[2023-03-18 23:11:06,976] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:11:06,976] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:11:06,976] [INFO] DQC Reference Directory: /var/lib/cwl/stga91bc19c-3f50-45c2-9d6e-d20c636aa7b5/dqc_reference
[2023-03-18 23:11:08,176] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:11:08,177] [INFO] Task started: Prodigal
[2023-03-18 23:11:08,177] [INFO] Running command: cat /var/lib/cwl/stg6a8174f6-34fa-4755-9cbc-105e480288ad/OceanDNA-b19601.fa | prodigal -d OceanDNA-b19601/cds.fna -a OceanDNA-b19601/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:11:18,988] [INFO] Task succeeded: Prodigal
[2023-03-18 23:11:18,988] [INFO] Task started: HMMsearch
[2023-03-18 23:11:18,988] [INFO] Running command: hmmsearch --tblout OceanDNA-b19601/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga91bc19c-3f50-45c2-9d6e-d20c636aa7b5/dqc_reference/reference_markers.hmm OceanDNA-b19601/protein.faa > /dev/null
[2023-03-18 23:11:19,220] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:11:19,221] [INFO] Found 6/6 markers.
[2023-03-18 23:11:19,240] [INFO] Query marker FASTA was written to OceanDNA-b19601/markers.fasta
[2023-03-18 23:11:19,241] [INFO] Task started: Blastn
[2023-03-18 23:11:19,241] [INFO] Running command: blastn -query OceanDNA-b19601/markers.fasta -db /var/lib/cwl/stga91bc19c-3f50-45c2-9d6e-d20c636aa7b5/dqc_reference/reference_markers.fasta -out OceanDNA-b19601/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:11:19,765] [INFO] Task succeeded: Blastn
[2023-03-18 23:11:19,766] [INFO] Selected 13 target genomes.
[2023-03-18 23:11:19,766] [INFO] Target genome list was writen to OceanDNA-b19601/target_genomes.txt
[2023-03-18 23:11:19,775] [INFO] Task started: fastANI
[2023-03-18 23:11:19,776] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a8174f6-34fa-4755-9cbc-105e480288ad/OceanDNA-b19601.fa --refList OceanDNA-b19601/target_genomes.txt --output OceanDNA-b19601/fastani_result.tsv --threads 1
[2023-03-18 23:11:25,056] [INFO] Task succeeded: fastANI
[2023-03-18 23:11:25,056] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga91bc19c-3f50-45c2-9d6e-d20c636aa7b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:11:25,057] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga91bc19c-3f50-45c2-9d6e-d20c636aa7b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:11:25,057] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:11:25,057] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 23:11:25,057] [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 23:11:25,057] [INFO] DFAST Taxonomy check result was written to OceanDNA-b19601/tc_result.tsv
[2023-03-18 23:11:25,057] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:11:25,057] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:11:25,058] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga91bc19c-3f50-45c2-9d6e-d20c636aa7b5/dqc_reference/checkm_data
[2023-03-18 23:11:25,060] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:11:25,065] [INFO] Task started: CheckM
[2023-03-18 23:11:25,065] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b19601/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b19601/checkm_input OceanDNA-b19601/checkm_result
[2023-03-18 23:11:56,144] [INFO] Task succeeded: CheckM
[2023-03-18 23:11:56,145] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.91%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 23:11:56,147] [INFO] ===== Completeness check finished =====
[2023-03-18 23:11:56,147] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:11:56,147] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b19601/markers.fasta)
[2023-03-18 23:11:56,147] [INFO] Task started: Blastn
[2023-03-18 23:11:56,148] [INFO] Running command: blastn -query OceanDNA-b19601/markers.fasta -db /var/lib/cwl/stga91bc19c-3f50-45c2-9d6e-d20c636aa7b5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b19601/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:11:56,873] [INFO] Task succeeded: Blastn
[2023-03-18 23:11:56,874] [INFO] Selected 23 target genomes.
[2023-03-18 23:11:56,875] [INFO] Target genome list was writen to OceanDNA-b19601/target_genomes_gtdb.txt
[2023-03-18 23:11:56,892] [INFO] Task started: fastANI
[2023-03-18 23:11:56,892] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a8174f6-34fa-4755-9cbc-105e480288ad/OceanDNA-b19601.fa --refList OceanDNA-b19601/target_genomes_gtdb.txt --output OceanDNA-b19601/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:12:04,129] [INFO] Task succeeded: fastANI
[2023-03-18 23:12:04,131] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 23:12:04,132] [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_002708715.1	s__GCA-002708715 sp002708715	75.6611	60	711	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__GCA-002708715	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002718285.1	s__UBA2134 sp002718285	75.3291	52	711	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__UBA2134	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 23:12:04,132] [INFO] GTDB search result was written to OceanDNA-b19601/result_gtdb.tsv
[2023-03-18 23:12:04,132] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:12:04,132] [INFO] DFAST_QC result json was written to OceanDNA-b19601/dqc_result.json
[2023-03-18 23:12:04,133] [INFO] DFAST_QC completed!
[2023-03-18 23:12:04,133] [INFO] Total running time: 0h0m57s