[2023-03-18 03:45:10,234] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:45:10,235] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:45:10,235] [INFO] DQC Reference Directory: /var/lib/cwl/stg172d6195-ac51-459f-831a-a50911c0bc63/dqc_reference
[2023-03-18 03:45:11,970] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:45:11,971] [INFO] Task started: Prodigal
[2023-03-18 03:45:11,971] [INFO] Running command: cat /var/lib/cwl/stg4a6faa27-2166-4bdb-bcbe-140ab14077c9/OceanDNA-b21665.fa | prodigal -d OceanDNA-b21665/cds.fna -a OceanDNA-b21665/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:45:17,109] [INFO] Task succeeded: Prodigal
[2023-03-18 03:45:17,110] [INFO] Task started: HMMsearch
[2023-03-18 03:45:17,110] [INFO] Running command: hmmsearch --tblout OceanDNA-b21665/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg172d6195-ac51-459f-831a-a50911c0bc63/dqc_reference/reference_markers.hmm OceanDNA-b21665/protein.faa > /dev/null
[2023-03-18 03:45:17,321] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:45:17,321] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4a6faa27-2166-4bdb-bcbe-140ab14077c9/OceanDNA-b21665.fa]
[2023-03-18 03:45:17,329] [INFO] Query marker FASTA was written to OceanDNA-b21665/markers.fasta
[2023-03-18 03:45:17,330] [INFO] Task started: Blastn
[2023-03-18 03:45:17,330] [INFO] Running command: blastn -query OceanDNA-b21665/markers.fasta -db /var/lib/cwl/stg172d6195-ac51-459f-831a-a50911c0bc63/dqc_reference/reference_markers.fasta -out OceanDNA-b21665/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:45:20,000] [INFO] Task succeeded: Blastn
[2023-03-18 03:45:20,000] [INFO] Selected 9 target genomes.
[2023-03-18 03:45:20,000] [INFO] Target genome list was writen to OceanDNA-b21665/target_genomes.txt
[2023-03-18 03:45:20,005] [INFO] Task started: fastANI
[2023-03-18 03:45:20,005] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a6faa27-2166-4bdb-bcbe-140ab14077c9/OceanDNA-b21665.fa --refList OceanDNA-b21665/target_genomes.txt --output OceanDNA-b21665/fastani_result.tsv --threads 1
[2023-03-18 03:45:23,221] [INFO] Task succeeded: fastANI
[2023-03-18 03:45:23,221] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg172d6195-ac51-459f-831a-a50911c0bc63/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:45:23,221] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg172d6195-ac51-459f-831a-a50911c0bc63/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:45:23,221] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 03:45:23,221] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 03:45:23,222] [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 03:45:23,222] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21665/tc_result.tsv
[2023-03-18 03:45:23,222] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:45:23,222] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:45:23,222] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg172d6195-ac51-459f-831a-a50911c0bc63/dqc_reference/checkm_data
[2023-03-18 03:45:23,224] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:45:23,226] [INFO] Task started: CheckM
[2023-03-18 03:45:23,227] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21665/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21665/checkm_input OceanDNA-b21665/checkm_result
[2023-03-18 03:45:42,847] [INFO] Task succeeded: CheckM
[2023-03-18 03:45:42,848] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.04%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 03:45:42,849] [INFO] ===== Completeness check finished =====
[2023-03-18 03:45:42,849] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:45:42,849] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21665/markers.fasta)
[2023-03-18 03:45:42,851] [INFO] Task started: Blastn
[2023-03-18 03:45:42,851] [INFO] Running command: blastn -query OceanDNA-b21665/markers.fasta -db /var/lib/cwl/stg172d6195-ac51-459f-831a-a50911c0bc63/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21665/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:45:43,635] [INFO] Task succeeded: Blastn
[2023-03-18 03:45:43,636] [INFO] Selected 16 target genomes.
[2023-03-18 03:45:43,636] [INFO] Target genome list was writen to OceanDNA-b21665/target_genomes_gtdb.txt
[2023-03-18 03:45:43,780] [INFO] Task started: fastANI
[2023-03-18 03:45:43,780] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a6faa27-2166-4bdb-bcbe-140ab14077c9/OceanDNA-b21665.fa --refList OceanDNA-b21665/target_genomes_gtdb.txt --output OceanDNA-b21665/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:45:48,944] [INFO] Task succeeded: fastANI
[2023-03-18 03:45:48,946] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 03:45:48,946] [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_018646985.1	s__JABBGTR01 sp018646985	99.9045	259	326	d__Bacteria;p__Patescibacteria;c__Microgenomatia;o__UBA1400;f__PJMF01;g__JABBGTR01	95.0	99.93	99.88	0.94	0.90	9	conclusive
GCA_018813375.1	s__JABBGTR01 sp018813375	76.9942	79	326	d__Bacteria;p__Patescibacteria;c__Microgenomatia;o__UBA1400;f__PJMF01;g__JABBGTR01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 03:45:48,947] [INFO] GTDB search result was written to OceanDNA-b21665/result_gtdb.tsv
[2023-03-18 03:45:48,947] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:45:48,947] [INFO] DFAST_QC result json was written to OceanDNA-b21665/dqc_result.json
[2023-03-18 03:45:48,947] [INFO] DFAST_QC completed!
[2023-03-18 03:45:48,947] [INFO] Total running time: 0h0m39s