[2023-03-19 03:22:59,866] [INFO] DFAST_QC pipeline started.
[2023-03-19 03:22:59,872] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 03:22:59,872] [INFO] DQC Reference Directory: /var/lib/cwl/stgc36a39ec-ae74-4950-9d55-bd821f3a183d/dqc_reference
[2023-03-19 03:23:00,955] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 03:23:00,956] [INFO] Task started: Prodigal
[2023-03-19 03:23:00,956] [INFO] Running command: cat /var/lib/cwl/stg18505aee-7b0e-4658-a377-ab98de813f62/OceanDNA-b45611.fa | prodigal -d OceanDNA-b45611/cds.fna -a OceanDNA-b45611/protein.faa -g 11 -q > /dev/null
[2023-03-19 03:23:10,247] [INFO] Task succeeded: Prodigal
[2023-03-19 03:23:10,248] [INFO] Task started: HMMsearch
[2023-03-19 03:23:10,248] [INFO] Running command: hmmsearch --tblout OceanDNA-b45611/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc36a39ec-ae74-4950-9d55-bd821f3a183d/dqc_reference/reference_markers.hmm OceanDNA-b45611/protein.faa > /dev/null
[2023-03-19 03:23:10,403] [INFO] Task succeeded: HMMsearch
[2023-03-19 03:23:10,404] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg18505aee-7b0e-4658-a377-ab98de813f62/OceanDNA-b45611.fa]
[2023-03-19 03:23:10,448] [INFO] Query marker FASTA was written to OceanDNA-b45611/markers.fasta
[2023-03-19 03:23:10,448] [INFO] Task started: Blastn
[2023-03-19 03:23:10,448] [INFO] Running command: blastn -query OceanDNA-b45611/markers.fasta -db /var/lib/cwl/stgc36a39ec-ae74-4950-9d55-bd821f3a183d/dqc_reference/reference_markers.fasta -out OceanDNA-b45611/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:23:10,979] [INFO] Task succeeded: Blastn
[2023-03-19 03:23:11,002] [INFO] Selected 17 target genomes.
[2023-03-19 03:23:11,002] [INFO] Target genome list was writen to OceanDNA-b45611/target_genomes.txt
[2023-03-19 03:23:11,010] [INFO] Task started: fastANI
[2023-03-19 03:23:11,010] [INFO] Running command: fastANI --query /var/lib/cwl/stg18505aee-7b0e-4658-a377-ab98de813f62/OceanDNA-b45611.fa --refList OceanDNA-b45611/target_genomes.txt --output OceanDNA-b45611/fastani_result.tsv --threads 1
[2023-03-19 03:23:21,406] [INFO] Task succeeded: fastANI
[2023-03-19 03:23:21,407] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc36a39ec-ae74-4950-9d55-bd821f3a183d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 03:23:21,407] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc36a39ec-ae74-4950-9d55-bd821f3a183d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 03:23:21,407] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 03:23:21,407] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 03:23:21,407] [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 03:23:21,414] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45611/tc_result.tsv
[2023-03-19 03:23:21,429] [INFO] ===== Taxonomy check completed =====
[2023-03-19 03:23:21,429] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 03:23:21,429] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc36a39ec-ae74-4950-9d55-bd821f3a183d/dqc_reference/checkm_data
[2023-03-19 03:23:21,432] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 03:23:21,438] [INFO] Task started: CheckM
[2023-03-19 03:23:21,438] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45611/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45611/checkm_input OceanDNA-b45611/checkm_result
[2023-03-19 03:23:49,719] [INFO] Task succeeded: CheckM
[2023-03-19 03:23:49,719] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 03:23:49,873] [INFO] ===== Completeness check finished =====
[2023-03-19 03:23:49,873] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:23:49,873] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45611/markers.fasta)
[2023-03-19 03:23:49,874] [INFO] Task started: Blastn
[2023-03-19 03:23:49,874] [INFO] Running command: blastn -query OceanDNA-b45611/markers.fasta -db /var/lib/cwl/stgc36a39ec-ae74-4950-9d55-bd821f3a183d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45611/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:23:50,685] [INFO] Task succeeded: Blastn
[2023-03-19 03:23:50,708] [INFO] Selected 17 target genomes.
[2023-03-19 03:23:50,709] [INFO] Target genome list was writen to OceanDNA-b45611/target_genomes_gtdb.txt
[2023-03-19 03:23:50,826] [INFO] Task started: fastANI
[2023-03-19 03:23:50,826] [INFO] Running command: fastANI --query /var/lib/cwl/stg18505aee-7b0e-4658-a377-ab98de813f62/OceanDNA-b45611.fa --refList OceanDNA-b45611/target_genomes_gtdb.txt --output OceanDNA-b45611/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:23:57,912] [INFO] Task succeeded: fastANI
[2023-03-19 03:23:57,916] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 03:23:57,916] [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_018645475.1	s__MB11C04 sp018645475	81.4013	291	426	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902580225.1	s__MB11C04 sp902580225	79.356	149	426	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018675995.1	s__MB11C04 sp018675995	79.2411	96	426	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478775.1	s__MB11C04 sp002477515	78.3475	135	426	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	98.93	98.38	0.86	0.80	5	-
--------------------------------------------------------------------------------
[2023-03-19 03:23:57,924] [INFO] GTDB search result was written to OceanDNA-b45611/result_gtdb.tsv
[2023-03-19 03:23:57,946] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:23:57,955] [INFO] DFAST_QC result json was written to OceanDNA-b45611/dqc_result.json
[2023-03-19 03:23:57,956] [INFO] DFAST_QC completed!
[2023-03-19 03:23:57,956] [INFO] Total running time: 0h0m58s