[2023-03-18 22:44:57,813] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:44:57,814] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:44:57,814] [INFO] DQC Reference Directory: /var/lib/cwl/stge69b1671-eafb-4115-99b2-cff550bed7aa/dqc_reference
[2023-03-18 22:44:58,938] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:44:58,938] [INFO] Task started: Prodigal
[2023-03-18 22:44:58,938] [INFO] Running command: cat /var/lib/cwl/stgdefc05da-4f3a-40ae-b9af-c7d5f256f44d/OceanDNA-b43740.fa | prodigal -d OceanDNA-b43740/cds.fna -a OceanDNA-b43740/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:45:14,915] [INFO] Task succeeded: Prodigal
[2023-03-18 22:45:14,915] [INFO] Task started: HMMsearch
[2023-03-18 22:45:14,915] [INFO] Running command: hmmsearch --tblout OceanDNA-b43740/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge69b1671-eafb-4115-99b2-cff550bed7aa/dqc_reference/reference_markers.hmm OceanDNA-b43740/protein.faa > /dev/null
[2023-03-18 22:45:15,103] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:45:15,103] [INFO] Found 6/6 markers.
[2023-03-18 22:45:15,119] [INFO] Query marker FASTA was written to OceanDNA-b43740/markers.fasta
[2023-03-18 22:45:15,120] [INFO] Task started: Blastn
[2023-03-18 22:45:15,120] [INFO] Running command: blastn -query OceanDNA-b43740/markers.fasta -db /var/lib/cwl/stge69b1671-eafb-4115-99b2-cff550bed7aa/dqc_reference/reference_markers.fasta -out OceanDNA-b43740/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:45:15,707] [INFO] Task succeeded: Blastn
[2023-03-18 22:45:15,708] [INFO] Selected 30 target genomes.
[2023-03-18 22:45:15,708] [INFO] Target genome list was writen to OceanDNA-b43740/target_genomes.txt
[2023-03-18 22:45:15,726] [INFO] Task started: fastANI
[2023-03-18 22:45:15,726] [INFO] Running command: fastANI --query /var/lib/cwl/stgdefc05da-4f3a-40ae-b9af-c7d5f256f44d/OceanDNA-b43740.fa --refList OceanDNA-b43740/target_genomes.txt --output OceanDNA-b43740/fastani_result.tsv --threads 1
[2023-03-18 22:45:32,851] [INFO] Task succeeded: fastANI
[2023-03-18 22:45:32,851] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge69b1671-eafb-4115-99b2-cff550bed7aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:45:32,852] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge69b1671-eafb-4115-99b2-cff550bed7aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:45:32,852] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 22:45:32,852] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 22:45:32,852] [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 22:45:32,852] [INFO] DFAST Taxonomy check result was written to OceanDNA-b43740/tc_result.tsv
[2023-03-18 22:45:32,852] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:45:32,852] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:45:32,852] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge69b1671-eafb-4115-99b2-cff550bed7aa/dqc_reference/checkm_data
[2023-03-18 22:45:32,855] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:45:32,860] [INFO] Task started: CheckM
[2023-03-18 22:45:32,860] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b43740/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b43740/checkm_input OceanDNA-b43740/checkm_result
[2023-03-18 22:46:16,228] [INFO] Task succeeded: CheckM
[2023-03-18 22:46:16,228] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 22:46:16,230] [INFO] ===== Completeness check finished =====
[2023-03-18 22:46:16,230] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:46:16,231] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b43740/markers.fasta)
[2023-03-18 22:46:16,232] [INFO] Task started: Blastn
[2023-03-18 22:46:16,232] [INFO] Running command: blastn -query OceanDNA-b43740/markers.fasta -db /var/lib/cwl/stge69b1671-eafb-4115-99b2-cff550bed7aa/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b43740/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:46:17,217] [INFO] Task succeeded: Blastn
[2023-03-18 22:46:17,217] [INFO] Selected 8 target genomes.
[2023-03-18 22:46:17,217] [INFO] Target genome list was writen to OceanDNA-b43740/target_genomes_gtdb.txt
[2023-03-18 22:46:17,265] [INFO] Task started: fastANI
[2023-03-18 22:46:17,265] [INFO] Running command: fastANI --query /var/lib/cwl/stgdefc05da-4f3a-40ae-b9af-c7d5f256f44d/OceanDNA-b43740.fa --refList OceanDNA-b43740/target_genomes_gtdb.txt --output OceanDNA-b43740/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:46:21,476] [INFO] Task succeeded: fastANI
[2023-03-18 22:46:21,480] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 22:46:21,481] [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_002477475.1	s__UBA868 sp002477475	99.7307	738	867	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA868	95.0	99.71	99.58	0.88	0.75	11	conclusive
GCA_011523045.1	s__UBA868 sp011523045	92.5028	644	867	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA868	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002713825.1	s__UBA868 sp002713825	90.2801	463	867	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA868	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002694065.1	s__UBA868 sp002694065	90.1916	503	867	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA868	95.0	97.83	97.76	0.76	0.75	3	-
GCA_002346525.1	s__UBA868 sp002346525	85.0243	432	867	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA868	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016845525.1	s__UBA868 sp016845525	84.8172	474	867	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA868	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 22:46:21,481] [INFO] GTDB search result was written to OceanDNA-b43740/result_gtdb.tsv
[2023-03-18 22:46:21,481] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:46:21,481] [INFO] DFAST_QC result json was written to OceanDNA-b43740/dqc_result.json
[2023-03-18 22:46:21,482] [INFO] DFAST_QC completed!
[2023-03-18 22:46:21,482] [INFO] Total running time: 0h1m24s