[2023-03-17 00:45:47,078] [INFO] DFAST_QC pipeline started.
[2023-03-17 00:45:47,078] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 00:45:47,078] [INFO] DQC Reference Directory: /var/lib/cwl/stgca137207-9113-48dd-933c-eab88106b411/dqc_reference
[2023-03-17 00:45:48,284] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 00:45:48,284] [INFO] Task started: Prodigal
[2023-03-17 00:45:48,284] [INFO] Running command: cat /var/lib/cwl/stgc61fe5e0-50d1-44a6-b120-a969c9d47004/OceanDNA-b12713.fa | prodigal -d OceanDNA-b12713/cds.fna -a OceanDNA-b12713/protein.faa -g 11 -q > /dev/null
[2023-03-17 00:45:59,856] [INFO] Task succeeded: Prodigal
[2023-03-17 00:45:59,856] [INFO] Task started: HMMsearch
[2023-03-17 00:45:59,856] [INFO] Running command: hmmsearch --tblout OceanDNA-b12713/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgca137207-9113-48dd-933c-eab88106b411/dqc_reference/reference_markers.hmm OceanDNA-b12713/protein.faa > /dev/null
[2023-03-17 00:46:00,009] [INFO] Task succeeded: HMMsearch
[2023-03-17 00:46:00,010] [INFO] Found 6/6 markers.
[2023-03-17 00:46:00,021] [INFO] Query marker FASTA was written to OceanDNA-b12713/markers.fasta
[2023-03-17 00:46:00,021] [INFO] Task started: Blastn
[2023-03-17 00:46:00,021] [INFO] Running command: blastn -query OceanDNA-b12713/markers.fasta -db /var/lib/cwl/stgca137207-9113-48dd-933c-eab88106b411/dqc_reference/reference_markers.fasta -out OceanDNA-b12713/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:46:00,536] [INFO] Task succeeded: Blastn
[2023-03-17 00:46:00,537] [INFO] Selected 28 target genomes.
[2023-03-17 00:46:00,537] [INFO] Target genome list was writen to OceanDNA-b12713/target_genomes.txt
[2023-03-17 00:46:00,582] [INFO] Task started: fastANI
[2023-03-17 00:46:00,582] [INFO] Running command: fastANI --query /var/lib/cwl/stgc61fe5e0-50d1-44a6-b120-a969c9d47004/OceanDNA-b12713.fa --refList OceanDNA-b12713/target_genomes.txt --output OceanDNA-b12713/fastani_result.tsv --threads 1
[2023-03-17 00:46:16,472] [INFO] Task succeeded: fastANI
[2023-03-17 00:46:16,472] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgca137207-9113-48dd-933c-eab88106b411/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 00:46:16,472] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgca137207-9113-48dd-933c-eab88106b411/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 00:46:16,473] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 00:46:16,473] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 00:46:16,473] [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 00:46:16,473] [INFO] DFAST Taxonomy check result was written to OceanDNA-b12713/tc_result.tsv
[2023-03-17 00:46:16,473] [INFO] ===== Taxonomy check completed =====
[2023-03-17 00:46:16,473] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 00:46:16,473] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgca137207-9113-48dd-933c-eab88106b411/dqc_reference/checkm_data
[2023-03-17 00:46:16,476] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 00:46:16,479] [INFO] Task started: CheckM
[2023-03-17 00:46:16,479] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b12713/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b12713/checkm_input OceanDNA-b12713/checkm_result
[2023-03-17 00:46:49,792] [INFO] Task succeeded: CheckM
[2023-03-17 00:46:49,793] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 00:46:49,795] [INFO] ===== Completeness check finished =====
[2023-03-17 00:46:49,795] [INFO] ===== Start GTDB Search =====
[2023-03-17 00:46:49,795] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b12713/markers.fasta)
[2023-03-17 00:46:49,796] [INFO] Task started: Blastn
[2023-03-17 00:46:49,796] [INFO] Running command: blastn -query OceanDNA-b12713/markers.fasta -db /var/lib/cwl/stgca137207-9113-48dd-933c-eab88106b411/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b12713/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:46:50,585] [INFO] Task succeeded: Blastn
[2023-03-17 00:46:50,586] [INFO] Selected 28 target genomes.
[2023-03-17 00:46:50,586] [INFO] Target genome list was writen to OceanDNA-b12713/target_genomes_gtdb.txt
[2023-03-17 00:46:51,238] [INFO] Task started: fastANI
[2023-03-17 00:46:51,238] [INFO] Running command: fastANI --query /var/lib/cwl/stgc61fe5e0-50d1-44a6-b120-a969c9d47004/OceanDNA-b12713.fa --refList OceanDNA-b12713/target_genomes_gtdb.txt --output OceanDNA-b12713/fastani_result_gtdb.tsv --threads 1
[2023-03-17 00:47:05,648] [INFO] Task succeeded: fastANI
[2023-03-17 00:47:05,653] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 00:47:05,653] [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_016779945.1	s__UBA9320 sp016779945	97.7161	460	585	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__NS11-12g;f__UBA9320;g__UBA9320	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013042025.1	s__UBA9320 sp013042025	76.9959	51	585	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__NS11-12g;f__UBA9320;g__UBA9320	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002746305.1	s__UBA9320 sp002746305	76.7437	81	585	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__NS11-12g;f__UBA9320;g__UBA9320	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402155.1	s__UBA9320 sp018402155	76.5919	61	585	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__NS11-12g;f__UBA9320;g__UBA9320	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018700895.1	s__UBA9320 sp018700895	76.3564	57	585	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__NS11-12g;f__UBA9320;g__UBA9320	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 00:47:05,653] [INFO] GTDB search result was written to OceanDNA-b12713/result_gtdb.tsv
[2023-03-17 00:47:05,653] [INFO] ===== GTDB Search completed =====
[2023-03-17 00:47:05,654] [INFO] DFAST_QC result json was written to OceanDNA-b12713/dqc_result.json
[2023-03-17 00:47:05,654] [INFO] DFAST_QC completed!
[2023-03-17 00:47:05,654] [INFO] Total running time: 0h1m19s