[2023-03-17 07:01:49,603] [INFO] DFAST_QC pipeline started.
[2023-03-17 07:01:49,603] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 07:01:49,603] [INFO] DQC Reference Directory: /var/lib/cwl/stg23a4e732-24d9-4810-b1bb-7625ecace4bf/dqc_reference
[2023-03-17 07:01:51,531] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 07:01:51,531] [INFO] Task started: Prodigal
[2023-03-17 07:01:51,531] [INFO] Running command: cat /var/lib/cwl/stg34245666-68a9-40fc-a5d3-985a6131236c/OceanDNA-b45250.fa | prodigal -d OceanDNA-b45250/cds.fna -a OceanDNA-b45250/protein.faa -g 11 -q > /dev/null
[2023-03-17 07:01:59,653] [INFO] Task succeeded: Prodigal
[2023-03-17 07:01:59,654] [INFO] Task started: HMMsearch
[2023-03-17 07:01:59,654] [INFO] Running command: hmmsearch --tblout OceanDNA-b45250/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg23a4e732-24d9-4810-b1bb-7625ecace4bf/dqc_reference/reference_markers.hmm OceanDNA-b45250/protein.faa > /dev/null
[2023-03-17 07:01:59,823] [INFO] Task succeeded: HMMsearch
[2023-03-17 07:01:59,824] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg34245666-68a9-40fc-a5d3-985a6131236c/OceanDNA-b45250.fa]
[2023-03-17 07:01:59,838] [INFO] Query marker FASTA was written to OceanDNA-b45250/markers.fasta
[2023-03-17 07:01:59,838] [INFO] Task started: Blastn
[2023-03-17 07:01:59,838] [INFO] Running command: blastn -query OceanDNA-b45250/markers.fasta -db /var/lib/cwl/stg23a4e732-24d9-4810-b1bb-7625ecace4bf/dqc_reference/reference_markers.fasta -out OceanDNA-b45250/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:02:00,336] [INFO] Task succeeded: Blastn
[2023-03-17 07:02:00,337] [INFO] Selected 10 target genomes.
[2023-03-17 07:02:00,337] [INFO] Target genome list was writen to OceanDNA-b45250/target_genomes.txt
[2023-03-17 07:02:00,343] [INFO] Task started: fastANI
[2023-03-17 07:02:00,343] [INFO] Running command: fastANI --query /var/lib/cwl/stg34245666-68a9-40fc-a5d3-985a6131236c/OceanDNA-b45250.fa --refList OceanDNA-b45250/target_genomes.txt --output OceanDNA-b45250/fastani_result.tsv --threads 1
[2023-03-17 07:02:05,757] [INFO] Task succeeded: fastANI
[2023-03-17 07:02:05,757] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg23a4e732-24d9-4810-b1bb-7625ecace4bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 07:02:05,758] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg23a4e732-24d9-4810-b1bb-7625ecace4bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 07:02:05,758] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 07:02:05,758] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 07:02:05,758] [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
--------------------------------------------------------------------------------
[2023-03-17 07:02:05,758] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45250/tc_result.tsv
[2023-03-17 07:02:05,758] [INFO] ===== Taxonomy check completed =====
[2023-03-17 07:02:05,758] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 07:02:05,758] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg23a4e732-24d9-4810-b1bb-7625ecace4bf/dqc_reference/checkm_data
[2023-03-17 07:02:05,761] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 07:02:05,765] [INFO] Task started: CheckM
[2023-03-17 07:02:05,765] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45250/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45250/checkm_input OceanDNA-b45250/checkm_result
[2023-03-17 07:02:31,192] [INFO] Task succeeded: CheckM
[2023-03-17 07:02:31,192] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 6.25%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 07:02:31,194] [INFO] ===== Completeness check finished =====
[2023-03-17 07:02:31,194] [INFO] ===== Start GTDB Search =====
[2023-03-17 07:02:31,195] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45250/markers.fasta)
[2023-03-17 07:02:31,195] [INFO] Task started: Blastn
[2023-03-17 07:02:31,195] [INFO] Running command: blastn -query OceanDNA-b45250/markers.fasta -db /var/lib/cwl/stg23a4e732-24d9-4810-b1bb-7625ecace4bf/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45250/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:02:31,769] [INFO] Task succeeded: Blastn
[2023-03-17 07:02:31,770] [INFO] Selected 12 target genomes.
[2023-03-17 07:02:31,770] [INFO] Target genome list was writen to OceanDNA-b45250/target_genomes_gtdb.txt
[2023-03-17 07:02:32,023] [INFO] Task started: fastANI
[2023-03-17 07:02:32,023] [INFO] Running command: fastANI --query /var/lib/cwl/stg34245666-68a9-40fc-a5d3-985a6131236c/OceanDNA-b45250.fa --refList OceanDNA-b45250/target_genomes_gtdb.txt --output OceanDNA-b45250/fastani_result_gtdb.tsv --threads 1
[2023-03-17 07:02:38,146] [INFO] Task succeeded: fastANI
[2023-03-17 07:02:38,148] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 07:02:38,148] [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_013297885.1	s__UBA2033 sp013297885	75.286	53	516	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__UBA2033	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 07:02:38,148] [INFO] GTDB search result was written to OceanDNA-b45250/result_gtdb.tsv
[2023-03-17 07:02:38,149] [INFO] ===== GTDB Search completed =====
[2023-03-17 07:02:38,149] [INFO] DFAST_QC result json was written to OceanDNA-b45250/dqc_result.json
[2023-03-17 07:02:38,149] [INFO] DFAST_QC completed!
[2023-03-17 07:02:38,149] [INFO] Total running time: 0h0m49s