[2023-03-18 23:56:04,507] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:56:04,508] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:56:04,508] [INFO] DQC Reference Directory: /var/lib/cwl/stg1d81a9fc-88e2-4338-8bc4-f295049aa16a/dqc_reference
[2023-03-18 23:56:05,620] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:56:05,621] [INFO] Task started: Prodigal
[2023-03-18 23:56:05,621] [INFO] Running command: cat /var/lib/cwl/stg2e2935a5-51d4-4de6-b933-8a4eac09e88f/OceanDNA-b32487.fa | prodigal -d OceanDNA-b32487/cds.fna -a OceanDNA-b32487/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:56:12,035] [INFO] Task succeeded: Prodigal
[2023-03-18 23:56:12,035] [INFO] Task started: HMMsearch
[2023-03-18 23:56:12,035] [INFO] Running command: hmmsearch --tblout OceanDNA-b32487/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1d81a9fc-88e2-4338-8bc4-f295049aa16a/dqc_reference/reference_markers.hmm OceanDNA-b32487/protein.faa > /dev/null
[2023-03-18 23:56:12,190] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:56:12,191] [INFO] Found 6/6 markers.
[2023-03-18 23:56:12,201] [INFO] Query marker FASTA was written to OceanDNA-b32487/markers.fasta
[2023-03-18 23:56:12,201] [INFO] Task started: Blastn
[2023-03-18 23:56:12,202] [INFO] Running command: blastn -query OceanDNA-b32487/markers.fasta -db /var/lib/cwl/stg1d81a9fc-88e2-4338-8bc4-f295049aa16a/dqc_reference/reference_markers.fasta -out OceanDNA-b32487/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:56:12,702] [INFO] Task succeeded: Blastn
[2023-03-18 23:56:12,703] [INFO] Selected 14 target genomes.
[2023-03-18 23:56:12,704] [INFO] Target genome list was writen to OceanDNA-b32487/target_genomes.txt
[2023-03-18 23:56:12,712] [INFO] Task started: fastANI
[2023-03-18 23:56:12,712] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e2935a5-51d4-4de6-b933-8a4eac09e88f/OceanDNA-b32487.fa --refList OceanDNA-b32487/target_genomes.txt --output OceanDNA-b32487/fastani_result.tsv --threads 1
[2023-03-18 23:56:20,237] [INFO] Task succeeded: fastANI
[2023-03-18 23:56:20,237] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1d81a9fc-88e2-4338-8bc4-f295049aa16a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:56:20,237] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1d81a9fc-88e2-4338-8bc4-f295049aa16a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:56:20,238] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:56:20,238] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 23:56:20,238] [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 23:56:20,238] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32487/tc_result.tsv
[2023-03-18 23:56:20,238] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:56:20,238] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:56:20,238] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1d81a9fc-88e2-4338-8bc4-f295049aa16a/dqc_reference/checkm_data
[2023-03-18 23:56:20,241] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:56:20,244] [INFO] Task started: CheckM
[2023-03-18 23:56:20,244] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32487/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32487/checkm_input OceanDNA-b32487/checkm_result
[2023-03-18 23:56:41,484] [INFO] Task succeeded: CheckM
[2023-03-18 23:56:41,485] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.42%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:56:41,487] [INFO] ===== Completeness check finished =====
[2023-03-18 23:56:41,487] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:56:41,487] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32487/markers.fasta)
[2023-03-18 23:56:41,487] [INFO] Task started: Blastn
[2023-03-18 23:56:41,487] [INFO] Running command: blastn -query OceanDNA-b32487/markers.fasta -db /var/lib/cwl/stg1d81a9fc-88e2-4338-8bc4-f295049aa16a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32487/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:56:42,203] [INFO] Task succeeded: Blastn
[2023-03-18 23:56:42,205] [INFO] Selected 19 target genomes.
[2023-03-18 23:56:42,205] [INFO] Target genome list was writen to OceanDNA-b32487/target_genomes_gtdb.txt
[2023-03-18 23:56:42,222] [INFO] Task started: fastANI
[2023-03-18 23:56:42,223] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e2935a5-51d4-4de6-b933-8a4eac09e88f/OceanDNA-b32487.fa --refList OceanDNA-b32487/target_genomes_gtdb.txt --output OceanDNA-b32487/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:56:46,342] [INFO] Task succeeded: fastANI
[2023-03-18 23:56:46,348] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 23:56:46,348] [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_002170595.1	s__TMED62 sp002170595	99.5932	394	442	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED131;g__TMED62	95.0	99.91	99.91	0.92	0.92	2	conclusive
GCA_902615805.1	s__TMED62 sp902615805	79.0182	219	442	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED131;g__TMED62	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902614225.1	s__TMED62 sp902614225	78.9746	171	442	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED131;g__TMED62	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902571315.1	s__TMED62 sp902571315	78.9576	159	442	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED131;g__TMED62	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902547175.1	s__TMED62 sp902547175	78.9266	137	442	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED131;g__TMED62	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902527765.1	s__TMED62 sp902527765	78.7304	159	442	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED131;g__TMED62	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902579545.1	s__CACHHO01 sp902579545	77.656	114	442	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED131;g__CACHHO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002690625.1	s__MED722 sp002690625	77.2532	58	442	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED131;g__MED722	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002715505.1	s__GCA-2715505 sp002715505	76.174	88	442	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED131;g__GCA-2715505	95.0	99.85	99.85	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2023-03-18 23:56:46,348] [INFO] GTDB search result was written to OceanDNA-b32487/result_gtdb.tsv
[2023-03-18 23:56:46,348] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:56:46,349] [INFO] DFAST_QC result json was written to OceanDNA-b32487/dqc_result.json
[2023-03-18 23:56:46,350] [INFO] DFAST_QC completed!
[2023-03-18 23:56:46,350] [INFO] Total running time: 0h0m42s