[2023-03-15 05:37:29,693] [INFO] DFAST_QC pipeline started.
[2023-03-15 05:37:29,693] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 05:37:29,693] [INFO] DQC Reference Directory: /var/lib/cwl/stgbc499e39-1987-4d1e-adf1-8146bd754b89/dqc_reference
[2023-03-15 05:37:30,777] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 05:37:30,777] [INFO] Task started: Prodigal
[2023-03-15 05:37:30,777] [INFO] Running command: cat /var/lib/cwl/stgb55e27f5-6e48-4f74-82b6-8955bd16c997/OceanDNA-b20294.fa | prodigal -d OceanDNA-b20294/cds.fna -a OceanDNA-b20294/protein.faa -g 11 -q > /dev/null
[2023-03-15 05:37:40,071] [INFO] Task succeeded: Prodigal
[2023-03-15 05:37:40,071] [INFO] Task started: HMMsearch
[2023-03-15 05:37:40,071] [INFO] Running command: hmmsearch --tblout OceanDNA-b20294/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbc499e39-1987-4d1e-adf1-8146bd754b89/dqc_reference/reference_markers.hmm OceanDNA-b20294/protein.faa > /dev/null
[2023-03-15 05:37:40,229] [INFO] Task succeeded: HMMsearch
[2023-03-15 05:37:40,230] [INFO] Found 6/6 markers.
[2023-03-15 05:37:40,242] [INFO] Query marker FASTA was written to OceanDNA-b20294/markers.fasta
[2023-03-15 05:37:40,242] [INFO] Task started: Blastn
[2023-03-15 05:37:40,242] [INFO] Running command: blastn -query OceanDNA-b20294/markers.fasta -db /var/lib/cwl/stgbc499e39-1987-4d1e-adf1-8146bd754b89/dqc_reference/reference_markers.fasta -out OceanDNA-b20294/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:37:40,748] [INFO] Task succeeded: Blastn
[2023-03-15 05:37:40,749] [INFO] Selected 15 target genomes.
[2023-03-15 05:37:40,749] [INFO] Target genome list was writen to OceanDNA-b20294/target_genomes.txt
[2023-03-15 05:37:40,755] [INFO] Task started: fastANI
[2023-03-15 05:37:40,756] [INFO] Running command: fastANI --query /var/lib/cwl/stgb55e27f5-6e48-4f74-82b6-8955bd16c997/OceanDNA-b20294.fa --refList OceanDNA-b20294/target_genomes.txt --output OceanDNA-b20294/fastani_result.tsv --threads 1
[2023-03-15 05:37:47,579] [INFO] Task succeeded: fastANI
[2023-03-15 05:37:47,579] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbc499e39-1987-4d1e-adf1-8146bd754b89/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 05:37:47,579] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbc499e39-1987-4d1e-adf1-8146bd754b89/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 05:37:47,579] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 05:37:47,579] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 05:37:47,580] [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 05:37:47,580] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20294/tc_result.tsv
[2023-03-15 05:37:47,580] [INFO] ===== Taxonomy check completed =====
[2023-03-15 05:37:47,580] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 05:37:47,580] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbc499e39-1987-4d1e-adf1-8146bd754b89/dqc_reference/checkm_data
[2023-03-15 05:37:47,582] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 05:37:47,586] [INFO] Task started: CheckM
[2023-03-15 05:37:47,586] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20294/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20294/checkm_input OceanDNA-b20294/checkm_result
[2023-03-15 05:38:15,716] [INFO] Task succeeded: CheckM
[2023-03-15 05:38:15,716] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.27%
Contamintation: 0.93%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 05:38:15,718] [INFO] ===== Completeness check finished =====
[2023-03-15 05:38:15,719] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:38:15,719] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20294/markers.fasta)
[2023-03-15 05:38:15,720] [INFO] Task started: Blastn
[2023-03-15 05:38:15,720] [INFO] Running command: blastn -query OceanDNA-b20294/markers.fasta -db /var/lib/cwl/stgbc499e39-1987-4d1e-adf1-8146bd754b89/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20294/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:38:16,437] [INFO] Task succeeded: Blastn
[2023-03-15 05:38:16,439] [INFO] Selected 16 target genomes.
[2023-03-15 05:38:16,439] [INFO] Target genome list was writen to OceanDNA-b20294/target_genomes_gtdb.txt
[2023-03-15 05:38:16,460] [INFO] Task started: fastANI
[2023-03-15 05:38:16,460] [INFO] Running command: fastANI --query /var/lib/cwl/stgb55e27f5-6e48-4f74-82b6-8955bd16c997/OceanDNA-b20294.fa --refList OceanDNA-b20294/target_genomes_gtdb.txt --output OceanDNA-b20294/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:38:22,509] [INFO] Task succeeded: fastANI
[2023-03-15 05:38:22,511] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 05:38:22,511] [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_002402135.1	s__UBA2128 sp002402135	96.8762	474	546	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA2128;g__UBA2128	95.0	98.48	98.38	0.92	0.90	5	conclusive
GCA_002471865.1	s__UBA2128 sp002471865	84.3964	350	546	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA2128;g__UBA2128	95.0	99.17	96.76	0.86	0.75	6	-
--------------------------------------------------------------------------------
[2023-03-15 05:38:22,512] [INFO] GTDB search result was written to OceanDNA-b20294/result_gtdb.tsv
[2023-03-15 05:38:22,512] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:38:22,513] [INFO] DFAST_QC result json was written to OceanDNA-b20294/dqc_result.json
[2023-03-15 05:38:22,513] [INFO] DFAST_QC completed!
[2023-03-15 05:38:22,513] [INFO] Total running time: 0h0m53s