[2023-03-19 03:50:07,840] [INFO] DFAST_QC pipeline started.
[2023-03-19 03:50:07,851] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 03:50:07,851] [INFO] DQC Reference Directory: /var/lib/cwl/stg50d999fb-399f-4ca3-9ecf-7638a9b9314f/dqc_reference
[2023-03-19 03:50:09,607] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 03:50:09,607] [INFO] Task started: Prodigal
[2023-03-19 03:50:09,607] [INFO] Running command: cat /var/lib/cwl/stg6e800e35-070b-41c9-85b4-0e498c3b4a90/OceanDNA-b41853.fa | prodigal -d OceanDNA-b41853/cds.fna -a OceanDNA-b41853/protein.faa -g 11 -q > /dev/null
[2023-03-19 03:50:15,493] [INFO] Task succeeded: Prodigal
[2023-03-19 03:50:15,493] [INFO] Task started: HMMsearch
[2023-03-19 03:50:15,493] [INFO] Running command: hmmsearch --tblout OceanDNA-b41853/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg50d999fb-399f-4ca3-9ecf-7638a9b9314f/dqc_reference/reference_markers.hmm OceanDNA-b41853/protein.faa > /dev/null
[2023-03-19 03:50:15,674] [INFO] Task succeeded: HMMsearch
[2023-03-19 03:50:15,674] [INFO] Found 6/6 markers.
[2023-03-19 03:50:15,682] [INFO] Query marker FASTA was written to OceanDNA-b41853/markers.fasta
[2023-03-19 03:50:15,682] [INFO] Task started: Blastn
[2023-03-19 03:50:15,682] [INFO] Running command: blastn -query OceanDNA-b41853/markers.fasta -db /var/lib/cwl/stg50d999fb-399f-4ca3-9ecf-7638a9b9314f/dqc_reference/reference_markers.fasta -out OceanDNA-b41853/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:50:16,253] [INFO] Task succeeded: Blastn
[2023-03-19 03:50:16,254] [INFO] Selected 12 target genomes.
[2023-03-19 03:50:16,254] [INFO] Target genome list was writen to OceanDNA-b41853/target_genomes.txt
[2023-03-19 03:50:16,261] [INFO] Task started: fastANI
[2023-03-19 03:50:16,261] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e800e35-070b-41c9-85b4-0e498c3b4a90/OceanDNA-b41853.fa --refList OceanDNA-b41853/target_genomes.txt --output OceanDNA-b41853/fastani_result.tsv --threads 1
[2023-03-19 03:50:22,218] [INFO] Task succeeded: fastANI
[2023-03-19 03:50:22,218] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg50d999fb-399f-4ca3-9ecf-7638a9b9314f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 03:50:22,219] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg50d999fb-399f-4ca3-9ecf-7638a9b9314f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 03:50:22,219] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 03:50:22,219] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 03:50:22,219] [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
--------------------------------------------------------------------------------
[2023-03-19 03:50:22,219] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41853/tc_result.tsv
[2023-03-19 03:50:22,219] [INFO] ===== Taxonomy check completed =====
[2023-03-19 03:50:22,219] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 03:50:22,219] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg50d999fb-399f-4ca3-9ecf-7638a9b9314f/dqc_reference/checkm_data
[2023-03-19 03:50:22,222] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 03:50:22,224] [INFO] Task started: CheckM
[2023-03-19 03:50:22,224] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41853/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41853/checkm_input OceanDNA-b41853/checkm_result
[2023-03-19 03:50:42,665] [INFO] Task succeeded: CheckM
[2023-03-19 03:50:42,665] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 03:50:42,666] [INFO] ===== Completeness check finished =====
[2023-03-19 03:50:42,667] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:50:42,667] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41853/markers.fasta)
[2023-03-19 03:50:42,667] [INFO] Task started: Blastn
[2023-03-19 03:50:42,667] [INFO] Running command: blastn -query OceanDNA-b41853/markers.fasta -db /var/lib/cwl/stg50d999fb-399f-4ca3-9ecf-7638a9b9314f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41853/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:50:43,583] [INFO] Task succeeded: Blastn
[2023-03-19 03:50:43,584] [INFO] Selected 22 target genomes.
[2023-03-19 03:50:43,584] [INFO] Target genome list was writen to OceanDNA-b41853/target_genomes_gtdb.txt
[2023-03-19 03:50:43,606] [INFO] Task started: fastANI
[2023-03-19 03:50:43,607] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e800e35-070b-41c9-85b4-0e498c3b4a90/OceanDNA-b41853.fa --refList OceanDNA-b41853/target_genomes_gtdb.txt --output OceanDNA-b41853/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:50:49,436] [INFO] Task succeeded: fastANI
[2023-03-19 03:50:49,440] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 03:50:49,440] [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_902593675.1	s__D2472 sp902593675	76.3274	50	379	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002172535.2	s__MED-G82 sp002172535	76.1885	53	379	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__MED-G82	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902601475.1	s__MED-G82 sp902601475	76.1364	54	379	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__MED-G82	95.0	95.97	95.73	0.86	0.83	4	-
GCA_902628925.1	s__MED-G82 sp902628925	76.1112	59	379	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__MED-G82	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902594515.1	s__MED-G82 sp902594515	76.0071	57	379	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__MED-G82	95.0	95.37	95.15	0.90	0.90	3	-
--------------------------------------------------------------------------------
[2023-03-19 03:50:49,440] [INFO] GTDB search result was written to OceanDNA-b41853/result_gtdb.tsv
[2023-03-19 03:50:49,440] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:50:49,441] [INFO] DFAST_QC result json was written to OceanDNA-b41853/dqc_result.json
[2023-03-19 03:50:49,441] [INFO] DFAST_QC completed!
[2023-03-19 03:50:49,441] [INFO] Total running time: 0h0m42s