[2023-03-16 10:20:34,791] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:20:34,791] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:20:34,791] [INFO] DQC Reference Directory: /var/lib/cwl/stg6fc10081-a85e-4de1-a7db-67fe919dd5ee/dqc_reference
[2023-03-16 10:20:36,024] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:20:36,025] [INFO] Task started: Prodigal
[2023-03-16 10:20:36,025] [INFO] Running command: cat /var/lib/cwl/stg7cbb4b29-754a-45ab-b479-4f7302c7a1a4/OceanDNA-b37709.fa | prodigal -d OceanDNA-b37709/cds.fna -a OceanDNA-b37709/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:20:41,678] [INFO] Task succeeded: Prodigal
[2023-03-16 10:20:41,679] [INFO] Task started: HMMsearch
[2023-03-16 10:20:41,679] [INFO] Running command: hmmsearch --tblout OceanDNA-b37709/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6fc10081-a85e-4de1-a7db-67fe919dd5ee/dqc_reference/reference_markers.hmm OceanDNA-b37709/protein.faa > /dev/null
[2023-03-16 10:20:41,903] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:20:41,904] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7cbb4b29-754a-45ab-b479-4f7302c7a1a4/OceanDNA-b37709.fa]
[2023-03-16 10:20:41,914] [INFO] Query marker FASTA was written to OceanDNA-b37709/markers.fasta
[2023-03-16 10:20:41,915] [INFO] Task started: Blastn
[2023-03-16 10:20:41,915] [INFO] Running command: blastn -query OceanDNA-b37709/markers.fasta -db /var/lib/cwl/stg6fc10081-a85e-4de1-a7db-67fe919dd5ee/dqc_reference/reference_markers.fasta -out OceanDNA-b37709/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:20:42,442] [INFO] Task succeeded: Blastn
[2023-03-16 10:20:42,443] [INFO] Selected 34 target genomes.
[2023-03-16 10:20:42,443] [INFO] Target genome list was writen to OceanDNA-b37709/target_genomes.txt
[2023-03-16 10:20:42,509] [INFO] Task started: fastANI
[2023-03-16 10:20:42,509] [INFO] Running command: fastANI --query /var/lib/cwl/stg7cbb4b29-754a-45ab-b479-4f7302c7a1a4/OceanDNA-b37709.fa --refList OceanDNA-b37709/target_genomes.txt --output OceanDNA-b37709/fastani_result.tsv --threads 1
[2023-03-16 10:21:04,433] [INFO] Task succeeded: fastANI
[2023-03-16 10:21:04,433] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6fc10081-a85e-4de1-a7db-67fe919dd5ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:21:04,434] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6fc10081-a85e-4de1-a7db-67fe919dd5ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:21:04,434] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 10:21:04,434] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 10:21:04,434] [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 10:21:04,434] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37709/tc_result.tsv
[2023-03-16 10:21:04,434] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:21:04,434] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:21:04,434] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6fc10081-a85e-4de1-a7db-67fe919dd5ee/dqc_reference/checkm_data
[2023-03-16 10:21:04,437] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:21:04,440] [INFO] Task started: CheckM
[2023-03-16 10:21:04,440] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37709/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37709/checkm_input OceanDNA-b37709/checkm_result
[2023-03-16 10:21:25,509] [INFO] Task succeeded: CheckM
[2023-03-16 10:21:25,510] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 51.04%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 10:21:25,512] [INFO] ===== Completeness check finished =====
[2023-03-16 10:21:25,513] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:21:25,513] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37709/markers.fasta)
[2023-03-16 10:21:25,514] [INFO] Task started: Blastn
[2023-03-16 10:21:25,514] [INFO] Running command: blastn -query OceanDNA-b37709/markers.fasta -db /var/lib/cwl/stg6fc10081-a85e-4de1-a7db-67fe919dd5ee/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37709/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:21:26,267] [INFO] Task succeeded: Blastn
[2023-03-16 10:21:26,269] [INFO] Selected 20 target genomes.
[2023-03-16 10:21:26,269] [INFO] Target genome list was writen to OceanDNA-b37709/target_genomes_gtdb.txt
[2023-03-16 10:21:26,310] [INFO] Task started: fastANI
[2023-03-16 10:21:26,310] [INFO] Running command: fastANI --query /var/lib/cwl/stg7cbb4b29-754a-45ab-b479-4f7302c7a1a4/OceanDNA-b37709.fa --refList OceanDNA-b37709/target_genomes_gtdb.txt --output OceanDNA-b37709/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:21:35,944] [INFO] Task succeeded: fastANI
[2023-03-16 10:21:35,947] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 10:21:35,947] [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_902631395.1	s__Luminiphilus sp902631395	98.3814	214	264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	98.59	98.59	0.74	0.74	2	conclusive
GCA_002721785.1	s__Luminiphilus sp002721785	79.82	176	264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	99.68	99.68	0.89	0.89	2	-
GCA_902623175.1	s__Luminiphilus sp902623175	77.6927	51	264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 10:21:35,948] [INFO] GTDB search result was written to OceanDNA-b37709/result_gtdb.tsv
[2023-03-16 10:21:35,948] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:21:35,949] [INFO] DFAST_QC result json was written to OceanDNA-b37709/dqc_result.json
[2023-03-16 10:21:35,949] [INFO] DFAST_QC completed!
[2023-03-16 10:21:35,949] [INFO] Total running time: 0h1m1s