[2023-03-15 22:25:05,829] [INFO] DFAST_QC pipeline started.
[2023-03-15 22:25:05,829] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 22:25:05,829] [INFO] DQC Reference Directory: /var/lib/cwl/stg2304b828-71fe-44c2-9ac2-015a149829a4/dqc_reference
[2023-03-15 22:25:06,957] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 22:25:06,957] [INFO] Task started: Prodigal
[2023-03-15 22:25:06,957] [INFO] Running command: cat /var/lib/cwl/stg1f25a7fb-56b0-4a6e-974d-b49237b537a9/OceanDNA-b26227.fa | prodigal -d OceanDNA-b26227/cds.fna -a OceanDNA-b26227/protein.faa -g 11 -q > /dev/null
[2023-03-15 22:25:12,263] [INFO] Task succeeded: Prodigal
[2023-03-15 22:25:12,264] [INFO] Task started: HMMsearch
[2023-03-15 22:25:12,264] [INFO] Running command: hmmsearch --tblout OceanDNA-b26227/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2304b828-71fe-44c2-9ac2-015a149829a4/dqc_reference/reference_markers.hmm OceanDNA-b26227/protein.faa > /dev/null
[2023-03-15 22:25:12,409] [INFO] Task succeeded: HMMsearch
[2023-03-15 22:25:12,409] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1f25a7fb-56b0-4a6e-974d-b49237b537a9/OceanDNA-b26227.fa]
[2023-03-15 22:25:12,423] [INFO] Query marker FASTA was written to OceanDNA-b26227/markers.fasta
[2023-03-15 22:25:12,423] [INFO] Task started: Blastn
[2023-03-15 22:25:12,423] [INFO] Running command: blastn -query OceanDNA-b26227/markers.fasta -db /var/lib/cwl/stg2304b828-71fe-44c2-9ac2-015a149829a4/dqc_reference/reference_markers.fasta -out OceanDNA-b26227/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:25:12,931] [INFO] Task succeeded: Blastn
[2023-03-15 22:25:12,932] [INFO] Selected 25 target genomes.
[2023-03-15 22:25:12,932] [INFO] Target genome list was writen to OceanDNA-b26227/target_genomes.txt
[2023-03-15 22:25:12,946] [INFO] Task started: fastANI
[2023-03-15 22:25:12,947] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f25a7fb-56b0-4a6e-974d-b49237b537a9/OceanDNA-b26227.fa --refList OceanDNA-b26227/target_genomes.txt --output OceanDNA-b26227/fastani_result.tsv --threads 1
[2023-03-15 22:25:25,943] [INFO] Task succeeded: fastANI
[2023-03-15 22:25:25,944] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2304b828-71fe-44c2-9ac2-015a149829a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 22:25:25,944] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2304b828-71fe-44c2-9ac2-015a149829a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 22:25:25,944] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 22:25:25,944] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 22:25:25,944] [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 22:25:25,945] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26227/tc_result.tsv
[2023-03-15 22:25:25,945] [INFO] ===== Taxonomy check completed =====
[2023-03-15 22:25:25,945] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 22:25:25,945] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2304b828-71fe-44c2-9ac2-015a149829a4/dqc_reference/checkm_data
[2023-03-15 22:25:25,947] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 22:25:25,984] [INFO] Task started: CheckM
[2023-03-15 22:25:25,984] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26227/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26227/checkm_input OceanDNA-b26227/checkm_result
[2023-03-15 22:25:45,877] [INFO] Task succeeded: CheckM
[2023-03-15 22:25:45,877] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 51.79%
Contamintation: 9.70%
Strain heterogeneity: 80.00%
--------------------------------------------------------------------------------
[2023-03-15 22:25:45,880] [INFO] ===== Completeness check finished =====
[2023-03-15 22:25:45,880] [INFO] ===== Start GTDB Search =====
[2023-03-15 22:25:45,880] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26227/markers.fasta)
[2023-03-15 22:25:45,880] [INFO] Task started: Blastn
[2023-03-15 22:25:45,880] [INFO] Running command: blastn -query OceanDNA-b26227/markers.fasta -db /var/lib/cwl/stg2304b828-71fe-44c2-9ac2-015a149829a4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26227/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:25:46,617] [INFO] Task succeeded: Blastn
[2023-03-15 22:25:46,618] [INFO] Selected 17 target genomes.
[2023-03-15 22:25:46,618] [INFO] Target genome list was writen to OceanDNA-b26227/target_genomes_gtdb.txt
[2023-03-15 22:25:46,681] [INFO] Task started: fastANI
[2023-03-15 22:25:46,681] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f25a7fb-56b0-4a6e-974d-b49237b537a9/OceanDNA-b26227.fa --refList OceanDNA-b26227/target_genomes_gtdb.txt --output OceanDNA-b26227/fastani_result_gtdb.tsv --threads 1
[2023-03-15 22:25:51,926] [INFO] Task succeeded: fastANI
[2023-03-15 22:25:51,929] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 22:25:51,929] [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_902559985.1	s__UBA3439 sp902559985	92.6411	72	118	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA3439	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003212345.1	s__UBA3439 sp003212345	92.5756	92	118	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA3439	95.0	98.67	97.33	0.87	0.74	3	-
GCA_003282865.1	s__UBA3439 sp003282865	88.4237	86	118	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA3439	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-15 22:25:51,929] [INFO] GTDB search result was written to OceanDNA-b26227/result_gtdb.tsv
[2023-03-15 22:25:51,929] [INFO] ===== GTDB Search completed =====
[2023-03-15 22:25:51,930] [INFO] DFAST_QC result json was written to OceanDNA-b26227/dqc_result.json
[2023-03-15 22:25:51,930] [INFO] DFAST_QC completed!
[2023-03-15 22:25:51,930] [INFO] Total running time: 0h0m46s