[2023-03-17 03:24:50,866] [INFO] DFAST_QC pipeline started.
[2023-03-17 03:24:50,867] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 03:24:50,867] [INFO] DQC Reference Directory: /var/lib/cwl/stga8a13651-e35b-4fad-912e-3d33fae7ffc3/dqc_reference
[2023-03-17 03:24:52,004] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 03:24:52,004] [INFO] Task started: Prodigal
[2023-03-17 03:24:52,004] [INFO] Running command: cat /var/lib/cwl/stgac520751-c29f-4b96-89b5-b48830b448c2/OceanDNA-b35580.fa | prodigal -d OceanDNA-b35580/cds.fna -a OceanDNA-b35580/protein.faa -g 11 -q > /dev/null
[2023-03-17 03:24:55,542] [INFO] Task succeeded: Prodigal
[2023-03-17 03:24:55,542] [INFO] Task started: HMMsearch
[2023-03-17 03:24:55,542] [INFO] Running command: hmmsearch --tblout OceanDNA-b35580/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga8a13651-e35b-4fad-912e-3d33fae7ffc3/dqc_reference/reference_markers.hmm OceanDNA-b35580/protein.faa > /dev/null
[2023-03-17 03:24:55,716] [INFO] Task succeeded: HMMsearch
[2023-03-17 03:24:55,717] [INFO] Found 6/6 markers.
[2023-03-17 03:24:55,725] [INFO] Query marker FASTA was written to OceanDNA-b35580/markers.fasta
[2023-03-17 03:24:55,726] [INFO] Task started: Blastn
[2023-03-17 03:24:55,726] [INFO] Running command: blastn -query OceanDNA-b35580/markers.fasta -db /var/lib/cwl/stga8a13651-e35b-4fad-912e-3d33fae7ffc3/dqc_reference/reference_markers.fasta -out OceanDNA-b35580/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:24:56,267] [INFO] Task succeeded: Blastn
[2023-03-17 03:24:56,268] [INFO] Selected 13 target genomes.
[2023-03-17 03:24:56,268] [INFO] Target genome list was writen to OceanDNA-b35580/target_genomes.txt
[2023-03-17 03:24:56,272] [INFO] Task started: fastANI
[2023-03-17 03:24:56,273] [INFO] Running command: fastANI --query /var/lib/cwl/stgac520751-c29f-4b96-89b5-b48830b448c2/OceanDNA-b35580.fa --refList OceanDNA-b35580/target_genomes.txt --output OceanDNA-b35580/fastani_result.tsv --threads 1
[2023-03-17 03:25:03,760] [INFO] Task succeeded: fastANI
[2023-03-17 03:25:03,760] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga8a13651-e35b-4fad-912e-3d33fae7ffc3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 03:25:03,760] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga8a13651-e35b-4fad-912e-3d33fae7ffc3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 03:25:03,761] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 03:25:03,761] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 03:25:03,761] [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 03:25:03,761] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35580/tc_result.tsv
[2023-03-17 03:25:03,761] [INFO] ===== Taxonomy check completed =====
[2023-03-17 03:25:03,761] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 03:25:03,761] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga8a13651-e35b-4fad-912e-3d33fae7ffc3/dqc_reference/checkm_data
[2023-03-17 03:25:03,764] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 03:25:03,961] [INFO] Task started: CheckM
[2023-03-17 03:25:03,961] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35580/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35580/checkm_input OceanDNA-b35580/checkm_result
[2023-03-17 03:25:19,442] [INFO] Task succeeded: CheckM
[2023-03-17 03:25:19,443] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.12%
Contamintation: 1.97%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 03:25:19,447] [INFO] ===== Completeness check finished =====
[2023-03-17 03:25:19,447] [INFO] ===== Start GTDB Search =====
[2023-03-17 03:25:19,447] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35580/markers.fasta)
[2023-03-17 03:25:19,448] [INFO] Task started: Blastn
[2023-03-17 03:25:19,448] [INFO] Running command: blastn -query OceanDNA-b35580/markers.fasta -db /var/lib/cwl/stga8a13651-e35b-4fad-912e-3d33fae7ffc3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35580/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:25:20,328] [INFO] Task succeeded: Blastn
[2023-03-17 03:25:20,332] [INFO] Selected 32 target genomes.
[2023-03-17 03:25:20,332] [INFO] Target genome list was writen to OceanDNA-b35580/target_genomes_gtdb.txt
[2023-03-17 03:25:20,411] [INFO] Task started: fastANI
[2023-03-17 03:25:20,411] [INFO] Running command: fastANI --query /var/lib/cwl/stgac520751-c29f-4b96-89b5-b48830b448c2/OceanDNA-b35580.fa --refList OceanDNA-b35580/target_genomes_gtdb.txt --output OceanDNA-b35580/fastani_result_gtdb.tsv --threads 1
[2023-03-17 03:25:26,990] [INFO] Task succeeded: fastANI
[2023-03-17 03:25:26,994] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 03:25:26,994] [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_018670435.1	s__GCA-2698665 sp018670435	77.8779	58	230	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-002705445;f__GCA-002716945;g__GCA-2698665	95.0	99.55	99.48	0.85	0.83	5	-
GCA_905479195.1	s__GCA-2698665 sp905479195	77.7674	80	230	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-002705445;f__GCA-002716945;g__GCA-2698665	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018667355.1	s__GCA-2698665 sp018667355	77.6128	64	230	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-002705445;f__GCA-002716945;g__GCA-2698665	95.0	99.95	99.92	0.96	0.95	8	-
GCA_002698665.1	s__GCA-2698665 sp002698665	77.0816	52	230	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-002705445;f__GCA-002716945;g__GCA-2698665	95.0	98.38	98.38	0.83	0.83	2	-
--------------------------------------------------------------------------------
[2023-03-17 03:25:26,994] [INFO] GTDB search result was written to OceanDNA-b35580/result_gtdb.tsv
[2023-03-17 03:25:26,994] [INFO] ===== GTDB Search completed =====
[2023-03-17 03:25:26,995] [INFO] DFAST_QC result json was written to OceanDNA-b35580/dqc_result.json
[2023-03-17 03:25:26,995] [INFO] DFAST_QC completed!
[2023-03-17 03:25:26,995] [INFO] Total running time: 0h0m36s