[2023-03-19 01:21:54,514] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:21:54,516] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:21:54,516] [INFO] DQC Reference Directory: /var/lib/cwl/stgac1c68a2-a87e-4214-9ba8-0513731c0ba7/dqc_reference
[2023-03-19 01:21:56,074] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:21:56,075] [INFO] Task started: Prodigal
[2023-03-19 01:21:56,075] [INFO] Running command: cat /var/lib/cwl/stg7185571b-901f-426c-a610-d88b48fa30eb/OceanDNA-b27110.fa | prodigal -d OceanDNA-b27110/cds.fna -a OceanDNA-b27110/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:22:02,543] [INFO] Task succeeded: Prodigal
[2023-03-19 01:22:02,544] [INFO] Task started: HMMsearch
[2023-03-19 01:22:02,544] [INFO] Running command: hmmsearch --tblout OceanDNA-b27110/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgac1c68a2-a87e-4214-9ba8-0513731c0ba7/dqc_reference/reference_markers.hmm OceanDNA-b27110/protein.faa > /dev/null
[2023-03-19 01:22:02,699] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:22:02,699] [INFO] Found 6/6 markers.
[2023-03-19 01:22:02,709] [INFO] Query marker FASTA was written to OceanDNA-b27110/markers.fasta
[2023-03-19 01:22:02,711] [INFO] Task started: Blastn
[2023-03-19 01:22:02,711] [INFO] Running command: blastn -query OceanDNA-b27110/markers.fasta -db /var/lib/cwl/stgac1c68a2-a87e-4214-9ba8-0513731c0ba7/dqc_reference/reference_markers.fasta -out OceanDNA-b27110/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:22:03,881] [INFO] Task succeeded: Blastn
[2023-03-19 01:22:03,882] [INFO] Selected 19 target genomes.
[2023-03-19 01:22:03,882] [INFO] Target genome list was writen to OceanDNA-b27110/target_genomes.txt
[2023-03-19 01:22:03,896] [INFO] Task started: fastANI
[2023-03-19 01:22:03,896] [INFO] Running command: fastANI --query /var/lib/cwl/stg7185571b-901f-426c-a610-d88b48fa30eb/OceanDNA-b27110.fa --refList OceanDNA-b27110/target_genomes.txt --output OceanDNA-b27110/fastani_result.tsv --threads 1
[2023-03-19 01:22:12,100] [INFO] Task succeeded: fastANI
[2023-03-19 01:22:12,100] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgac1c68a2-a87e-4214-9ba8-0513731c0ba7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:22:12,101] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgac1c68a2-a87e-4214-9ba8-0513731c0ba7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:22:12,101] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:22:12,101] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 01:22:12,101] [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
--------------------------------------------------------------------------------
[2023-03-19 01:22:12,101] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27110/tc_result.tsv
[2023-03-19 01:22:12,101] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:22:12,101] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:22:12,101] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgac1c68a2-a87e-4214-9ba8-0513731c0ba7/dqc_reference/checkm_data
[2023-03-19 01:22:12,105] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:22:12,107] [INFO] Task started: CheckM
[2023-03-19 01:22:12,107] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27110/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27110/checkm_input OceanDNA-b27110/checkm_result
[2023-03-19 01:22:33,497] [INFO] Task succeeded: CheckM
[2023-03-19 01:22:33,497] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 01:22:33,498] [INFO] ===== Completeness check finished =====
[2023-03-19 01:22:33,499] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:22:33,499] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27110/markers.fasta)
[2023-03-19 01:22:33,500] [INFO] Task started: Blastn
[2023-03-19 01:22:33,500] [INFO] Running command: blastn -query OceanDNA-b27110/markers.fasta -db /var/lib/cwl/stgac1c68a2-a87e-4214-9ba8-0513731c0ba7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27110/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:22:34,360] [INFO] Task succeeded: Blastn
[2023-03-19 01:22:34,361] [INFO] Selected 27 target genomes.
[2023-03-19 01:22:34,361] [INFO] Target genome list was writen to OceanDNA-b27110/target_genomes_gtdb.txt
[2023-03-19 01:22:34,389] [INFO] Task started: fastANI
[2023-03-19 01:22:34,389] [INFO] Running command: fastANI --query /var/lib/cwl/stg7185571b-901f-426c-a610-d88b48fa30eb/OceanDNA-b27110.fa --refList OceanDNA-b27110/target_genomes_gtdb.txt --output OceanDNA-b27110/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:22:40,487] [INFO] Task succeeded: fastANI
[2023-03-19 01:22:40,491] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 01:22:40,491] [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_002731945.1	s__GCA-002731945 sp002731945	94.8727	335	417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__GCA-002731945	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002726005.1	s__AG-430-B22 sp002726005	76.4467	73	417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__AG-430-B22	95.0	98.76	98.76	0.74	0.74	2	-
GCA_902533755.1	s__AG-430-B22 sp902533755	76.3854	56	417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__AG-430-B22	95.0	99.48	99.48	0.87	0.87	3	-
GCA_003212795.1	s__AG-430-B22 sp003212795	76.2998	82	417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__AG-430-B22	95.0	98.52	95.66	0.95	0.87	7	-
GCA_002728335.1	s__AG-430-B22 sp002728335	76.0692	50	417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__AG-430-B22	95.0	97.53	96.38	0.78	0.71	4	-
--------------------------------------------------------------------------------
[2023-03-19 01:22:40,491] [INFO] GTDB search result was written to OceanDNA-b27110/result_gtdb.tsv
[2023-03-19 01:22:40,492] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:22:40,492] [INFO] DFAST_QC result json was written to OceanDNA-b27110/dqc_result.json
[2023-03-19 01:22:40,492] [INFO] DFAST_QC completed!
[2023-03-19 01:22:40,492] [INFO] Total running time: 0h0m46s