[2023-03-15 08:55:06,630] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:55:06,630] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:55:06,630] [INFO] DQC Reference Directory: /var/lib/cwl/stgaad63589-0fda-474e-ad49-7a1a1c1062bd/dqc_reference
[2023-03-15 08:55:08,350] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:55:08,350] [INFO] Task started: Prodigal
[2023-03-15 08:55:08,350] [INFO] Running command: cat /var/lib/cwl/stgba3bd850-cfef-47f7-a491-fb2ff58b2ec3/OceanDNA-b38596.fa | prodigal -d OceanDNA-b38596/cds.fna -a OceanDNA-b38596/protein.faa -g 11 -q > /dev/null
[2023-03-15 08:55:14,938] [INFO] Task succeeded: Prodigal
[2023-03-15 08:55:14,938] [INFO] Task started: HMMsearch
[2023-03-15 08:55:14,938] [INFO] Running command: hmmsearch --tblout OceanDNA-b38596/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaad63589-0fda-474e-ad49-7a1a1c1062bd/dqc_reference/reference_markers.hmm OceanDNA-b38596/protein.faa > /dev/null
[2023-03-15 08:55:15,156] [INFO] Task succeeded: HMMsearch
[2023-03-15 08:55:15,157] [INFO] Found 6/6 markers.
[2023-03-15 08:55:15,170] [INFO] Query marker FASTA was written to OceanDNA-b38596/markers.fasta
[2023-03-15 08:55:15,170] [INFO] Task started: Blastn
[2023-03-15 08:55:15,170] [INFO] Running command: blastn -query OceanDNA-b38596/markers.fasta -db /var/lib/cwl/stgaad63589-0fda-474e-ad49-7a1a1c1062bd/dqc_reference/reference_markers.fasta -out OceanDNA-b38596/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:55:15,876] [INFO] Task succeeded: Blastn
[2023-03-15 08:55:15,877] [INFO] Selected 12 target genomes.
[2023-03-15 08:55:15,877] [INFO] Target genome list was writen to OceanDNA-b38596/target_genomes.txt
[2023-03-15 08:55:15,881] [INFO] Task started: fastANI
[2023-03-15 08:55:15,881] [INFO] Running command: fastANI --query /var/lib/cwl/stgba3bd850-cfef-47f7-a491-fb2ff58b2ec3/OceanDNA-b38596.fa --refList OceanDNA-b38596/target_genomes.txt --output OceanDNA-b38596/fastani_result.tsv --threads 1
[2023-03-15 08:55:20,874] [INFO] Task succeeded: fastANI
[2023-03-15 08:55:20,875] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaad63589-0fda-474e-ad49-7a1a1c1062bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 08:55:20,875] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaad63589-0fda-474e-ad49-7a1a1c1062bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 08:55:20,880] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 08:55:20,880] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 08:55:20,880] [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
Moraxella osloensis	strain=FDAARGOS_870	GCA_016028755.1	34062	34062	suspected-type	True	94.4515	255	287	95	below_threshold
Moraxella osloensis	strain=CCUG 350	GCA_001553955.1	34062	34062	suspected-type	True	94.4034	256	287	95	below_threshold
Moraxella osloensis	strain=NCTC10465	GCA_900453115.1	34062	34062	suspected-type	True	94.4006	256	287	95	below_threshold
Moraxella osloensis	strain=CCUG 350	GCA_001679175.1	34062	34062	suspected-type	True	94.3712	254	287	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 08:55:20,880] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38596/tc_result.tsv
[2023-03-15 08:55:20,881] [INFO] ===== Taxonomy check completed =====
[2023-03-15 08:55:20,881] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 08:55:20,881] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaad63589-0fda-474e-ad49-7a1a1c1062bd/dqc_reference/checkm_data
[2023-03-15 08:55:20,881] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 08:55:20,886] [INFO] Task started: CheckM
[2023-03-15 08:55:20,886] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38596/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38596/checkm_input OceanDNA-b38596/checkm_result
[2023-03-15 08:55:44,102] [INFO] Task succeeded: CheckM
[2023-03-15 08:55:44,103] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.20%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 08:55:44,105] [INFO] ===== Completeness check finished =====
[2023-03-15 08:55:44,105] [INFO] ===== Start GTDB Search =====
[2023-03-15 08:55:44,105] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38596/markers.fasta)
[2023-03-15 08:55:44,105] [INFO] Task started: Blastn
[2023-03-15 08:55:44,105] [INFO] Running command: blastn -query OceanDNA-b38596/markers.fasta -db /var/lib/cwl/stgaad63589-0fda-474e-ad49-7a1a1c1062bd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38596/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:55:44,897] [INFO] Task succeeded: Blastn
[2023-03-15 08:55:44,898] [INFO] Selected 19 target genomes.
[2023-03-15 08:55:44,898] [INFO] Target genome list was writen to OceanDNA-b38596/target_genomes_gtdb.txt
[2023-03-15 08:55:44,953] [INFO] Task started: fastANI
[2023-03-15 08:55:44,954] [INFO] Running command: fastANI --query /var/lib/cwl/stgba3bd850-cfef-47f7-a491-fb2ff58b2ec3/OceanDNA-b38596.fa --refList OceanDNA-b38596/target_genomes_gtdb.txt --output OceanDNA-b38596/fastani_result_gtdb.tsv --threads 1
[2023-03-15 08:55:53,496] [INFO] Task succeeded: fastANI
[2023-03-15 08:55:53,499] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 08:55:53,499] [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_014647715.1	s__Moraxella_A cinereus	94.6615	254	287	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella_A	95.0	95.56	95.32	0.87	0.85	40	-
GCF_009867135.1	s__Moraxella_A sp002478835	94.44	255	287	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella_A	95.0237	96.28	95.11	0.93	0.88	7	-
GCF_001553955.1	s__Moraxella_A osloensis	94.4034	256	287	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella_A	95.0237	96.88	95.23	0.89	0.83	12	-
--------------------------------------------------------------------------------
[2023-03-15 08:55:53,499] [INFO] GTDB search result was written to OceanDNA-b38596/result_gtdb.tsv
[2023-03-15 08:55:53,499] [INFO] ===== GTDB Search completed =====
[2023-03-15 08:55:53,500] [INFO] DFAST_QC result json was written to OceanDNA-b38596/dqc_result.json
[2023-03-15 08:55:53,500] [INFO] DFAST_QC completed!
[2023-03-15 08:55:53,500] [INFO] Total running time: 0h0m47s