[2023-03-15 21:52:21,352] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:52:21,352] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:52:21,352] [INFO] DQC Reference Directory: /var/lib/cwl/stgd3d9d730-af79-45b4-bdda-8e7a8860cbea/dqc_reference
[2023-03-15 21:52:22,486] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:52:22,486] [INFO] Task started: Prodigal
[2023-03-15 21:52:22,486] [INFO] Running command: cat /var/lib/cwl/stg5b97aa22-df0a-42fa-93b8-8ca153cbccdd/OceanDNA-b32391.fa | prodigal -d OceanDNA-b32391/cds.fna -a OceanDNA-b32391/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:52:25,181] [INFO] Task succeeded: Prodigal
[2023-03-15 21:52:25,182] [INFO] Task started: HMMsearch
[2023-03-15 21:52:25,182] [INFO] Running command: hmmsearch --tblout OceanDNA-b32391/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd3d9d730-af79-45b4-bdda-8e7a8860cbea/dqc_reference/reference_markers.hmm OceanDNA-b32391/protein.faa > /dev/null
[2023-03-15 21:52:25,329] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:52:25,330] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg5b97aa22-df0a-42fa-93b8-8ca153cbccdd/OceanDNA-b32391.fa]
[2023-03-15 21:52:25,341] [INFO] Query marker FASTA was written to OceanDNA-b32391/markers.fasta
[2023-03-15 21:52:25,344] [INFO] Task started: Blastn
[2023-03-15 21:52:25,344] [INFO] Running command: blastn -query OceanDNA-b32391/markers.fasta -db /var/lib/cwl/stgd3d9d730-af79-45b4-bdda-8e7a8860cbea/dqc_reference/reference_markers.fasta -out OceanDNA-b32391/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:52:26,028] [INFO] Task succeeded: Blastn
[2023-03-15 21:52:26,029] [INFO] Selected 10 target genomes.
[2023-03-15 21:52:26,029] [INFO] Target genome list was writen to OceanDNA-b32391/target_genomes.txt
[2023-03-15 21:52:26,038] [INFO] Task started: fastANI
[2023-03-15 21:52:26,038] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b97aa22-df0a-42fa-93b8-8ca153cbccdd/OceanDNA-b32391.fa --refList OceanDNA-b32391/target_genomes.txt --output OceanDNA-b32391/fastani_result.tsv --threads 1
[2023-03-15 21:52:29,312] [INFO] Task succeeded: fastANI
[2023-03-15 21:52:29,312] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd3d9d730-af79-45b4-bdda-8e7a8860cbea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:52:29,312] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd3d9d730-af79-45b4-bdda-8e7a8860cbea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:52:29,313] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:52:29,313] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 21:52:29,313] [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
--------------------------------------------------------------------------------
[2023-03-15 21:52:29,313] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32391/tc_result.tsv
[2023-03-15 21:52:29,313] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:52:29,313] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:52:29,313] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd3d9d730-af79-45b4-bdda-8e7a8860cbea/dqc_reference/checkm_data
[2023-03-15 21:52:29,316] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:52:29,320] [INFO] Task started: CheckM
[2023-03-15 21:52:29,320] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32391/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32391/checkm_input OceanDNA-b32391/checkm_result
[2023-03-15 21:52:47,768] [INFO] Task succeeded: CheckM
[2023-03-15 21:52:47,768] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.61%
Contamintation: 9.18%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 21:52:47,770] [INFO] ===== Completeness check finished =====
[2023-03-15 21:52:47,770] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:52:47,770] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32391/markers.fasta)
[2023-03-15 21:52:47,772] [INFO] Task started: Blastn
[2023-03-15 21:52:47,773] [INFO] Running command: blastn -query OceanDNA-b32391/markers.fasta -db /var/lib/cwl/stgd3d9d730-af79-45b4-bdda-8e7a8860cbea/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32391/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:52:49,297] [INFO] Task succeeded: Blastn
[2023-03-15 21:52:49,298] [INFO] Selected 10 target genomes.
[2023-03-15 21:52:49,298] [INFO] Target genome list was writen to OceanDNA-b32391/target_genomes_gtdb.txt
[2023-03-15 21:52:49,563] [INFO] Task started: fastANI
[2023-03-15 21:52:49,563] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b97aa22-df0a-42fa-93b8-8ca153cbccdd/OceanDNA-b32391.fa --refList OceanDNA-b32391/target_genomes_gtdb.txt --output OceanDNA-b32391/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:52:51,562] [INFO] Task succeeded: fastANI
[2023-03-15 21:52:51,564] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 21:52:51,565] [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_002720535.1	s__TMED109 sp002720535	85.9226	66	78	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED109;g__TMED109	95.0	95.89	95.27	0.82	0.81	3	-
GCA_002171375.1	s__TMED109 sp002171375	83.3178	59	78	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED109;g__TMED109	95.0	98.96	97.53	0.84	0.73	4	-
GCA_002937655.1	s__TMED109 sp002937655	82.7141	65	78	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED109;g__TMED109	95.0	99.81	99.81	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2023-03-15 21:52:51,565] [INFO] GTDB search result was written to OceanDNA-b32391/result_gtdb.tsv
[2023-03-15 21:52:51,565] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:52:51,566] [INFO] DFAST_QC result json was written to OceanDNA-b32391/dqc_result.json
[2023-03-15 21:52:51,566] [INFO] DFAST_QC completed!
[2023-03-15 21:52:51,566] [INFO] Total running time: 0h0m30s