[2023-03-18 10:20:22,473] [INFO] DFAST_QC pipeline started.
[2023-03-18 10:20:22,473] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 10:20:22,473] [INFO] DQC Reference Directory: /var/lib/cwl/stg0df1e32a-6b7a-469f-b18a-cd4d5ca43681/dqc_reference
[2023-03-18 10:20:23,597] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 10:20:23,597] [INFO] Task started: Prodigal
[2023-03-18 10:20:23,597] [INFO] Running command: cat /var/lib/cwl/stgee382aa5-557e-4a05-b83b-d187275d728d/OceanDNA-b11568.fa | prodigal -d OceanDNA-b11568/cds.fna -a OceanDNA-b11568/protein.faa -g 11 -q > /dev/null
[2023-03-18 10:20:30,865] [INFO] Task succeeded: Prodigal
[2023-03-18 10:20:30,865] [INFO] Task started: HMMsearch
[2023-03-18 10:20:30,866] [INFO] Running command: hmmsearch --tblout OceanDNA-b11568/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0df1e32a-6b7a-469f-b18a-cd4d5ca43681/dqc_reference/reference_markers.hmm OceanDNA-b11568/protein.faa > /dev/null
[2023-03-18 10:20:31,048] [INFO] Task succeeded: HMMsearch
[2023-03-18 10:20:31,048] [INFO] Found 6/6 markers.
[2023-03-18 10:20:31,058] [INFO] Query marker FASTA was written to OceanDNA-b11568/markers.fasta
[2023-03-18 10:20:31,060] [INFO] Task started: Blastn
[2023-03-18 10:20:31,060] [INFO] Running command: blastn -query OceanDNA-b11568/markers.fasta -db /var/lib/cwl/stg0df1e32a-6b7a-469f-b18a-cd4d5ca43681/dqc_reference/reference_markers.fasta -out OceanDNA-b11568/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:20:31,566] [INFO] Task succeeded: Blastn
[2023-03-18 10:20:31,567] [INFO] Selected 21 target genomes.
[2023-03-18 10:20:31,567] [INFO] Target genome list was writen to OceanDNA-b11568/target_genomes.txt
[2023-03-18 10:20:31,578] [INFO] Task started: fastANI
[2023-03-18 10:20:31,578] [INFO] Running command: fastANI --query /var/lib/cwl/stgee382aa5-557e-4a05-b83b-d187275d728d/OceanDNA-b11568.fa --refList OceanDNA-b11568/target_genomes.txt --output OceanDNA-b11568/fastani_result.tsv --threads 1
[2023-03-18 10:20:42,808] [INFO] Task succeeded: fastANI
[2023-03-18 10:20:42,808] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0df1e32a-6b7a-469f-b18a-cd4d5ca43681/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 10:20:42,809] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0df1e32a-6b7a-469f-b18a-cd4d5ca43681/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 10:20:42,809] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 10:20:42,809] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 10:20:42,809] [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
--------------------------------------------------------------------------------
[2023-03-18 10:20:42,809] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11568/tc_result.tsv
[2023-03-18 10:20:42,809] [INFO] ===== Taxonomy check completed =====
[2023-03-18 10:20:42,809] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 10:20:42,809] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0df1e32a-6b7a-469f-b18a-cd4d5ca43681/dqc_reference/checkm_data
[2023-03-18 10:20:42,813] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 10:20:42,815] [INFO] Task started: CheckM
[2023-03-18 10:20:42,816] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11568/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11568/checkm_input OceanDNA-b11568/checkm_result
[2023-03-18 10:21:06,346] [INFO] Task succeeded: CheckM
[2023-03-18 10:21:06,347] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.12%
Contamintation: 4.55%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-18 10:21:06,349] [INFO] ===== Completeness check finished =====
[2023-03-18 10:21:06,349] [INFO] ===== Start GTDB Search =====
[2023-03-18 10:21:06,349] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11568/markers.fasta)
[2023-03-18 10:21:06,351] [INFO] Task started: Blastn
[2023-03-18 10:21:06,351] [INFO] Running command: blastn -query OceanDNA-b11568/markers.fasta -db /var/lib/cwl/stg0df1e32a-6b7a-469f-b18a-cd4d5ca43681/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11568/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:21:07,084] [INFO] Task succeeded: Blastn
[2023-03-18 10:21:07,085] [INFO] Selected 21 target genomes.
[2023-03-18 10:21:07,086] [INFO] Target genome list was writen to OceanDNA-b11568/target_genomes_gtdb.txt
[2023-03-18 10:21:07,379] [INFO] Task started: fastANI
[2023-03-18 10:21:07,379] [INFO] Running command: fastANI --query /var/lib/cwl/stgee382aa5-557e-4a05-b83b-d187275d728d/OceanDNA-b11568.fa --refList OceanDNA-b11568/target_genomes_gtdb.txt --output OceanDNA-b11568/fastani_result_gtdb.tsv --threads 1
[2023-03-18 10:21:13,726] [INFO] Task succeeded: fastANI
[2023-03-18 10:21:13,732] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 10:21:13,732] [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_002713285.1	s__SP256 sp002713285	98.6375	342	383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__SP256	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002722215.1	s__SP256 sp002722215	78.7957	221	383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__SP256	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002714185.1	s__SP256 sp002714185	78.653	197	383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__SP256	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002707245.1	s__GCA-002707245 sp002707245	77.4678	124	383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__GCA-002707245	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002701365.1	s__GCA-002701365 sp002701365	77.205	162	383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__GCA-002701365	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002696965.1	s__GCA-2696965 sp002696965	76.9618	85	383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__GCA-2696965	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002171975.2	s__GCA-2696965 sp002171975	76.873	114	383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__GCA-2696965	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002718895.1	s__GCA-2718895 sp002718895	76.05	87	383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__GCA-2718895	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 10:21:13,733] [INFO] GTDB search result was written to OceanDNA-b11568/result_gtdb.tsv
[2023-03-18 10:21:13,733] [INFO] ===== GTDB Search completed =====
[2023-03-18 10:21:13,735] [INFO] DFAST_QC result json was written to OceanDNA-b11568/dqc_result.json
[2023-03-18 10:21:13,735] [INFO] DFAST_QC completed!
[2023-03-18 10:21:13,735] [INFO] Total running time: 0h0m51s