[2023-03-18 07:06:20,702] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:06:20,702] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:06:20,702] [INFO] DQC Reference Directory: /var/lib/cwl/stg2ee38b71-fc05-4bed-ab85-998a9e19100a/dqc_reference
[2023-03-18 07:06:22,302] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:06:22,303] [INFO] Task started: Prodigal
[2023-03-18 07:06:22,303] [INFO] Running command: cat /var/lib/cwl/stg40174b6a-b1a2-48a4-a65b-4fd9f7e86355/OceanDNA-b45832.fa | prodigal -d OceanDNA-b45832/cds.fna -a OceanDNA-b45832/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:06:39,067] [INFO] Task succeeded: Prodigal
[2023-03-18 07:06:39,067] [INFO] Task started: HMMsearch
[2023-03-18 07:06:39,067] [INFO] Running command: hmmsearch --tblout OceanDNA-b45832/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2ee38b71-fc05-4bed-ab85-998a9e19100a/dqc_reference/reference_markers.hmm OceanDNA-b45832/protein.faa > /dev/null
[2023-03-18 07:06:39,238] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:06:39,238] [INFO] Found 6/6 markers.
[2023-03-18 07:06:39,257] [INFO] Query marker FASTA was written to OceanDNA-b45832/markers.fasta
[2023-03-18 07:06:39,257] [INFO] Task started: Blastn
[2023-03-18 07:06:39,257] [INFO] Running command: blastn -query OceanDNA-b45832/markers.fasta -db /var/lib/cwl/stg2ee38b71-fc05-4bed-ab85-998a9e19100a/dqc_reference/reference_markers.fasta -out OceanDNA-b45832/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:06:39,814] [INFO] Task succeeded: Blastn
[2023-03-18 07:06:39,815] [INFO] Selected 12 target genomes.
[2023-03-18 07:06:39,815] [INFO] Target genome list was writen to OceanDNA-b45832/target_genomes.txt
[2023-03-18 07:06:39,821] [INFO] Task started: fastANI
[2023-03-18 07:06:39,821] [INFO] Running command: fastANI --query /var/lib/cwl/stg40174b6a-b1a2-48a4-a65b-4fd9f7e86355/OceanDNA-b45832.fa --refList OceanDNA-b45832/target_genomes.txt --output OceanDNA-b45832/fastani_result.tsv --threads 1
[2023-03-18 07:06:46,732] [INFO] Task succeeded: fastANI
[2023-03-18 07:06:46,733] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2ee38b71-fc05-4bed-ab85-998a9e19100a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:06:46,733] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2ee38b71-fc05-4bed-ab85-998a9e19100a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:06:46,733] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 07:06:46,733] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 07:06:46,733] [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
--------------------------------------------------------------------------------
[2023-03-18 07:06:46,733] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45832/tc_result.tsv
[2023-03-18 07:06:46,733] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:06:46,733] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:06:46,734] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2ee38b71-fc05-4bed-ab85-998a9e19100a/dqc_reference/checkm_data
[2023-03-18 07:06:46,736] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:06:46,750] [INFO] Task started: CheckM
[2023-03-18 07:06:46,750] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45832/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45832/checkm_input OceanDNA-b45832/checkm_result
[2023-03-18 07:07:32,069] [INFO] Task succeeded: CheckM
[2023-03-18 07:07:32,070] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.91%
Contamintation: 4.55%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 07:07:32,072] [INFO] ===== Completeness check finished =====
[2023-03-18 07:07:32,072] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:07:32,072] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45832/markers.fasta)
[2023-03-18 07:07:32,073] [INFO] Task started: Blastn
[2023-03-18 07:07:32,073] [INFO] Running command: blastn -query OceanDNA-b45832/markers.fasta -db /var/lib/cwl/stg2ee38b71-fc05-4bed-ab85-998a9e19100a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45832/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:07:32,992] [INFO] Task succeeded: Blastn
[2023-03-18 07:07:32,993] [INFO] Selected 20 target genomes.
[2023-03-18 07:07:32,993] [INFO] Target genome list was writen to OceanDNA-b45832/target_genomes_gtdb.txt
[2023-03-18 07:07:33,460] [INFO] Task started: fastANI
[2023-03-18 07:07:33,460] [INFO] Running command: fastANI --query /var/lib/cwl/stg40174b6a-b1a2-48a4-a65b-4fd9f7e86355/OceanDNA-b45832.fa --refList OceanDNA-b45832/target_genomes_gtdb.txt --output OceanDNA-b45832/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:07:44,818] [INFO] Task succeeded: fastANI
[2023-03-18 07:07:44,821] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 07:07:44,821] [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_002474325.1	s__UBA5691 sp002474325	83.9905	342	570	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA5691	95.0	98.86	98.86	0.81	0.81	2	-
GCA_002694885.1	s__UBA5691 sp002694885	80.6835	324	570	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA5691	95.0	99.79	99.79	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2023-03-18 07:07:44,821] [INFO] GTDB search result was written to OceanDNA-b45832/result_gtdb.tsv
[2023-03-18 07:07:44,821] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:07:44,821] [INFO] DFAST_QC result json was written to OceanDNA-b45832/dqc_result.json
[2023-03-18 07:07:44,822] [INFO] DFAST_QC completed!
[2023-03-18 07:07:44,822] [INFO] Total running time: 0h1m24s