[2023-03-16 08:50:59,666] [INFO] DFAST_QC pipeline started.
[2023-03-16 08:50:59,666] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 08:50:59,666] [INFO] DQC Reference Directory: /var/lib/cwl/stga9d2a260-11e1-4469-89bb-9e8033d2a90f/dqc_reference
[2023-03-16 08:51:00,791] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 08:51:00,792] [INFO] Task started: Prodigal
[2023-03-16 08:51:00,792] [INFO] Running command: cat /var/lib/cwl/stga9a5559e-4a2d-4a0c-a845-61f3ad4a5bd0/OceanDNA-b21568.fa | prodigal -d OceanDNA-b21568/cds.fna -a OceanDNA-b21568/protein.faa -g 11 -q > /dev/null
[2023-03-16 08:51:08,506] [INFO] Task succeeded: Prodigal
[2023-03-16 08:51:08,507] [INFO] Task started: HMMsearch
[2023-03-16 08:51:08,507] [INFO] Running command: hmmsearch --tblout OceanDNA-b21568/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga9d2a260-11e1-4469-89bb-9e8033d2a90f/dqc_reference/reference_markers.hmm OceanDNA-b21568/protein.faa > /dev/null
[2023-03-16 08:51:08,694] [INFO] Task succeeded: HMMsearch
[2023-03-16 08:51:08,695] [INFO] Found 6/6 markers.
[2023-03-16 08:51:08,707] [INFO] Query marker FASTA was written to OceanDNA-b21568/markers.fasta
[2023-03-16 08:51:08,707] [INFO] Task started: Blastn
[2023-03-16 08:51:08,707] [INFO] Running command: blastn -query OceanDNA-b21568/markers.fasta -db /var/lib/cwl/stga9d2a260-11e1-4469-89bb-9e8033d2a90f/dqc_reference/reference_markers.fasta -out OceanDNA-b21568/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:51:09,310] [INFO] Task succeeded: Blastn
[2023-03-16 08:51:09,312] [INFO] Selected 15 target genomes.
[2023-03-16 08:51:09,312] [INFO] Target genome list was writen to OceanDNA-b21568/target_genomes.txt
[2023-03-16 08:51:09,326] [INFO] Task started: fastANI
[2023-03-16 08:51:09,326] [INFO] Running command: fastANI --query /var/lib/cwl/stga9a5559e-4a2d-4a0c-a845-61f3ad4a5bd0/OceanDNA-b21568.fa --refList OceanDNA-b21568/target_genomes.txt --output OceanDNA-b21568/fastani_result.tsv --threads 1
[2023-03-16 08:51:18,668] [INFO] Task succeeded: fastANI
[2023-03-16 08:51:18,669] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga9d2a260-11e1-4469-89bb-9e8033d2a90f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 08:51:18,669] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga9d2a260-11e1-4469-89bb-9e8033d2a90f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 08:51:18,669] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 08:51:18,669] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 08:51:18,669] [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
--------------------------------------------------------------------------------
[2023-03-16 08:51:18,672] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21568/tc_result.tsv
[2023-03-16 08:51:18,673] [INFO] ===== Taxonomy check completed =====
[2023-03-16 08:51:18,673] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 08:51:18,673] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga9d2a260-11e1-4469-89bb-9e8033d2a90f/dqc_reference/checkm_data
[2023-03-16 08:51:18,677] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 08:51:18,681] [INFO] Task started: CheckM
[2023-03-16 08:51:18,682] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21568/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21568/checkm_input OceanDNA-b21568/checkm_result
[2023-03-16 08:51:44,057] [INFO] Task succeeded: CheckM
[2023-03-16 08:51:44,058] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 08:51:44,073] [INFO] ===== Completeness check finished =====
[2023-03-16 08:51:44,073] [INFO] ===== Start GTDB Search =====
[2023-03-16 08:51:44,073] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21568/markers.fasta)
[2023-03-16 08:51:44,074] [INFO] Task started: Blastn
[2023-03-16 08:51:44,074] [INFO] Running command: blastn -query OceanDNA-b21568/markers.fasta -db /var/lib/cwl/stga9d2a260-11e1-4469-89bb-9e8033d2a90f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21568/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:51:44,816] [INFO] Task succeeded: Blastn
[2023-03-16 08:51:44,818] [INFO] Selected 19 target genomes.
[2023-03-16 08:51:44,818] [INFO] Target genome list was writen to OceanDNA-b21568/target_genomes_gtdb.txt
[2023-03-16 08:51:44,848] [INFO] Task started: fastANI
[2023-03-16 08:51:44,848] [INFO] Running command: fastANI --query /var/lib/cwl/stga9a5559e-4a2d-4a0c-a845-61f3ad4a5bd0/OceanDNA-b21568.fa --refList OceanDNA-b21568/target_genomes_gtdb.txt --output OceanDNA-b21568/fastani_result_gtdb.tsv --threads 1
[2023-03-16 08:51:52,197] [INFO] Task succeeded: fastANI
[2023-03-16 08:51:52,199] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 08:51:52,199] [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_018652955.1	s__UBA2170 sp018652955	78.7354	164	319	d__Bacteria;p__Patescibacteria;c__Gracilibacteria;o__Peribacterales;f__Peribacteraceae;g__UBA2170	95.0	99.95	99.94	0.98	0.97	8	-
GCA_002436205.1	s__UBA2170 sp002436205	78.292	134	319	d__Bacteria;p__Patescibacteria;c__Gracilibacteria;o__Peribacterales;f__Peribacteraceae;g__UBA2170	95.0	99.80	99.74	0.86	0.81	3	-
--------------------------------------------------------------------------------
[2023-03-16 08:51:52,201] [INFO] GTDB search result was written to OceanDNA-b21568/result_gtdb.tsv
[2023-03-16 08:51:52,202] [INFO] ===== GTDB Search completed =====
[2023-03-16 08:51:52,204] [INFO] DFAST_QC result json was written to OceanDNA-b21568/dqc_result.json
[2023-03-16 08:51:52,204] [INFO] DFAST_QC completed!
[2023-03-16 08:51:52,204] [INFO] Total running time: 0h0m53s