[2023-03-15 14:53:55,870] [INFO] DFAST_QC pipeline started.
[2023-03-15 14:53:55,874] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 14:53:55,874] [INFO] DQC Reference Directory: /var/lib/cwl/stg12a061f6-2951-474d-8816-3e851970b20e/dqc_reference
[2023-03-15 14:53:57,655] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 14:53:57,656] [INFO] Task started: Prodigal
[2023-03-15 14:53:57,656] [INFO] Running command: cat /var/lib/cwl/stg3703a467-7124-42e4-8c4f-e408a46f246d/OceanDNA-b40612.fa | prodigal -d OceanDNA-b40612/cds.fna -a OceanDNA-b40612/protein.faa -g 11 -q > /dev/null
[2023-03-15 14:54:05,632] [INFO] Task succeeded: Prodigal
[2023-03-15 14:54:05,633] [INFO] Task started: HMMsearch
[2023-03-15 14:54:05,633] [INFO] Running command: hmmsearch --tblout OceanDNA-b40612/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg12a061f6-2951-474d-8816-3e851970b20e/dqc_reference/reference_markers.hmm OceanDNA-b40612/protein.faa > /dev/null
[2023-03-15 14:54:05,806] [INFO] Task succeeded: HMMsearch
[2023-03-15 14:54:05,807] [INFO] Found 6/6 markers.
[2023-03-15 14:54:05,875] [INFO] Query marker FASTA was written to OceanDNA-b40612/markers.fasta
[2023-03-15 14:54:05,877] [INFO] Task started: Blastn
[2023-03-15 14:54:05,877] [INFO] Running command: blastn -query OceanDNA-b40612/markers.fasta -db /var/lib/cwl/stg12a061f6-2951-474d-8816-3e851970b20e/dqc_reference/reference_markers.fasta -out OceanDNA-b40612/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:54:06,458] [INFO] Task succeeded: Blastn
[2023-03-15 14:54:06,481] [INFO] Selected 17 target genomes.
[2023-03-15 14:54:06,481] [INFO] Target genome list was writen to OceanDNA-b40612/target_genomes.txt
[2023-03-15 14:54:06,491] [INFO] Task started: fastANI
[2023-03-15 14:54:06,491] [INFO] Running command: fastANI --query /var/lib/cwl/stg3703a467-7124-42e4-8c4f-e408a46f246d/OceanDNA-b40612.fa --refList OceanDNA-b40612/target_genomes.txt --output OceanDNA-b40612/fastani_result.tsv --threads 1
[2023-03-15 14:54:17,224] [INFO] Task succeeded: fastANI
[2023-03-15 14:54:17,224] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg12a061f6-2951-474d-8816-3e851970b20e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 14:54:17,225] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg12a061f6-2951-474d-8816-3e851970b20e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 14:54:17,225] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 14:54:17,225] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 14:54:17,225] [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 14:54:17,233] [INFO] DFAST Taxonomy check result was written to OceanDNA-b40612/tc_result.tsv
[2023-03-15 14:54:17,246] [INFO] ===== Taxonomy check completed =====
[2023-03-15 14:54:17,247] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 14:54:17,247] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg12a061f6-2951-474d-8816-3e851970b20e/dqc_reference/checkm_data
[2023-03-15 14:54:17,250] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 14:54:17,272] [INFO] Task started: CheckM
[2023-03-15 14:54:17,272] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b40612/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b40612/checkm_input OceanDNA-b40612/checkm_result
[2023-03-15 14:54:42,809] [INFO] Task succeeded: CheckM
[2023-03-15 14:54:42,810] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.25%
Contamintation: 4.69%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 14:54:42,946] [INFO] ===== Completeness check finished =====
[2023-03-15 14:54:42,946] [INFO] ===== Start GTDB Search =====
[2023-03-15 14:54:42,947] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b40612/markers.fasta)
[2023-03-15 14:54:42,948] [INFO] Task started: Blastn
[2023-03-15 14:54:42,948] [INFO] Running command: blastn -query OceanDNA-b40612/markers.fasta -db /var/lib/cwl/stg12a061f6-2951-474d-8816-3e851970b20e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b40612/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:54:43,675] [INFO] Task succeeded: Blastn
[2023-03-15 14:54:43,708] [INFO] Selected 26 target genomes.
[2023-03-15 14:54:43,708] [INFO] Target genome list was writen to OceanDNA-b40612/target_genomes_gtdb.txt
[2023-03-15 14:54:43,932] [INFO] Task started: fastANI
[2023-03-15 14:54:43,932] [INFO] Running command: fastANI --query /var/lib/cwl/stg3703a467-7124-42e4-8c4f-e408a46f246d/OceanDNA-b40612.fa --refList OceanDNA-b40612/target_genomes_gtdb.txt --output OceanDNA-b40612/fastani_result_gtdb.tsv --threads 1
[2023-03-15 14:54:53,645] [INFO] Task succeeded: fastANI
[2023-03-15 14:54:53,648] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 14:54:53,649] [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_902531515.1	s__UBA9145 sp902531515	92.7179	304	459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002714195.1	s__UBA9145 sp002714195	85.0626	255	459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002172295.1	s__UBA9145 sp002172295	79.482	91	459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	100.00	100.00	0.99	0.99	2	-
GCA_902591495.1	s__UBA9145 sp902591495	79.3665	166	459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 14:54:53,661] [INFO] GTDB search result was written to OceanDNA-b40612/result_gtdb.tsv
[2023-03-15 14:54:53,681] [INFO] ===== GTDB Search completed =====
[2023-03-15 14:54:53,695] [INFO] DFAST_QC result json was written to OceanDNA-b40612/dqc_result.json
[2023-03-15 14:54:53,695] [INFO] DFAST_QC completed!
[2023-03-15 14:54:53,695] [INFO] Total running time: 0h0m58s