[2023-03-17 11:25:37,061] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:25:37,076] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:25:37,077] [INFO] DQC Reference Directory: /var/lib/cwl/stgf8de6093-dcef-49f4-9e5d-5b86479c3695/dqc_reference
[2023-03-17 11:25:38,139] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:25:38,139] [INFO] Task started: Prodigal
[2023-03-17 11:25:38,139] [INFO] Running command: cat /var/lib/cwl/stg3d0c5f3a-e9c5-4351-8d44-554febe7a831/OceanDNA-b17796.fa | prodigal -d OceanDNA-b17796/cds.fna -a OceanDNA-b17796/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:25:45,647] [INFO] Task succeeded: Prodigal
[2023-03-17 11:25:45,648] [INFO] Task started: HMMsearch
[2023-03-17 11:25:45,648] [INFO] Running command: hmmsearch --tblout OceanDNA-b17796/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf8de6093-dcef-49f4-9e5d-5b86479c3695/dqc_reference/reference_markers.hmm OceanDNA-b17796/protein.faa > /dev/null
[2023-03-17 11:25:45,830] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:25:45,831] [INFO] Found 6/6 markers.
[2023-03-17 11:25:45,980] [INFO] Query marker FASTA was written to OceanDNA-b17796/markers.fasta
[2023-03-17 11:25:45,981] [INFO] Task started: Blastn
[2023-03-17 11:25:45,981] [INFO] Running command: blastn -query OceanDNA-b17796/markers.fasta -db /var/lib/cwl/stgf8de6093-dcef-49f4-9e5d-5b86479c3695/dqc_reference/reference_markers.fasta -out OceanDNA-b17796/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:25:46,498] [INFO] Task succeeded: Blastn
[2023-03-17 11:25:46,550] [INFO] Selected 15 target genomes.
[2023-03-17 11:25:46,551] [INFO] Target genome list was writen to OceanDNA-b17796/target_genomes.txt
[2023-03-17 11:25:46,587] [INFO] Task started: fastANI
[2023-03-17 11:25:46,587] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d0c5f3a-e9c5-4351-8d44-554febe7a831/OceanDNA-b17796.fa --refList OceanDNA-b17796/target_genomes.txt --output OceanDNA-b17796/fastani_result.tsv --threads 1
[2023-03-17 11:25:52,949] [INFO] Task succeeded: fastANI
[2023-03-17 11:25:52,949] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf8de6093-dcef-49f4-9e5d-5b86479c3695/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:25:52,950] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf8de6093-dcef-49f4-9e5d-5b86479c3695/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:25:52,950] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:25:52,950] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 11:25:52,950] [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 11:25:52,967] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17796/tc_result.tsv
[2023-03-17 11:25:53,001] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:25:53,001] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:25:53,002] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf8de6093-dcef-49f4-9e5d-5b86479c3695/dqc_reference/checkm_data
[2023-03-17 11:25:53,004] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:25:53,010] [INFO] Task started: CheckM
[2023-03-17 11:25:53,010] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17796/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17796/checkm_input OceanDNA-b17796/checkm_result
[2023-03-17 11:26:17,073] [INFO] Task succeeded: CheckM
[2023-03-17 11:26:17,073] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.86%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 11:26:17,197] [INFO] ===== Completeness check finished =====
[2023-03-17 11:26:17,197] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:26:17,197] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17796/markers.fasta)
[2023-03-17 11:26:17,197] [INFO] Task started: Blastn
[2023-03-17 11:26:17,197] [INFO] Running command: blastn -query OceanDNA-b17796/markers.fasta -db /var/lib/cwl/stgf8de6093-dcef-49f4-9e5d-5b86479c3695/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17796/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:26:17,905] [INFO] Task succeeded: Blastn
[2023-03-17 11:26:17,960] [INFO] Selected 15 target genomes.
[2023-03-17 11:26:17,960] [INFO] Target genome list was writen to OceanDNA-b17796/target_genomes_gtdb.txt
[2023-03-17 11:26:17,976] [INFO] Task started: fastANI
[2023-03-17 11:26:17,976] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d0c5f3a-e9c5-4351-8d44-554febe7a831/OceanDNA-b17796.fa --refList OceanDNA-b17796/target_genomes_gtdb.txt --output OceanDNA-b17796/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:26:23,121] [INFO] Task succeeded: fastANI
[2023-03-17 11:26:23,124] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 11:26:23,124] [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_002697535.1	s__GCA-002719695 sp002697535	99.7344	457	501	d__Bacteria;p__Margulisbacteria;c__Marinamargulisbacteria;o__GCA-2716485;f__GCA-002719695;g__GCA-002719695	95.0	96.60	95.39	0.86	0.85	4	conclusive
GCA_002716725.1	s__GCA-002719695 sp002716725	81.8645	266	501	d__Bacteria;p__Margulisbacteria;c__Marinamargulisbacteria;o__GCA-2716485;f__GCA-002719695;g__GCA-002719695	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002719695.1	s__GCA-002719695 sp002719695	81.344	194	501	d__Bacteria;p__Margulisbacteria;c__Marinamargulisbacteria;o__GCA-2716485;f__GCA-002719695;g__GCA-002719695	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 11:26:23,129] [INFO] GTDB search result was written to OceanDNA-b17796/result_gtdb.tsv
[2023-03-17 11:26:23,134] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:26:23,139] [INFO] DFAST_QC result json was written to OceanDNA-b17796/dqc_result.json
[2023-03-17 11:26:23,139] [INFO] DFAST_QC completed!
[2023-03-17 11:26:23,139] [INFO] Total running time: 0h0m46s