[2023-03-15 18:39:12,230] [INFO] DFAST_QC pipeline started.
[2023-03-15 18:39:12,230] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 18:39:12,230] [INFO] DQC Reference Directory: /var/lib/cwl/stg3f93c650-1db0-47af-bb53-b7eca3a0d442/dqc_reference
[2023-03-15 18:39:13,657] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 18:39:13,657] [INFO] Task started: Prodigal
[2023-03-15 18:39:13,657] [INFO] Running command: cat /var/lib/cwl/stg1869d85c-cfcd-4d64-b10e-85fce6404d78/OceanDNA-b19627.fa | prodigal -d OceanDNA-b19627/cds.fna -a OceanDNA-b19627/protein.faa -g 11 -q > /dev/null
[2023-03-15 18:39:23,660] [INFO] Task succeeded: Prodigal
[2023-03-15 18:39:23,661] [INFO] Task started: HMMsearch
[2023-03-15 18:39:23,661] [INFO] Running command: hmmsearch --tblout OceanDNA-b19627/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3f93c650-1db0-47af-bb53-b7eca3a0d442/dqc_reference/reference_markers.hmm OceanDNA-b19627/protein.faa > /dev/null
[2023-03-15 18:39:23,833] [INFO] Task succeeded: HMMsearch
[2023-03-15 18:39:23,833] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1869d85c-cfcd-4d64-b10e-85fce6404d78/OceanDNA-b19627.fa]
[2023-03-15 18:39:23,848] [INFO] Query marker FASTA was written to OceanDNA-b19627/markers.fasta
[2023-03-15 18:39:23,848] [INFO] Task started: Blastn
[2023-03-15 18:39:23,848] [INFO] Running command: blastn -query OceanDNA-b19627/markers.fasta -db /var/lib/cwl/stg3f93c650-1db0-47af-bb53-b7eca3a0d442/dqc_reference/reference_markers.fasta -out OceanDNA-b19627/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:39:24,351] [INFO] Task succeeded: Blastn
[2023-03-15 18:39:24,352] [INFO] Selected 10 target genomes.
[2023-03-15 18:39:24,352] [INFO] Target genome list was writen to OceanDNA-b19627/target_genomes.txt
[2023-03-15 18:39:24,359] [INFO] Task started: fastANI
[2023-03-15 18:39:24,359] [INFO] Running command: fastANI --query /var/lib/cwl/stg1869d85c-cfcd-4d64-b10e-85fce6404d78/OceanDNA-b19627.fa --refList OceanDNA-b19627/target_genomes.txt --output OceanDNA-b19627/fastani_result.tsv --threads 1
[2023-03-15 18:39:28,283] [INFO] Task succeeded: fastANI
[2023-03-15 18:39:28,283] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3f93c650-1db0-47af-bb53-b7eca3a0d442/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 18:39:28,283] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3f93c650-1db0-47af-bb53-b7eca3a0d442/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 18:39:28,283] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 18:39:28,283] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 18:39:28,284] [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 18:39:28,284] [INFO] DFAST Taxonomy check result was written to OceanDNA-b19627/tc_result.tsv
[2023-03-15 18:39:28,284] [INFO] ===== Taxonomy check completed =====
[2023-03-15 18:39:28,284] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 18:39:28,284] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3f93c650-1db0-47af-bb53-b7eca3a0d442/dqc_reference/checkm_data
[2023-03-15 18:39:28,286] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 18:39:28,290] [INFO] Task started: CheckM
[2023-03-15 18:39:28,290] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b19627/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b19627/checkm_input OceanDNA-b19627/checkm_result
[2023-03-15 18:39:57,634] [INFO] Task succeeded: CheckM
[2023-03-15 18:39:57,634] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 18:39:57,636] [INFO] ===== Completeness check finished =====
[2023-03-15 18:39:57,636] [INFO] ===== Start GTDB Search =====
[2023-03-15 18:39:57,636] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b19627/markers.fasta)
[2023-03-15 18:39:57,637] [INFO] Task started: Blastn
[2023-03-15 18:39:57,637] [INFO] Running command: blastn -query OceanDNA-b19627/markers.fasta -db /var/lib/cwl/stg3f93c650-1db0-47af-bb53-b7eca3a0d442/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b19627/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:39:58,339] [INFO] Task succeeded: Blastn
[2023-03-15 18:39:58,340] [INFO] Selected 23 target genomes.
[2023-03-15 18:39:58,340] [INFO] Target genome list was writen to OceanDNA-b19627/target_genomes_gtdb.txt
[2023-03-15 18:39:59,115] [INFO] Task started: fastANI
[2023-03-15 18:39:59,115] [INFO] Running command: fastANI --query /var/lib/cwl/stg1869d85c-cfcd-4d64-b10e-85fce6404d78/OceanDNA-b19627.fa --refList OceanDNA-b19627/target_genomes_gtdb.txt --output OceanDNA-b19627/fastani_result_gtdb.tsv --threads 1
[2023-03-15 18:40:07,149] [INFO] Task succeeded: fastANI
[2023-03-15 18:40:07,151] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 18:40:07,151] [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_902562835.1	s__CACEUX01 sp902562835	76.2925	50	624	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__CACEUX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002167345.2	s__CACEUX01 sp002167345	76.208	60	624	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__CACEUX01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 18:40:07,151] [INFO] GTDB search result was written to OceanDNA-b19627/result_gtdb.tsv
[2023-03-15 18:40:07,152] [INFO] ===== GTDB Search completed =====
[2023-03-15 18:40:07,152] [INFO] DFAST_QC result json was written to OceanDNA-b19627/dqc_result.json
[2023-03-15 18:40:07,152] [INFO] DFAST_QC completed!
[2023-03-15 18:40:07,152] [INFO] Total running time: 0h0m55s