[2023-03-15 22:44:22,109] [INFO] DFAST_QC pipeline started.
[2023-03-15 22:44:22,109] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 22:44:22,109] [INFO] DQC Reference Directory: /var/lib/cwl/stgd14fab9c-8fa7-43a0-aa28-92d5a6eb6b14/dqc_reference
[2023-03-15 22:44:23,185] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 22:44:23,187] [INFO] Task started: Prodigal
[2023-03-15 22:44:23,187] [INFO] Running command: cat /var/lib/cwl/stg5ceccec1-55dc-4cd2-9ecf-71e449e404c1/OceanDNA-b44522.fa | prodigal -d OceanDNA-b44522/cds.fna -a OceanDNA-b44522/protein.faa -g 11 -q > /dev/null
[2023-03-15 22:44:32,403] [INFO] Task succeeded: Prodigal
[2023-03-15 22:44:32,404] [INFO] Task started: HMMsearch
[2023-03-15 22:44:32,404] [INFO] Running command: hmmsearch --tblout OceanDNA-b44522/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd14fab9c-8fa7-43a0-aa28-92d5a6eb6b14/dqc_reference/reference_markers.hmm OceanDNA-b44522/protein.faa > /dev/null
[2023-03-15 22:44:32,584] [INFO] Task succeeded: HMMsearch
[2023-03-15 22:44:32,585] [INFO] Found 6/6 markers.
[2023-03-15 22:44:32,602] [INFO] Query marker FASTA was written to OceanDNA-b44522/markers.fasta
[2023-03-15 22:44:32,602] [INFO] Task started: Blastn
[2023-03-15 22:44:32,602] [INFO] Running command: blastn -query OceanDNA-b44522/markers.fasta -db /var/lib/cwl/stgd14fab9c-8fa7-43a0-aa28-92d5a6eb6b14/dqc_reference/reference_markers.fasta -out OceanDNA-b44522/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:44:33,137] [INFO] Task succeeded: Blastn
[2023-03-15 22:44:33,144] [INFO] Selected 21 target genomes.
[2023-03-15 22:44:33,145] [INFO] Target genome list was writen to OceanDNA-b44522/target_genomes.txt
[2023-03-15 22:44:33,156] [INFO] Task started: fastANI
[2023-03-15 22:44:33,156] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ceccec1-55dc-4cd2-9ecf-71e449e404c1/OceanDNA-b44522.fa --refList OceanDNA-b44522/target_genomes.txt --output OceanDNA-b44522/fastani_result.tsv --threads 1
[2023-03-15 22:44:42,105] [INFO] Task succeeded: fastANI
[2023-03-15 22:44:42,105] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd14fab9c-8fa7-43a0-aa28-92d5a6eb6b14/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 22:44:42,106] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd14fab9c-8fa7-43a0-aa28-92d5a6eb6b14/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 22:44:42,106] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 22:44:42,106] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 22:44:42,106] [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
--------------------------------------------------------------------------------
[2023-03-15 22:44:42,120] [INFO] DFAST Taxonomy check result was written to OceanDNA-b44522/tc_result.tsv
[2023-03-15 22:44:42,151] [INFO] ===== Taxonomy check completed =====
[2023-03-15 22:44:42,151] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 22:44:42,151] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd14fab9c-8fa7-43a0-aa28-92d5a6eb6b14/dqc_reference/checkm_data
[2023-03-15 22:44:42,154] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 22:44:42,194] [INFO] Task started: CheckM
[2023-03-15 22:44:42,194] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b44522/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b44522/checkm_input OceanDNA-b44522/checkm_result
[2023-03-15 22:45:10,081] [INFO] Task succeeded: CheckM
[2023-03-15 22:45:10,081] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 22:45:10,293] [INFO] ===== Completeness check finished =====
[2023-03-15 22:45:10,294] [INFO] ===== Start GTDB Search =====
[2023-03-15 22:45:10,294] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b44522/markers.fasta)
[2023-03-15 22:45:10,295] [INFO] Task started: Blastn
[2023-03-15 22:45:10,295] [INFO] Running command: blastn -query OceanDNA-b44522/markers.fasta -db /var/lib/cwl/stgd14fab9c-8fa7-43a0-aa28-92d5a6eb6b14/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b44522/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:45:11,111] [INFO] Task succeeded: Blastn
[2023-03-15 22:45:11,117] [INFO] Selected 29 target genomes.
[2023-03-15 22:45:11,117] [INFO] Target genome list was writen to OceanDNA-b44522/target_genomes_gtdb.txt
[2023-03-15 22:45:11,333] [INFO] Task started: fastANI
[2023-03-15 22:45:11,333] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ceccec1-55dc-4cd2-9ecf-71e449e404c1/OceanDNA-b44522.fa --refList OceanDNA-b44522/target_genomes_gtdb.txt --output OceanDNA-b44522/fastani_result_gtdb.tsv --threads 1
[2023-03-15 22:45:22,102] [INFO] Task succeeded: fastANI
[2023-03-15 22:45:22,105] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 22:45:22,105] [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_905182415.1	s__SP4260 sp905182415	99.7704	520	575	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__SP4260	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902510755.1	s__SP4260 sp902510755	77.6737	104	575	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__SP4260	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 22:45:22,118] [INFO] GTDB search result was written to OceanDNA-b44522/result_gtdb.tsv
[2023-03-15 22:45:22,146] [INFO] ===== GTDB Search completed =====
[2023-03-15 22:45:22,162] [INFO] DFAST_QC result json was written to OceanDNA-b44522/dqc_result.json
[2023-03-15 22:45:22,162] [INFO] DFAST_QC completed!
[2023-03-15 22:45:22,162] [INFO] Total running time: 0h1m0s