[2023-03-15 22:15:27,637] [INFO] DFAST_QC pipeline started.
[2023-03-15 22:15:27,637] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 22:15:27,637] [INFO] DQC Reference Directory: /var/lib/cwl/stg0f768263-d1a4-4abc-bdc3-5ab7226ad50a/dqc_reference
[2023-03-15 22:15:29,360] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 22:15:29,361] [INFO] Task started: Prodigal
[2023-03-15 22:15:29,361] [INFO] Running command: cat /var/lib/cwl/stg32f589c4-1ed2-43ec-b270-1eae26f5bb2d/OceanDNA-b3690.fa | prodigal -d OceanDNA-b3690/cds.fna -a OceanDNA-b3690/protein.faa -g 11 -q > /dev/null
[2023-03-15 22:15:58,335] [INFO] Task succeeded: Prodigal
[2023-03-15 22:15:58,336] [INFO] Task started: HMMsearch
[2023-03-15 22:15:58,336] [INFO] Running command: hmmsearch --tblout OceanDNA-b3690/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0f768263-d1a4-4abc-bdc3-5ab7226ad50a/dqc_reference/reference_markers.hmm OceanDNA-b3690/protein.faa > /dev/null
[2023-03-15 22:15:58,584] [INFO] Task succeeded: HMMsearch
[2023-03-15 22:15:58,584] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg32f589c4-1ed2-43ec-b270-1eae26f5bb2d/OceanDNA-b3690.fa]
[2023-03-15 22:15:58,634] [INFO] Query marker FASTA was written to OceanDNA-b3690/markers.fasta
[2023-03-15 22:15:58,635] [INFO] Task started: Blastn
[2023-03-15 22:15:58,635] [INFO] Running command: blastn -query OceanDNA-b3690/markers.fasta -db /var/lib/cwl/stg0f768263-d1a4-4abc-bdc3-5ab7226ad50a/dqc_reference/reference_markers.fasta -out OceanDNA-b3690/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:15:59,132] [INFO] Task succeeded: Blastn
[2023-03-15 22:15:59,135] [INFO] Selected 17 target genomes.
[2023-03-15 22:15:59,135] [INFO] Target genome list was writen to OceanDNA-b3690/target_genomes.txt
[2023-03-15 22:15:59,145] [INFO] Task started: fastANI
[2023-03-15 22:15:59,145] [INFO] Running command: fastANI --query /var/lib/cwl/stg32f589c4-1ed2-43ec-b270-1eae26f5bb2d/OceanDNA-b3690.fa --refList OceanDNA-b3690/target_genomes.txt --output OceanDNA-b3690/fastani_result.tsv --threads 1
[2023-03-15 22:16:09,880] [INFO] Task succeeded: fastANI
[2023-03-15 22:16:09,880] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0f768263-d1a4-4abc-bdc3-5ab7226ad50a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 22:16:09,880] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0f768263-d1a4-4abc-bdc3-5ab7226ad50a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 22:16:09,880] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 22:16:09,880] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 22:16:09,880] [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 22:16:09,882] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3690/tc_result.tsv
[2023-03-15 22:16:09,884] [INFO] ===== Taxonomy check completed =====
[2023-03-15 22:16:09,884] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 22:16:09,884] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0f768263-d1a4-4abc-bdc3-5ab7226ad50a/dqc_reference/checkm_data
[2023-03-15 22:16:09,887] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 22:16:09,901] [INFO] Task started: CheckM
[2023-03-15 22:16:09,901] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3690/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3690/checkm_input OceanDNA-b3690/checkm_result
[2023-03-15 22:17:22,753] [INFO] Task succeeded: CheckM
[2023-03-15 22:17:22,754] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.74%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 22:17:22,925] [INFO] ===== Completeness check finished =====
[2023-03-15 22:17:22,925] [INFO] ===== Start GTDB Search =====
[2023-03-15 22:17:22,925] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3690/markers.fasta)
[2023-03-15 22:17:22,927] [INFO] Task started: Blastn
[2023-03-15 22:17:22,927] [INFO] Running command: blastn -query OceanDNA-b3690/markers.fasta -db /var/lib/cwl/stg0f768263-d1a4-4abc-bdc3-5ab7226ad50a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3690/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:17:23,595] [INFO] Task succeeded: Blastn
[2023-03-15 22:17:23,601] [INFO] Selected 18 target genomes.
[2023-03-15 22:17:23,601] [INFO] Target genome list was writen to OceanDNA-b3690/target_genomes_gtdb.txt
[2023-03-15 22:17:23,724] [INFO] Task started: fastANI
[2023-03-15 22:17:23,725] [INFO] Running command: fastANI --query /var/lib/cwl/stg32f589c4-1ed2-43ec-b270-1eae26f5bb2d/OceanDNA-b3690.fa --refList OceanDNA-b3690/target_genomes_gtdb.txt --output OceanDNA-b3690/fastani_result_gtdb.tsv --threads 1
[2023-03-15 22:17:34,704] [INFO] Task succeeded: fastANI
[2023-03-15 22:17:34,707] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 22:17:34,707] [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
GCF_000724545.1	s__Aureispira sp000724545	77.1364	179	925	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Aureispira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902727865.1	s__Aureispira sp902727865	76.7957	134	925	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Aureispira	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 22:17:34,709] [INFO] GTDB search result was written to OceanDNA-b3690/result_gtdb.tsv
[2023-03-15 22:17:34,712] [INFO] ===== GTDB Search completed =====
[2023-03-15 22:17:34,715] [INFO] DFAST_QC result json was written to OceanDNA-b3690/dqc_result.json
[2023-03-15 22:17:34,715] [INFO] DFAST_QC completed!
[2023-03-15 22:17:34,715] [INFO] Total running time: 0h2m7s