txt
[2023-03-17 11:29:36,987] [INFO] Task started: fastANI
[2023-03-17 11:29:36,987] [INFO] Running command: fastANI --query /var/lib/cwl/stg72ebdbe7-33d6-4d00-8883-f4488dcfc6c5/OceanDNA-b41859.fa --refList OceanDNA-b41859/target_genomes.txt --output OceanDNA-b41859/fastani_result.tsv --threads 1
[2023-03-17 11:29:40,271] [INFO] Task succeeded: fastANI
[2023-03-17 11:29:40,272] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg01eb73b3-8c24-425e-b6e5-a14a8e9f1b4a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:29:40,272] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg01eb73b3-8c24-425e-b6e5-a14a8e9f1b4a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:29:40,272] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:29:40,272] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 11:29:40,272] [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
--------------------------------------------------------------------------------
[2023-03-17 11:29:40,273] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41859/tc_result.tsv
[2023-03-17 11:29:40,273] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:29:40,273] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:29:40,273] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg01eb73b3-8c24-425e-b6e5-a14a8e9f1b4a/dqc_reference/checkm_data
[2023-03-17 11:29:40,277] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:29:40,384] [INFO] Task started: CheckM
[2023-03-17 11:29:40,384] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41859/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41859/checkm_input OceanDNA-b41859/checkm_result
[2023-03-17 11:29:58,397] [INFO] Task succeeded: CheckM
[2023-03-17 11:29:58,397] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.81%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 11:29:58,399] [INFO] ===== Completeness check finished =====
[2023-03-17 11:29:58,399] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:29:58,399] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41859/markers.fasta)
[2023-03-17 11:29:58,400] [INFO] Task started: Blastn
[2023-03-17 11:29:58,400] [INFO] Running command: blastn -query OceanDNA-b41859/markers.fasta -db /var/lib/cwl/stg01eb73b3-8c24-425e-b6e5-a14a8e9f1b4a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41859/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:29:59,277] [INFO] Task succeeded: Blastn
[2023-03-17 11:29:59,278] [INFO] Selected 19 target genomes.
[2023-03-17 11:29:59,278] [INFO] Target genome list was writen to OceanDNA-b41859/target_genomes_gtdb.txt
[2023-03-17 11:29:59,300] [INFO] Task started: fastANI
[2023-03-17 11:29:59,300] [INFO] Running command: fastANI --query /var/lib/cwl/stg72ebdbe7-33d6-4d00-8883-f4488dcfc6c5/OceanDNA-b41859.fa --refList OceanDNA-b41859/target_genomes_gtdb.txt --output OceanDNA-b41859/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:30:03,176] [INFO] Task succeeded: fastANI
[2023-03-17 11:30:03,183] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 11:30:03,184] [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_902514105.1	s__MED-G78 sp902514105	95.7814	211	317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__MED-G78	95.0	98.38	98.38	0.65	0.65	2	conclusive
GCA_905181955.1	s__MED-G78 sp905181955	78.69	159	317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__MED-G78	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902509965.1	s__MED-G78 sp902509965	78.6456	134	317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__MED-G78	95.0	96.76	96.76	0.83	0.83	2	-
GCA_905181645.1	s__MED-G78 sp905181645	78.4511	150	317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__MED-G78	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902557645.1	s__MED-G78 sp902558645	78.4041	166	317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__MED-G78	95.0	98.05	95.16	0.89	0.87	6	-
GCA_902559345.1	s__SAR86A sp902559345	77.1012	53	317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000384935.1	s__SCGC-AAA076-P13 sp000384935	76.8614	50	317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902583575.1	s__SAR86A sp902583575	76.7714	56	317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000385055.1	s__SCGC-AAA076-P13 sp000385055	76.7688	65	317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	98.19	98.19	0.89	0.89	2	-
GCA_902517505.1	s__SAR86A sp902517505	76.6605	53	317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.73	97.59	0.82	0.80	3	-
GCA_905478035.1	s__SCGC-AAA076-P13 sp905478035	76.5887	55	317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902560315.1	s__SAR86A sp902560315	76.4053	55	317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	95.47	95.47	0.82	0.82	2	-
GCA_902591565.1	s__SCGC-AAA076-P13 sp902591565	76.4013	52	317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 11:30:03,184] [INFO] GTDB search result was written to OceanDNA-b41859/result_gtdb.tsv
[2023-03-17 11:30:03,184] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:30:03,188] [INFO] DFAST_QC result json was written to OceanDNA-b41859/dqc_result.json
[2023-03-17 11:30:03,188] [INFO] DFAST_QC completed!
[2023-03-17 11:30:03,188] [INFO] Total running time: 0h0m33s