[2023-03-16 09:50:26,314] [INFO] DFAST_QC pipeline started.
[2023-03-16 09:50:26,314] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 09:50:26,315] [INFO] DQC Reference Directory: /var/lib/cwl/stg7c5d9271-5388-445b-82d3-1b61c4bc724c/dqc_reference
[2023-03-16 09:50:27,435] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 09:50:27,436] [INFO] Task started: Prodigal
[2023-03-16 09:50:27,436] [INFO] Running command: cat /var/lib/cwl/stg447f197d-75d6-4611-85d1-ccb49207acc3/OceanDNA-b24775.fa | prodigal -d OceanDNA-b24775/cds.fna -a OceanDNA-b24775/protein.faa -g 11 -q > /dev/null
[2023-03-16 09:50:39,232] [INFO] Task succeeded: Prodigal
[2023-03-16 09:50:39,233] [INFO] Task started: HMMsearch
[2023-03-16 09:50:39,233] [INFO] Running command: hmmsearch --tblout OceanDNA-b24775/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7c5d9271-5388-445b-82d3-1b61c4bc724c/dqc_reference/reference_markers.hmm OceanDNA-b24775/protein.faa > /dev/null
[2023-03-16 09:50:39,422] [INFO] Task succeeded: HMMsearch
[2023-03-16 09:50:39,422] [INFO] Found 6/6 markers.
[2023-03-16 09:50:39,443] [INFO] Query marker FASTA was written to OceanDNA-b24775/markers.fasta
[2023-03-16 09:50:39,445] [INFO] Task started: Blastn
[2023-03-16 09:50:39,445] [INFO] Running command: blastn -query OceanDNA-b24775/markers.fasta -db /var/lib/cwl/stg7c5d9271-5388-445b-82d3-1b61c4bc724c/dqc_reference/reference_markers.fasta -out OceanDNA-b24775/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:50:40,080] [INFO] Task succeeded: Blastn
[2023-03-16 09:50:40,081] [INFO] Selected 22 target genomes.
[2023-03-16 09:50:40,081] [INFO] Target genome list was writen to OceanDNA-b24775/target_genomes.txt
[2023-03-16 09:50:40,097] [INFO] Task started: fastANI
[2023-03-16 09:50:40,097] [INFO] Running command: fastANI --query /var/lib/cwl/stg447f197d-75d6-4611-85d1-ccb49207acc3/OceanDNA-b24775.fa --refList OceanDNA-b24775/target_genomes.txt --output OceanDNA-b24775/fastani_result.tsv --threads 1
[2023-03-16 09:50:49,498] [INFO] Task succeeded: fastANI
[2023-03-16 09:50:49,498] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7c5d9271-5388-445b-82d3-1b61c4bc724c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 09:50:49,498] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7c5d9271-5388-445b-82d3-1b61c4bc724c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 09:50:49,499] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 09:50:49,499] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 09:50:49,499] [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
--------------------------------------------------------------------------------
[2023-03-16 09:50:49,499] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24775/tc_result.tsv
[2023-03-16 09:50:49,500] [INFO] ===== Taxonomy check completed =====
[2023-03-16 09:50:49,500] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 09:50:49,500] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7c5d9271-5388-445b-82d3-1b61c4bc724c/dqc_reference/checkm_data
[2023-03-16 09:50:49,503] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 09:50:49,533] [INFO] Task started: CheckM
[2023-03-16 09:50:49,533] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24775/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24775/checkm_input OceanDNA-b24775/checkm_result
[2023-03-16 09:51:23,157] [INFO] Task succeeded: CheckM
[2023-03-16 09:51:23,157] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.45%
Contamintation: 3.88%
Strain heterogeneity: 60.00%
--------------------------------------------------------------------------------
[2023-03-16 09:51:23,170] [INFO] ===== Completeness check finished =====
[2023-03-16 09:51:23,170] [INFO] ===== Start GTDB Search =====
[2023-03-16 09:51:23,170] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24775/markers.fasta)
[2023-03-16 09:51:23,171] [INFO] Task started: Blastn
[2023-03-16 09:51:23,171] [INFO] Running command: blastn -query OceanDNA-b24775/markers.fasta -db /var/lib/cwl/stg7c5d9271-5388-445b-82d3-1b61c4bc724c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24775/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:51:24,050] [INFO] Task succeeded: Blastn
[2023-03-16 09:51:24,052] [INFO] Selected 9 target genomes.
[2023-03-16 09:51:24,052] [INFO] Target genome list was writen to OceanDNA-b24775/target_genomes_gtdb.txt
[2023-03-16 09:51:24,103] [INFO] Task started: fastANI
[2023-03-16 09:51:24,103] [INFO] Running command: fastANI --query /var/lib/cwl/stg447f197d-75d6-4611-85d1-ccb49207acc3/OceanDNA-b24775.fa --refList OceanDNA-b24775/target_genomes_gtdb.txt --output OceanDNA-b24775/fastani_result_gtdb.tsv --threads 1
[2023-03-16 09:51:27,859] [INFO] Task succeeded: fastANI
[2023-03-16 09:51:27,864] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 09:51:27,864] [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_002730675.1	s__GCA-002701455 sp002730675	98.5573	463	678	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__GCA-002701455	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902589475.1	s__GCA-002701455 sp902589475	90.5392	403	678	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__GCA-002701455	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002690995.1	s__GCA-002701455 sp002690995	90.5314	563	678	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__GCA-002701455	95.0	95.85	95.85	0.80	0.80	2	-
GCA_902578675.1	s__GCA-002701455 sp902578675	89.5943	314	678	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__GCA-002701455	95.0	97.96	97.96	0.68	0.68	2	-
GCA_902629125.1	s__GCA-002701455 sp902629125	89.2453	467	678	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__GCA-002701455	95.0	98.54	98.54	0.68	0.68	2	-
GCA_002701455.1	s__GCA-002701455 sp002701455	78.1795	275	678	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__GCA-002701455	95.0	98.37	98.37	0.80	0.80	2	-
--------------------------------------------------------------------------------
[2023-03-16 09:51:27,864] [INFO] GTDB search result was written to OceanDNA-b24775/result_gtdb.tsv
[2023-03-16 09:51:27,865] [INFO] ===== GTDB Search completed =====
[2023-03-16 09:51:27,866] [INFO] DFAST_QC result json was written to OceanDNA-b24775/dqc_result.json
[2023-03-16 09:51:27,867] [INFO] DFAST_QC completed!
[2023-03-16 09:51:27,867] [INFO] Total running time: 0h1m2s