[2023-03-16 12:26:51,225] [INFO] DFAST_QC pipeline started.
[2023-03-16 12:26:51,225] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 12:26:51,225] [INFO] DQC Reference Directory: /var/lib/cwl/stg824f4d96-dbce-45c6-ab21-2d08aa66b609/dqc_reference
[2023-03-16 12:26:53,736] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 12:26:53,736] [INFO] Task started: Prodigal
[2023-03-16 12:26:53,736] [INFO] Running command: cat /var/lib/cwl/stgc06b51ff-87ee-485b-b127-6e17f14ea265/OceanDNA-b18386.fa | prodigal -d OceanDNA-b18386/cds.fna -a OceanDNA-b18386/protein.faa -g 11 -q > /dev/null
[2023-03-16 12:27:00,450] [INFO] Task succeeded: Prodigal
[2023-03-16 12:27:00,451] [INFO] Task started: HMMsearch
[2023-03-16 12:27:00,451] [INFO] Running command: hmmsearch --tblout OceanDNA-b18386/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg824f4d96-dbce-45c6-ab21-2d08aa66b609/dqc_reference/reference_markers.hmm OceanDNA-b18386/protein.faa > /dev/null
[2023-03-16 12:27:00,712] [INFO] Task succeeded: HMMsearch
[2023-03-16 12:27:00,713] [INFO] Found 6/6 markers.
[2023-03-16 12:27:00,722] [INFO] Query marker FASTA was written to OceanDNA-b18386/markers.fasta
[2023-03-16 12:27:00,722] [INFO] Task started: Blastn
[2023-03-16 12:27:00,723] [INFO] Running command: blastn -query OceanDNA-b18386/markers.fasta -db /var/lib/cwl/stg824f4d96-dbce-45c6-ab21-2d08aa66b609/dqc_reference/reference_markers.fasta -out OceanDNA-b18386/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 12:27:01,557] [INFO] Task succeeded: Blastn
[2023-03-16 12:27:01,558] [INFO] Selected 18 target genomes.
[2023-03-16 12:27:01,558] [INFO] Target genome list was writen to OceanDNA-b18386/target_genomes.txt
[2023-03-16 12:27:01,569] [INFO] Task started: fastANI
[2023-03-16 12:27:01,569] [INFO] Running command: fastANI --query /var/lib/cwl/stgc06b51ff-87ee-485b-b127-6e17f14ea265/OceanDNA-b18386.fa --refList OceanDNA-b18386/target_genomes.txt --output OceanDNA-b18386/fastani_result.tsv --threads 1
[2023-03-16 12:27:07,920] [INFO] Task succeeded: fastANI
[2023-03-16 12:27:07,920] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg824f4d96-dbce-45c6-ab21-2d08aa66b609/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 12:27:07,920] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg824f4d96-dbce-45c6-ab21-2d08aa66b609/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 12:27:07,921] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 12:27:07,921] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 12:27:07,921] [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
--------------------------------------------------------------------------------
[2023-03-16 12:27:07,921] [INFO] DFAST Taxonomy check result was written to OceanDNA-b18386/tc_result.tsv
[2023-03-16 12:27:07,921] [INFO] ===== Taxonomy check completed =====
[2023-03-16 12:27:07,921] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 12:27:07,921] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg824f4d96-dbce-45c6-ab21-2d08aa66b609/dqc_reference/checkm_data
[2023-03-16 12:27:07,974] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 12:27:07,977] [INFO] Task started: CheckM
[2023-03-16 12:27:07,977] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b18386/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b18386/checkm_input OceanDNA-b18386/checkm_result
[2023-03-16 12:27:43,255] [INFO] Task succeeded: CheckM
[2023-03-16 12:27:43,256] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.29%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 12:27:43,257] [INFO] ===== Completeness check finished =====
[2023-03-16 12:27:43,257] [INFO] ===== Start GTDB Search =====
[2023-03-16 12:27:43,257] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b18386/markers.fasta)
[2023-03-16 12:27:43,259] [INFO] Task started: Blastn
[2023-03-16 12:27:43,259] [INFO] Running command: blastn -query OceanDNA-b18386/markers.fasta -db /var/lib/cwl/stg824f4d96-dbce-45c6-ab21-2d08aa66b609/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b18386/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 12:27:44,891] [INFO] Task succeeded: Blastn
[2023-03-16 12:27:44,892] [INFO] Selected 21 target genomes.
[2023-03-16 12:27:44,892] [INFO] Target genome list was writen to OceanDNA-b18386/target_genomes_gtdb.txt
[2023-03-16 12:27:45,445] [INFO] Task started: fastANI
[2023-03-16 12:27:45,445] [INFO] Running command: fastANI --query /var/lib/cwl/stgc06b51ff-87ee-485b-b127-6e17f14ea265/OceanDNA-b18386.fa --refList OceanDNA-b18386/target_genomes_gtdb.txt --output OceanDNA-b18386/fastani_result_gtdb.tsv --threads 1
[2023-03-16 12:27:52,655] [INFO] Task succeeded: fastANI
[2023-03-16 12:27:52,658] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 12:27:52,658] [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_002691365.1	s__GCA-002707905 sp002691365	97.0846	401	452	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__S15-B10;g__GCA-002707905	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_002707905.1	s__GCA-002707905 sp002707905	85.4531	265	452	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__S15-B10;g__GCA-002707905	95.0	97.67	97.67	0.67	0.67	2	-
--------------------------------------------------------------------------------
[2023-03-16 12:27:52,658] [INFO] GTDB search result was written to OceanDNA-b18386/result_gtdb.tsv
[2023-03-16 12:27:52,658] [INFO] ===== GTDB Search completed =====
[2023-03-16 12:27:52,659] [INFO] DFAST_QC result json was written to OceanDNA-b18386/dqc_result.json
[2023-03-16 12:27:52,659] [INFO] DFAST_QC completed!
[2023-03-16 12:27:52,659] [INFO] Total running time: 0h1m1s