[2023-03-18 05:53:16,847] [INFO] DFAST_QC pipeline started.
[2023-03-18 05:53:16,847] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 05:53:16,847] [INFO] DQC Reference Directory: /var/lib/cwl/stg8199b645-6204-47a6-81fa-6976cdea46b6/dqc_reference
[2023-03-18 05:53:17,976] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 05:53:17,976] [INFO] Task started: Prodigal
[2023-03-18 05:53:17,976] [INFO] Running command: cat /var/lib/cwl/stg1ed57c53-a1be-443a-ae4a-5d9796d7d38a/OceanDNA-b35530.fa | prodigal -d OceanDNA-b35530/cds.fna -a OceanDNA-b35530/protein.faa -g 11 -q > /dev/null
[2023-03-18 05:53:20,693] [INFO] Task succeeded: Prodigal
[2023-03-18 05:53:20,693] [INFO] Task started: HMMsearch
[2023-03-18 05:53:20,693] [INFO] Running command: hmmsearch --tblout OceanDNA-b35530/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8199b645-6204-47a6-81fa-6976cdea46b6/dqc_reference/reference_markers.hmm OceanDNA-b35530/protein.faa > /dev/null
[2023-03-18 05:53:20,868] [INFO] Task succeeded: HMMsearch
[2023-03-18 05:53:20,869] [INFO] Found 6/6 markers.
[2023-03-18 05:53:20,875] [INFO] Query marker FASTA was written to OceanDNA-b35530/markers.fasta
[2023-03-18 05:53:20,877] [INFO] Task started: Blastn
[2023-03-18 05:53:20,877] [INFO] Running command: blastn -query OceanDNA-b35530/markers.fasta -db /var/lib/cwl/stg8199b645-6204-47a6-81fa-6976cdea46b6/dqc_reference/reference_markers.fasta -out OceanDNA-b35530/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:53:21,588] [INFO] Task succeeded: Blastn
[2023-03-18 05:53:21,589] [INFO] Selected 13 target genomes.
[2023-03-18 05:53:21,589] [INFO] Target genome list was writen to OceanDNA-b35530/target_genomes.txt
[2023-03-18 05:53:21,601] [INFO] Task started: fastANI
[2023-03-18 05:53:21,601] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ed57c53-a1be-443a-ae4a-5d9796d7d38a/OceanDNA-b35530.fa --refList OceanDNA-b35530/target_genomes.txt --output OceanDNA-b35530/fastani_result.tsv --threads 1
[2023-03-18 05:53:27,425] [INFO] Task succeeded: fastANI
[2023-03-18 05:53:27,425] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8199b645-6204-47a6-81fa-6976cdea46b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 05:53:27,426] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8199b645-6204-47a6-81fa-6976cdea46b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 05:53:27,426] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 05:53:27,426] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 05:53:27,426] [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 05:53:27,426] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35530/tc_result.tsv
[2023-03-18 05:53:27,426] [INFO] ===== Taxonomy check completed =====
[2023-03-18 05:53:27,426] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 05:53:27,426] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8199b645-6204-47a6-81fa-6976cdea46b6/dqc_reference/checkm_data
[2023-03-18 05:53:27,429] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 05:53:27,431] [INFO] Task started: CheckM
[2023-03-18 05:53:27,431] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35530/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35530/checkm_input OceanDNA-b35530/checkm_result
[2023-03-18 05:53:44,832] [INFO] Task succeeded: CheckM
[2023-03-18 05:53:44,832] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 05:53:44,834] [INFO] ===== Completeness check finished =====
[2023-03-18 05:53:44,834] [INFO] ===== Start GTDB Search =====
[2023-03-18 05:53:44,834] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35530/markers.fasta)
[2023-03-18 05:53:44,836] [INFO] Task started: Blastn
[2023-03-18 05:53:44,836] [INFO] Running command: blastn -query OceanDNA-b35530/markers.fasta -db /var/lib/cwl/stg8199b645-6204-47a6-81fa-6976cdea46b6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35530/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:53:46,046] [INFO] Task succeeded: Blastn
[2023-03-18 05:53:46,047] [INFO] Selected 21 target genomes.
[2023-03-18 05:53:46,047] [INFO] Target genome list was writen to OceanDNA-b35530/target_genomes_gtdb.txt
[2023-03-18 05:53:46,108] [INFO] Task started: fastANI
[2023-03-18 05:53:46,108] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ed57c53-a1be-443a-ae4a-5d9796d7d38a/OceanDNA-b35530.fa --refList OceanDNA-b35530/target_genomes_gtdb.txt --output OceanDNA-b35530/fastani_result_gtdb.tsv --threads 1
[2023-03-18 05:53:51,058] [INFO] Task succeeded: fastANI
[2023-03-18 05:53:51,061] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 05:53:51,061] [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_902559355.1	s__CACLCV01 sp902559355	95.187	164	171	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-002705445;f__GCA-002716945;g__CACLCV01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902605525.1	s__CACLCV01 sp902605525	94.3625	113	171	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-002705445;f__GCA-002716945;g__CACLCV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016779485.1	s__CACLCV01 sp016779485	78.9207	94	171	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-002705445;f__GCA-002716945;g__CACLCV01	95.0	99.98	99.97	0.94	0.91	3	-
GCA_902521725.1	s__CACLCV01 sp902521725	78.312	54	171	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-002705445;f__GCA-002716945;g__CACLCV01	95.0	99.92	99.92	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2023-03-18 05:53:51,061] [INFO] GTDB search result was written to OceanDNA-b35530/result_gtdb.tsv
[2023-03-18 05:53:51,061] [INFO] ===== GTDB Search completed =====
[2023-03-18 05:53:51,062] [INFO] DFAST_QC result json was written to OceanDNA-b35530/dqc_result.json
[2023-03-18 05:53:51,062] [INFO] DFAST_QC completed!
[2023-03-18 05:53:51,062] [INFO] Total running time: 0h0m34s