[2023-03-15 22:23:01,926] [INFO] DFAST_QC pipeline started.
[2023-03-15 22:23:01,926] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 22:23:01,926] [INFO] DQC Reference Directory: /var/lib/cwl/stg34f9f91b-4117-4eb8-9c9c-5e49e1dcc718/dqc_reference
[2023-03-15 22:23:03,672] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 22:23:03,673] [INFO] Task started: Prodigal
[2023-03-15 22:23:03,673] [INFO] Running command: cat /var/lib/cwl/stg2ddbf15b-760d-478f-ac4a-9e6ed82cf0c7/OceanDNA-b32785.fa | prodigal -d OceanDNA-b32785/cds.fna -a OceanDNA-b32785/protein.faa -g 11 -q > /dev/null
[2023-03-15 22:23:13,684] [INFO] Task succeeded: Prodigal
[2023-03-15 22:23:13,684] [INFO] Task started: HMMsearch
[2023-03-15 22:23:13,684] [INFO] Running command: hmmsearch --tblout OceanDNA-b32785/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg34f9f91b-4117-4eb8-9c9c-5e49e1dcc718/dqc_reference/reference_markers.hmm OceanDNA-b32785/protein.faa > /dev/null
[2023-03-15 22:23:13,853] [INFO] Task succeeded: HMMsearch
[2023-03-15 22:23:13,853] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2ddbf15b-760d-478f-ac4a-9e6ed82cf0c7/OceanDNA-b32785.fa]
[2023-03-15 22:23:13,868] [INFO] Query marker FASTA was written to OceanDNA-b32785/markers.fasta
[2023-03-15 22:23:13,869] [INFO] Task started: Blastn
[2023-03-15 22:23:13,869] [INFO] Running command: blastn -query OceanDNA-b32785/markers.fasta -db /var/lib/cwl/stg34f9f91b-4117-4eb8-9c9c-5e49e1dcc718/dqc_reference/reference_markers.fasta -out OceanDNA-b32785/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:23:14,456] [INFO] Task succeeded: Blastn
[2023-03-15 22:23:14,457] [INFO] Selected 35 target genomes.
[2023-03-15 22:23:14,457] [INFO] Target genome list was writen to OceanDNA-b32785/target_genomes.txt
[2023-03-15 22:23:14,480] [INFO] Task started: fastANI
[2023-03-15 22:23:14,480] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ddbf15b-760d-478f-ac4a-9e6ed82cf0c7/OceanDNA-b32785.fa --refList OceanDNA-b32785/target_genomes.txt --output OceanDNA-b32785/fastani_result.tsv --threads 1
[2023-03-15 22:23:37,272] [INFO] Task succeeded: fastANI
[2023-03-15 22:23:37,273] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg34f9f91b-4117-4eb8-9c9c-5e49e1dcc718/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 22:23:37,273] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg34f9f91b-4117-4eb8-9c9c-5e49e1dcc718/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 22:23:37,273] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 22:23:37,273] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 22:23:37,273] [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 22:23:37,273] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32785/tc_result.tsv
[2023-03-15 22:23:37,273] [INFO] ===== Taxonomy check completed =====
[2023-03-15 22:23:37,273] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 22:23:37,274] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg34f9f91b-4117-4eb8-9c9c-5e49e1dcc718/dqc_reference/checkm_data
[2023-03-15 22:23:37,277] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 22:23:37,280] [INFO] Task started: CheckM
[2023-03-15 22:23:37,280] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32785/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32785/checkm_input OceanDNA-b32785/checkm_result
[2023-03-15 22:24:06,769] [INFO] Task succeeded: CheckM
[2023-03-15 22:24:06,769] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.09%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 22:24:06,772] [INFO] ===== Completeness check finished =====
[2023-03-15 22:24:06,772] [INFO] ===== Start GTDB Search =====
[2023-03-15 22:24:06,772] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32785/markers.fasta)
[2023-03-15 22:24:06,773] [INFO] Task started: Blastn
[2023-03-15 22:24:06,773] [INFO] Running command: blastn -query OceanDNA-b32785/markers.fasta -db /var/lib/cwl/stg34f9f91b-4117-4eb8-9c9c-5e49e1dcc718/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32785/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:24:07,944] [INFO] Task succeeded: Blastn
[2023-03-15 22:24:07,945] [INFO] Selected 17 target genomes.
[2023-03-15 22:24:07,945] [INFO] Target genome list was writen to OceanDNA-b32785/target_genomes_gtdb.txt
[2023-03-15 22:24:07,957] [INFO] Task started: fastANI
[2023-03-15 22:24:07,957] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ddbf15b-760d-478f-ac4a-9e6ed82cf0c7/OceanDNA-b32785.fa --refList OceanDNA-b32785/target_genomes_gtdb.txt --output OceanDNA-b32785/fastani_result_gtdb.tsv --threads 1
[2023-03-15 22:24:16,707] [INFO] Task succeeded: fastANI
[2023-03-15 22:24:16,711] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 22:24:16,711] [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_002722515.1	s__UBA8079 sp002722515	99.9223	479	548	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002724635.1	s__UBA8079 sp002724635	77.9727	229	548	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018667335.1	s__UBA8079 sp018667335	77.7658	230	548	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	99.89	99.79	0.96	0.96	6	-
GCA_018702955.1	s__UBA8079 sp018702955	77.7623	218	548	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	99.54	99.39	0.93	0.91	5	-
GCA_002727315.1	s__UBA8079 sp002727315	77.098	122	548	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 22:24:16,711] [INFO] GTDB search result was written to OceanDNA-b32785/result_gtdb.tsv
[2023-03-15 22:24:16,711] [INFO] ===== GTDB Search completed =====
[2023-03-15 22:24:16,712] [INFO] DFAST_QC result json was written to OceanDNA-b32785/dqc_result.json
[2023-03-15 22:24:16,712] [INFO] DFAST_QC completed!
[2023-03-15 22:24:16,712] [INFO] Total running time: 0h1m15s