[2023-03-18 09:26:42,710] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:26:42,714] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:26:42,714] [INFO] DQC Reference Directory: /var/lib/cwl/stgfa2fe9b8-e300-430d-8b18-3552250be69d/dqc_reference
[2023-03-18 09:26:43,866] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:26:43,866] [INFO] Task started: Prodigal
[2023-03-18 09:26:43,866] [INFO] Running command: cat /var/lib/cwl/stgcf36b923-9482-4422-a97a-bf3a95dc7308/OceanDNA-b16777.fa | prodigal -d OceanDNA-b16777/cds.fna -a OceanDNA-b16777/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:27:27,228] [INFO] Task succeeded: Prodigal
[2023-03-18 09:27:27,229] [INFO] Task started: HMMsearch
[2023-03-18 09:27:27,229] [INFO] Running command: hmmsearch --tblout OceanDNA-b16777/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfa2fe9b8-e300-430d-8b18-3552250be69d/dqc_reference/reference_markers.hmm OceanDNA-b16777/protein.faa > /dev/null
[2023-03-18 09:27:27,496] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:27:27,497] [INFO] Found 6/6 markers.
[2023-03-18 09:27:27,538] [INFO] Query marker FASTA was written to OceanDNA-b16777/markers.fasta
[2023-03-18 09:27:27,538] [INFO] Task started: Blastn
[2023-03-18 09:27:27,538] [INFO] Running command: blastn -query OceanDNA-b16777/markers.fasta -db /var/lib/cwl/stgfa2fe9b8-e300-430d-8b18-3552250be69d/dqc_reference/reference_markers.fasta -out OceanDNA-b16777/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:27:28,047] [INFO] Task succeeded: Blastn
[2023-03-18 09:27:28,047] [INFO] Selected 11 target genomes.
[2023-03-18 09:27:28,048] [INFO] Target genome list was writen to OceanDNA-b16777/target_genomes.txt
[2023-03-18 09:27:28,052] [INFO] Task started: fastANI
[2023-03-18 09:27:28,053] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf36b923-9482-4422-a97a-bf3a95dc7308/OceanDNA-b16777.fa --refList OceanDNA-b16777/target_genomes.txt --output OceanDNA-b16777/fastani_result.tsv --threads 1
[2023-03-18 09:27:34,824] [INFO] Task succeeded: fastANI
[2023-03-18 09:27:34,825] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfa2fe9b8-e300-430d-8b18-3552250be69d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:27:34,825] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfa2fe9b8-e300-430d-8b18-3552250be69d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:27:34,825] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:27:34,825] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 09:27:34,825] [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 09:27:34,825] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16777/tc_result.tsv
[2023-03-18 09:27:34,825] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:27:34,825] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:27:34,826] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfa2fe9b8-e300-430d-8b18-3552250be69d/dqc_reference/checkm_data
[2023-03-18 09:27:34,828] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:27:34,908] [INFO] Task started: CheckM
[2023-03-18 09:27:34,908] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16777/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16777/checkm_input OceanDNA-b16777/checkm_result
[2023-03-18 09:29:18,772] [INFO] Task succeeded: CheckM
[2023-03-18 09:29:18,772] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 09:29:18,777] [INFO] ===== Completeness check finished =====
[2023-03-18 09:29:18,777] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:29:18,777] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16777/markers.fasta)
[2023-03-18 09:29:18,777] [INFO] Task started: Blastn
[2023-03-18 09:29:18,777] [INFO] Running command: blastn -query OceanDNA-b16777/markers.fasta -db /var/lib/cwl/stgfa2fe9b8-e300-430d-8b18-3552250be69d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16777/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:29:19,498] [INFO] Task succeeded: Blastn
[2023-03-18 09:29:19,499] [INFO] Selected 19 target genomes.
[2023-03-18 09:29:19,499] [INFO] Target genome list was writen to OceanDNA-b16777/target_genomes_gtdb.txt
[2023-03-18 09:29:19,581] [INFO] Task started: fastANI
[2023-03-18 09:29:19,581] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf36b923-9482-4422-a97a-bf3a95dc7308/OceanDNA-b16777.fa --refList OceanDNA-b16777/target_genomes_gtdb.txt --output OceanDNA-b16777/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:29:32,944] [INFO] Task succeeded: fastANI
[2023-03-18 09:29:32,947] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 09:29:32,948] [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_013997645.1	s__QKMZ01 sp013997645	76.6077	57	2413	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Obscuribacterales;f__Obscuribacteraceae;g__QKMZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003242885.1	s__QKMZ01 sp003242885	76.5764	90	2413	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Obscuribacterales;f__Obscuribacteraceae;g__QKMZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016212515.1	s__Obscuribacter sp016212515	76.3542	57	2413	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Obscuribacterales;f__Obscuribacteraceae;g__Obscuribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018266255.1	s__PALSA-1081 sp018266255	76.2884	52	2413	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Obscuribacterales;f__Obscuribacteraceae;g__PALSA-1081	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124935.1	s__RI-106 sp016124935	76.146	56	2413	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Obscuribacterales;f__Obscuribacteraceae;g__RI-106	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 09:29:32,948] [INFO] GTDB search result was written to OceanDNA-b16777/result_gtdb.tsv
[2023-03-18 09:29:32,948] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:29:32,949] [INFO] DFAST_QC result json was written to OceanDNA-b16777/dqc_result.json
[2023-03-18 09:29:32,949] [INFO] DFAST_QC completed!
[2023-03-18 09:29:32,949] [INFO] Total running time: 0h2m50s