[2023-03-18 09:41:09,231] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:41:09,231] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:41:09,231] [INFO] DQC Reference Directory: /var/lib/cwl/stgf9e4caf4-8af2-462f-a0d6-faca27687947/dqc_reference
[2023-03-18 09:41:10,373] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:41:10,374] [INFO] Task started: Prodigal
[2023-03-18 09:41:10,374] [INFO] Running command: cat /var/lib/cwl/stgd45dc3f7-65ac-4128-809e-9126b23a259b/OceanDNA-b32709.fa | prodigal -d OceanDNA-b32709/cds.fna -a OceanDNA-b32709/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:41:19,876] [INFO] Task succeeded: Prodigal
[2023-03-18 09:41:19,877] [INFO] Task started: HMMsearch
[2023-03-18 09:41:19,877] [INFO] Running command: hmmsearch --tblout OceanDNA-b32709/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf9e4caf4-8af2-462f-a0d6-faca27687947/dqc_reference/reference_markers.hmm OceanDNA-b32709/protein.faa > /dev/null
[2023-03-18 09:41:20,071] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:41:20,071] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd45dc3f7-65ac-4128-809e-9126b23a259b/OceanDNA-b32709.fa]
[2023-03-18 09:41:20,090] [INFO] Query marker FASTA was written to OceanDNA-b32709/markers.fasta
[2023-03-18 09:41:20,090] [INFO] Task started: Blastn
[2023-03-18 09:41:20,090] [INFO] Running command: blastn -query OceanDNA-b32709/markers.fasta -db /var/lib/cwl/stgf9e4caf4-8af2-462f-a0d6-faca27687947/dqc_reference/reference_markers.fasta -out OceanDNA-b32709/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:41:20,735] [INFO] Task succeeded: Blastn
[2023-03-18 09:41:20,736] [INFO] Selected 31 target genomes.
[2023-03-18 09:41:20,736] [INFO] Target genome list was writen to OceanDNA-b32709/target_genomes.txt
[2023-03-18 09:41:20,756] [INFO] Task started: fastANI
[2023-03-18 09:41:20,756] [INFO] Running command: fastANI --query /var/lib/cwl/stgd45dc3f7-65ac-4128-809e-9126b23a259b/OceanDNA-b32709.fa --refList OceanDNA-b32709/target_genomes.txt --output OceanDNA-b32709/fastani_result.tsv --threads 1
[2023-03-18 09:41:46,988] [INFO] Task succeeded: fastANI
[2023-03-18 09:41:46,988] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf9e4caf4-8af2-462f-a0d6-faca27687947/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:41:46,988] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf9e4caf4-8af2-462f-a0d6-faca27687947/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:41:46,989] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:41:46,989] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 09:41:46,989] [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 09:41:46,989] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32709/tc_result.tsv
[2023-03-18 09:41:46,989] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:41:46,989] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:41:46,989] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf9e4caf4-8af2-462f-a0d6-faca27687947/dqc_reference/checkm_data
[2023-03-18 09:41:46,991] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:41:46,995] [INFO] Task started: CheckM
[2023-03-18 09:41:46,995] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32709/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32709/checkm_input OceanDNA-b32709/checkm_result
[2023-03-18 09:42:15,602] [INFO] Task succeeded: CheckM
[2023-03-18 09:42:15,603] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.25%
Contamintation: 9.32%
Strain heterogeneity: 25.00%
--------------------------------------------------------------------------------
[2023-03-18 09:42:15,605] [INFO] ===== Completeness check finished =====
[2023-03-18 09:42:15,605] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:42:15,605] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32709/markers.fasta)
[2023-03-18 09:42:15,605] [INFO] Task started: Blastn
[2023-03-18 09:42:15,605] [INFO] Running command: blastn -query OceanDNA-b32709/markers.fasta -db /var/lib/cwl/stgf9e4caf4-8af2-462f-a0d6-faca27687947/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32709/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:42:16,689] [INFO] Task succeeded: Blastn
[2023-03-18 09:42:16,689] [INFO] Selected 23 target genomes.
[2023-03-18 09:42:16,690] [INFO] Target genome list was writen to OceanDNA-b32709/target_genomes_gtdb.txt
[2023-03-18 09:42:16,710] [INFO] Task started: fastANI
[2023-03-18 09:42:16,710] [INFO] Running command: fastANI --query /var/lib/cwl/stgd45dc3f7-65ac-4128-809e-9126b23a259b/OceanDNA-b32709.fa --refList OceanDNA-b32709/target_genomes_gtdb.txt --output OceanDNA-b32709/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:42:29,917] [INFO] Task succeeded: fastANI
[2023-03-18 09:42:29,924] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 09:42:29,924] [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_018666195.1	s__JABJAG01 sp018666195	78.5837	189	386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__JABJAG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018667335.1	s__UBA8079 sp018667335	77.9992	187	386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	99.89	99.79	0.96	0.96	6	-
GCA_018702955.1	s__UBA8079 sp018702955	77.9276	162	386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	99.54	99.39	0.93	0.91	5	-
GCA_002727315.1	s__UBA8079 sp002727315	77.6097	112	386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017643325.1	s__JABJAG01 sp017643325	77.393	116	386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__JABJAG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002724635.1	s__UBA8079 sp002724635	76.8238	104	386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013003285.1	s__JABDJY01 sp013003285	76.5979	53	386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__JABDJY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011087645.1	s__JABDJY01 sp011087645	76.3079	81	386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__JABDJY01	95.0	99.97	99.97	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2023-03-18 09:42:29,924] [INFO] GTDB search result was written to OceanDNA-b32709/result_gtdb.tsv
[2023-03-18 09:42:29,924] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:42:29,925] [INFO] DFAST_QC result json was written to OceanDNA-b32709/dqc_result.json
[2023-03-18 09:42:29,925] [INFO] DFAST_QC completed!
[2023-03-18 09:42:29,925] [INFO] Total running time: 0h1m21s