[2023-03-18 05:35:37,307] [INFO] DFAST_QC pipeline started.
[2023-03-18 05:35:37,308] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 05:35:37,308] [INFO] DQC Reference Directory: /var/lib/cwl/stg222f36d3-8fc3-4d0e-b0be-deb213bb8047/dqc_reference
[2023-03-18 05:35:38,963] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 05:35:38,963] [INFO] Task started: Prodigal
[2023-03-18 05:35:38,964] [INFO] Running command: cat /var/lib/cwl/stg8fc6f0b1-f173-45ca-813c-f2f0f38092a6/OceanDNA-b41982.fa | prodigal -d OceanDNA-b41982/cds.fna -a OceanDNA-b41982/protein.faa -g 11 -q > /dev/null
[2023-03-18 05:35:43,259] [INFO] Task succeeded: Prodigal
[2023-03-18 05:35:43,259] [INFO] Task started: HMMsearch
[2023-03-18 05:35:43,259] [INFO] Running command: hmmsearch --tblout OceanDNA-b41982/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg222f36d3-8fc3-4d0e-b0be-deb213bb8047/dqc_reference/reference_markers.hmm OceanDNA-b41982/protein.faa > /dev/null
[2023-03-18 05:35:43,387] [INFO] Task succeeded: HMMsearch
[2023-03-18 05:35:43,388] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg8fc6f0b1-f173-45ca-813c-f2f0f38092a6/OceanDNA-b41982.fa]
[2023-03-18 05:35:43,407] [INFO] Query marker FASTA was written to OceanDNA-b41982/markers.fasta
[2023-03-18 05:35:43,408] [INFO] Task started: Blastn
[2023-03-18 05:35:43,408] [INFO] Running command: blastn -query OceanDNA-b41982/markers.fasta -db /var/lib/cwl/stg222f36d3-8fc3-4d0e-b0be-deb213bb8047/dqc_reference/reference_markers.fasta -out OceanDNA-b41982/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:35:44,658] [INFO] Task succeeded: Blastn
[2023-03-18 05:35:44,666] [INFO] Selected 10 target genomes.
[2023-03-18 05:35:44,667] [INFO] Target genome list was writen to OceanDNA-b41982/target_genomes.txt
[2023-03-18 05:35:44,674] [INFO] Task started: fastANI
[2023-03-18 05:35:44,674] [INFO] Running command: fastANI --query /var/lib/cwl/stg8fc6f0b1-f173-45ca-813c-f2f0f38092a6/OceanDNA-b41982.fa --refList OceanDNA-b41982/target_genomes.txt --output OceanDNA-b41982/fastani_result.tsv --threads 1
[2023-03-18 05:35:48,234] [INFO] Task succeeded: fastANI
[2023-03-18 05:35:48,235] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg222f36d3-8fc3-4d0e-b0be-deb213bb8047/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 05:35:48,235] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg222f36d3-8fc3-4d0e-b0be-deb213bb8047/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 05:35:48,235] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 05:35:48,235] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 05:35:48,235] [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 05:35:48,243] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41982/tc_result.tsv
[2023-03-18 05:35:48,249] [INFO] ===== Taxonomy check completed =====
[2023-03-18 05:35:48,249] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 05:35:48,249] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg222f36d3-8fc3-4d0e-b0be-deb213bb8047/dqc_reference/checkm_data
[2023-03-18 05:35:48,253] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 05:35:48,256] [INFO] Task started: CheckM
[2023-03-18 05:35:48,256] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41982/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41982/checkm_input OceanDNA-b41982/checkm_result
[2023-03-18 05:36:04,268] [INFO] Task succeeded: CheckM
[2023-03-18 05:36:04,268] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 43.75%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 05:36:04,289] [INFO] ===== Completeness check finished =====
[2023-03-18 05:36:04,289] [INFO] ===== Start GTDB Search =====
[2023-03-18 05:36:04,289] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41982/markers.fasta)
[2023-03-18 05:36:04,290] [INFO] Task started: Blastn
[2023-03-18 05:36:04,290] [INFO] Running command: blastn -query OceanDNA-b41982/markers.fasta -db /var/lib/cwl/stg222f36d3-8fc3-4d0e-b0be-deb213bb8047/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41982/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:36:04,908] [INFO] Task succeeded: Blastn
[2023-03-18 05:36:04,913] [INFO] Selected 15 target genomes.
[2023-03-18 05:36:04,913] [INFO] Target genome list was writen to OceanDNA-b41982/target_genomes_gtdb.txt
[2023-03-18 05:36:04,929] [INFO] Task started: fastANI
[2023-03-18 05:36:04,929] [INFO] Running command: fastANI --query /var/lib/cwl/stg8fc6f0b1-f173-45ca-813c-f2f0f38092a6/OceanDNA-b41982.fa --refList OceanDNA-b41982/target_genomes_gtdb.txt --output OceanDNA-b41982/fastani_result_gtdb.tsv --threads 1
[2023-03-18 05:36:07,865] [INFO] Task succeeded: fastANI
[2023-03-18 05:36:07,868] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 05:36:07,868] [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_902559885.1	s__CACEJU01 sp902559885	95.7711	208	254	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__CACEJU01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902558395.1	s__SCGC-AAA076-P13 sp902558395	76.4464	60	254	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	97.77	97.77	0.94	0.94	2	-
GCA_000385055.1	s__SCGC-AAA076-P13 sp000385055	76.3599	53	254	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	98.19	98.19	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-03-18 05:36:07,870] [INFO] GTDB search result was written to OceanDNA-b41982/result_gtdb.tsv
[2023-03-18 05:36:07,872] [INFO] ===== GTDB Search completed =====
[2023-03-18 05:36:07,875] [INFO] DFAST_QC result json was written to OceanDNA-b41982/dqc_result.json
[2023-03-18 05:36:07,876] [INFO] DFAST_QC completed!
[2023-03-18 05:36:07,876] [INFO] Total running time: 0h0m31s