[2023-03-14 11:33:34,927] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:33:34,927] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:33:34,927] [INFO] DQC Reference Directory: /var/lib/cwl/stg382e113f-586d-4be9-9665-7119dd736d9f/dqc_reference
[2023-03-14 11:33:36,124] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:33:36,125] [INFO] Task started: Prodigal
[2023-03-14 11:33:36,125] [INFO] Running command: cat /var/lib/cwl/stg7683e3ae-9bc9-4981-8dd7-dac2b09562fe/OceanDNA-b41926.fa | prodigal -d OceanDNA-b41926/cds.fna -a OceanDNA-b41926/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:33:42,180] [INFO] Task succeeded: Prodigal
[2023-03-14 11:33:42,181] [INFO] Task started: HMMsearch
[2023-03-14 11:33:42,181] [INFO] Running command: hmmsearch --tblout OceanDNA-b41926/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg382e113f-586d-4be9-9665-7119dd736d9f/dqc_reference/reference_markers.hmm OceanDNA-b41926/protein.faa > /dev/null
[2023-03-14 11:33:42,402] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:33:42,403] [INFO] Found 6/6 markers.
[2023-03-14 11:33:42,412] [INFO] Query marker FASTA was written to OceanDNA-b41926/markers.fasta
[2023-03-14 11:33:42,412] [INFO] Task started: Blastn
[2023-03-14 11:33:42,412] [INFO] Running command: blastn -query OceanDNA-b41926/markers.fasta -db /var/lib/cwl/stg382e113f-586d-4be9-9665-7119dd736d9f/dqc_reference/reference_markers.fasta -out OceanDNA-b41926/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:33:43,034] [INFO] Task succeeded: Blastn
[2023-03-14 11:33:43,035] [INFO] Selected 18 target genomes.
[2023-03-14 11:33:43,035] [INFO] Target genome list was writen to OceanDNA-b41926/target_genomes.txt
[2023-03-14 11:33:43,045] [INFO] Task started: fastANI
[2023-03-14 11:33:43,045] [INFO] Running command: fastANI --query /var/lib/cwl/stg7683e3ae-9bc9-4981-8dd7-dac2b09562fe/OceanDNA-b41926.fa --refList OceanDNA-b41926/target_genomes.txt --output OceanDNA-b41926/fastani_result.tsv --threads 1
[2023-03-14 11:33:50,435] [INFO] Task succeeded: fastANI
[2023-03-14 11:33:50,435] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg382e113f-586d-4be9-9665-7119dd736d9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:33:50,436] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg382e113f-586d-4be9-9665-7119dd736d9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:33:50,436] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:33:50,436] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 11:33:50,436] [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
--------------------------------------------------------------------------------
[2023-03-14 11:33:50,436] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41926/tc_result.tsv
[2023-03-14 11:33:50,436] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:33:50,437] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:33:50,437] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg382e113f-586d-4be9-9665-7119dd736d9f/dqc_reference/checkm_data
[2023-03-14 11:33:50,439] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:33:50,443] [INFO] Task started: CheckM
[2023-03-14 11:33:50,443] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41926/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41926/checkm_input OceanDNA-b41926/checkm_result
[2023-03-14 11:34:11,785] [INFO] Task succeeded: CheckM
[2023-03-14 11:34:11,785] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:34:11,787] [INFO] ===== Completeness check finished =====
[2023-03-14 11:34:11,787] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:34:11,788] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41926/markers.fasta)
[2023-03-14 11:34:11,788] [INFO] Task started: Blastn
[2023-03-14 11:34:11,788] [INFO] Running command: blastn -query OceanDNA-b41926/markers.fasta -db /var/lib/cwl/stg382e113f-586d-4be9-9665-7119dd736d9f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41926/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:34:12,763] [INFO] Task succeeded: Blastn
[2023-03-14 11:34:12,765] [INFO] Selected 16 target genomes.
[2023-03-14 11:34:12,765] [INFO] Target genome list was writen to OceanDNA-b41926/target_genomes_gtdb.txt
[2023-03-14 11:34:12,790] [INFO] Task started: fastANI
[2023-03-14 11:34:12,790] [INFO] Running command: fastANI --query /var/lib/cwl/stg7683e3ae-9bc9-4981-8dd7-dac2b09562fe/OceanDNA-b41926.fa --refList OceanDNA-b41926/target_genomes_gtdb.txt --output OceanDNA-b41926/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:34:16,515] [INFO] Task succeeded: fastANI
[2023-03-14 11:34:16,524] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 11:34:16,524] [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_905181955.1	s__MED-G78 sp905181955	99.7677	386	399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__MED-G78	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_905181645.1	s__MED-G78 sp905181645	94.3546	394	399	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	82.0684	248	399	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_902557645.1	s__MED-G78 sp902558645	79.0777	230	399	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_902514105.1	s__MED-G78 sp902514105	78.5448	141	399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__MED-G78	95.0	98.38	98.38	0.65	0.65	2	-
GCA_902591665.1	s__SCGC-AAA076-P13 sp902591665	77.2444	69	399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	99.81	99.81	0.85	0.85	2	-
GCA_902557705.1	s__SCGC-AAA076-P13 sp902557705	77.0926	55	399	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_902591565.1	s__SCGC-AAA076-P13 sp902591565	76.824	57	399	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_902551185.1	s__SAR86A sp902551185	76.4523	50	399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	99.17	99.17	0.78	0.78	2	-
GCA_902630885.1	s__SAR86A sp902630885	76.4306	59	399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902632555.1	s__SAR86A sp902632555	76.4218	53	399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902558095.1	s__SAR86A sp902558095	76.4177	64	399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902631785.1	s__SAR86A sp902631785	76.3748	53	399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.84	96.84	0.79	0.79	2	-
GCA_905478015.1	s__CAJQGY01 sp905478015	76.3407	60	399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__CAJQGY01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 11:34:16,524] [INFO] GTDB search result was written to OceanDNA-b41926/result_gtdb.tsv
[2023-03-14 11:34:16,524] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:34:16,525] [INFO] DFAST_QC result json was written to OceanDNA-b41926/dqc_result.json
[2023-03-14 11:34:16,526] [INFO] DFAST_QC completed!
[2023-03-14 11:34:16,526] [INFO] Total running time: 0h0m42s