[2023-03-16 22:45:35,372] [INFO] DFAST_QC pipeline started.
[2023-03-16 22:45:35,372] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 22:45:35,372] [INFO] DQC Reference Directory: /var/lib/cwl/stg31a25c7c-2a8b-42b1-a120-43ef41ae137a/dqc_reference
[2023-03-16 22:45:37,282] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 22:45:37,282] [INFO] Task started: Prodigal
[2023-03-16 22:45:37,283] [INFO] Running command: cat /var/lib/cwl/stg2a48319c-0638-474b-8449-5504080483bc/OceanDNA-b887.fa | prodigal -d OceanDNA-b887/cds.fna -a OceanDNA-b887/protein.faa -g 11 -q > /dev/null
[2023-03-16 22:45:45,612] [INFO] Task succeeded: Prodigal
[2023-03-16 22:45:45,613] [INFO] Task started: HMMsearch
[2023-03-16 22:45:45,613] [INFO] Running command: hmmsearch --tblout OceanDNA-b887/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg31a25c7c-2a8b-42b1-a120-43ef41ae137a/dqc_reference/reference_markers.hmm OceanDNA-b887/protein.faa > /dev/null
[2023-03-16 22:45:45,778] [INFO] Task succeeded: HMMsearch
[2023-03-16 22:45:45,778] [INFO] Found 6/6 markers.
[2023-03-16 22:45:45,790] [INFO] Query marker FASTA was written to OceanDNA-b887/markers.fasta
[2023-03-16 22:45:45,791] [INFO] Task started: Blastn
[2023-03-16 22:45:45,791] [INFO] Running command: blastn -query OceanDNA-b887/markers.fasta -db /var/lib/cwl/stg31a25c7c-2a8b-42b1-a120-43ef41ae137a/dqc_reference/reference_markers.fasta -out OceanDNA-b887/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 22:45:46,345] [INFO] Task succeeded: Blastn
[2023-03-16 22:45:46,346] [INFO] Selected 15 target genomes.
[2023-03-16 22:45:46,346] [INFO] Target genome list was writen to OceanDNA-b887/target_genomes.txt
[2023-03-16 22:45:46,355] [INFO] Task started: fastANI
[2023-03-16 22:45:46,355] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a48319c-0638-474b-8449-5504080483bc/OceanDNA-b887.fa --refList OceanDNA-b887/target_genomes.txt --output OceanDNA-b887/fastani_result.tsv --threads 1
[2023-03-16 22:45:55,042] [INFO] Task succeeded: fastANI
[2023-03-16 22:45:55,043] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg31a25c7c-2a8b-42b1-a120-43ef41ae137a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 22:45:55,043] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg31a25c7c-2a8b-42b1-a120-43ef41ae137a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 22:45:55,043] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 22:45:55,043] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 22:45:55,043] [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 22:45:55,044] [INFO] DFAST Taxonomy check result was written to OceanDNA-b887/tc_result.tsv
[2023-03-16 22:45:55,044] [INFO] ===== Taxonomy check completed =====
[2023-03-16 22:45:55,044] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 22:45:55,044] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg31a25c7c-2a8b-42b1-a120-43ef41ae137a/dqc_reference/checkm_data
[2023-03-16 22:45:55,046] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 22:45:55,049] [INFO] Task started: CheckM
[2023-03-16 22:45:55,050] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b887/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b887/checkm_input OceanDNA-b887/checkm_result
[2023-03-16 22:46:20,493] [INFO] Task succeeded: CheckM
[2023-03-16 22:46:20,493] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 22:46:20,495] [INFO] ===== Completeness check finished =====
[2023-03-16 22:46:20,495] [INFO] ===== Start GTDB Search =====
[2023-03-16 22:46:20,495] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b887/markers.fasta)
[2023-03-16 22:46:20,495] [INFO] Task started: Blastn
[2023-03-16 22:46:20,496] [INFO] Running command: blastn -query OceanDNA-b887/markers.fasta -db /var/lib/cwl/stg31a25c7c-2a8b-42b1-a120-43ef41ae137a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b887/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 22:46:21,413] [INFO] Task succeeded: Blastn
[2023-03-16 22:46:21,414] [INFO] Selected 20 target genomes.
[2023-03-16 22:46:21,414] [INFO] Target genome list was writen to OceanDNA-b887/target_genomes_gtdb.txt
[2023-03-16 22:46:22,190] [INFO] Task started: fastANI
[2023-03-16 22:46:22,190] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a48319c-0638-474b-8449-5504080483bc/OceanDNA-b887.fa --refList OceanDNA-b887/target_genomes_gtdb.txt --output OceanDNA-b887/fastani_result_gtdb.tsv --threads 1
[2023-03-16 22:46:27,986] [INFO] Task succeeded: fastANI
[2023-03-16 22:46:27,989] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 22:46:27,989] [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_902634555.1	s__MedAcidi-G2B sp902634555	83.6396	262	487	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__MedAcidi-G2B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000817115.1	s__MedAcidi-G2B sp000817115	83.3614	330	487	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__MedAcidi-G2B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003215175.1	s__MedAcidi-G2B sp003215175	78.4559	192	487	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__MedAcidi-G2B	95.0	98.07	96.28	0.80	0.69	6	-
--------------------------------------------------------------------------------
[2023-03-16 22:46:27,989] [INFO] GTDB search result was written to OceanDNA-b887/result_gtdb.tsv
[2023-03-16 22:46:27,989] [INFO] ===== GTDB Search completed =====
[2023-03-16 22:46:27,990] [INFO] DFAST_QC result json was written to OceanDNA-b887/dqc_result.json
[2023-03-16 22:46:27,990] [INFO] DFAST_QC completed!
[2023-03-16 22:46:27,990] [INFO] Total running time: 0h0m53s