[2023-03-15 10:34:47,897] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:34:47,917] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:34:47,917] [INFO] DQC Reference Directory: /var/lib/cwl/stgb01cc743-8be6-4449-bed6-3bf7730d2426/dqc_reference
[2023-03-15 10:34:49,422] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:34:49,423] [INFO] Task started: Prodigal
[2023-03-15 10:34:49,423] [INFO] Running command: cat /var/lib/cwl/stg0b08b4ea-9daa-429a-b44b-1551b5584ee8/OceanDNA-b37029.fa | prodigal -d OceanDNA-b37029/cds.fna -a OceanDNA-b37029/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:35:02,926] [INFO] Task succeeded: Prodigal
[2023-03-15 10:35:02,927] [INFO] Task started: HMMsearch
[2023-03-15 10:35:02,927] [INFO] Running command: hmmsearch --tblout OceanDNA-b37029/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb01cc743-8be6-4449-bed6-3bf7730d2426/dqc_reference/reference_markers.hmm OceanDNA-b37029/protein.faa > /dev/null
[2023-03-15 10:35:03,110] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:35:03,111] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg0b08b4ea-9daa-429a-b44b-1551b5584ee8/OceanDNA-b37029.fa]
[2023-03-15 10:35:03,245] [INFO] Query marker FASTA was written to OceanDNA-b37029/markers.fasta
[2023-03-15 10:35:03,247] [INFO] Task started: Blastn
[2023-03-15 10:35:03,247] [INFO] Running command: blastn -query OceanDNA-b37029/markers.fasta -db /var/lib/cwl/stgb01cc743-8be6-4449-bed6-3bf7730d2426/dqc_reference/reference_markers.fasta -out OceanDNA-b37029/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:35:03,804] [INFO] Task succeeded: Blastn
[2023-03-15 10:35:03,851] [INFO] Selected 24 target genomes.
[2023-03-15 10:35:03,851] [INFO] Target genome list was writen to OceanDNA-b37029/target_genomes.txt
[2023-03-15 10:35:03,860] [INFO] Task started: fastANI
[2023-03-15 10:35:03,860] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b08b4ea-9daa-429a-b44b-1551b5584ee8/OceanDNA-b37029.fa --refList OceanDNA-b37029/target_genomes.txt --output OceanDNA-b37029/fastani_result.tsv --threads 1
[2023-03-15 10:35:17,798] [INFO] Task succeeded: fastANI
[2023-03-15 10:35:17,799] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb01cc743-8be6-4449-bed6-3bf7730d2426/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:35:17,799] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb01cc743-8be6-4449-bed6-3bf7730d2426/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:35:17,799] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:35:17,799] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 10:35:17,799] [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 10:35:17,815] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37029/tc_result.tsv
[2023-03-15 10:35:17,843] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:35:17,843] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:35:17,843] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb01cc743-8be6-4449-bed6-3bf7730d2426/dqc_reference/checkm_data
[2023-03-15 10:35:17,846] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:35:17,877] [INFO] Task started: CheckM
[2023-03-15 10:35:17,877] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37029/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37029/checkm_input OceanDNA-b37029/checkm_result
[2023-03-15 10:35:54,782] [INFO] Task succeeded: CheckM
[2023-03-15 10:35:54,783] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.94%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 10:35:55,044] [INFO] ===== Completeness check finished =====
[2023-03-15 10:35:55,044] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:35:55,045] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37029/markers.fasta)
[2023-03-15 10:35:55,046] [INFO] Task started: Blastn
[2023-03-15 10:35:55,046] [INFO] Running command: blastn -query OceanDNA-b37029/markers.fasta -db /var/lib/cwl/stgb01cc743-8be6-4449-bed6-3bf7730d2426/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37029/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:35:55,806] [INFO] Task succeeded: Blastn
[2023-03-15 10:35:55,853] [INFO] Selected 16 target genomes.
[2023-03-15 10:35:55,853] [INFO] Target genome list was writen to OceanDNA-b37029/target_genomes_gtdb.txt
[2023-03-15 10:35:56,473] [INFO] Task started: fastANI
[2023-03-15 10:35:56,473] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b08b4ea-9daa-429a-b44b-1551b5584ee8/OceanDNA-b37029.fa --refList OceanDNA-b37029/target_genomes_gtdb.txt --output OceanDNA-b37029/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:36:04,743] [INFO] Task succeeded: fastANI
[2023-03-15 10:36:04,747] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 10:36:04,747] [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_009886205.1	s__UBA4421 sp009886205	85.0724	585	782	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	98.44	96.05	0.88	0.79	9	-
GCA_905182095.1	s__UBA4421 sp905182095	82.1597	483	782	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002336645.1	s__UBA4421 sp002336645	80.995	465	782	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182905.1	s__UBA4421 sp002390555	78.4393	338	782	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	99.65	99.65	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2023-03-15 10:36:04,762] [INFO] GTDB search result was written to OceanDNA-b37029/result_gtdb.tsv
[2023-03-15 10:36:04,793] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:36:04,811] [INFO] DFAST_QC result json was written to OceanDNA-b37029/dqc_result.json
[2023-03-15 10:36:04,811] [INFO] DFAST_QC completed!
[2023-03-15 10:36:04,811] [INFO] Total running time: 0h1m17s