[2023-03-14 13:23:14,579] [INFO] DFAST_QC pipeline started.
[2023-03-14 13:23:14,579] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 13:23:14,579] [INFO] DQC Reference Directory: /var/lib/cwl/stg16b0059c-6002-457a-ba7b-477592252b06/dqc_reference
[2023-03-14 13:23:16,086] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 13:23:16,086] [INFO] Task started: Prodigal
[2023-03-14 13:23:16,087] [INFO] Running command: cat /var/lib/cwl/stg5b92c40f-7ab4-44cb-90d6-ca6ae4309195/OceanDNA-b41945.fa | prodigal -d OceanDNA-b41945/cds.fna -a OceanDNA-b41945/protein.faa -g 11 -q > /dev/null
[2023-03-14 13:23:19,387] [INFO] Task succeeded: Prodigal
[2023-03-14 13:23:19,387] [INFO] Task started: HMMsearch
[2023-03-14 13:23:19,387] [INFO] Running command: hmmsearch --tblout OceanDNA-b41945/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg16b0059c-6002-457a-ba7b-477592252b06/dqc_reference/reference_markers.hmm OceanDNA-b41945/protein.faa > /dev/null
[2023-03-14 13:23:19,515] [INFO] Task succeeded: HMMsearch
[2023-03-14 13:23:19,516] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg5b92c40f-7ab4-44cb-90d6-ca6ae4309195/OceanDNA-b41945.fa]
[2023-03-14 13:23:19,525] [INFO] Query marker FASTA was written to OceanDNA-b41945/markers.fasta
[2023-03-14 13:23:19,526] [INFO] Task started: Blastn
[2023-03-14 13:23:19,526] [INFO] Running command: blastn -query OceanDNA-b41945/markers.fasta -db /var/lib/cwl/stg16b0059c-6002-457a-ba7b-477592252b06/dqc_reference/reference_markers.fasta -out OceanDNA-b41945/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:23:20,000] [INFO] Task succeeded: Blastn
[2023-03-14 13:23:20,001] [INFO] Selected 5 target genomes.
[2023-03-14 13:23:20,001] [INFO] Target genome list was writen to OceanDNA-b41945/target_genomes.txt
[2023-03-14 13:23:20,004] [INFO] Task started: fastANI
[2023-03-14 13:23:20,004] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b92c40f-7ab4-44cb-90d6-ca6ae4309195/OceanDNA-b41945.fa --refList OceanDNA-b41945/target_genomes.txt --output OceanDNA-b41945/fastani_result.tsv --threads 1
[2023-03-14 13:23:23,389] [INFO] Task succeeded: fastANI
[2023-03-14 13:23:23,390] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg16b0059c-6002-457a-ba7b-477592252b06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 13:23:23,390] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg16b0059c-6002-457a-ba7b-477592252b06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 13:23:23,390] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 13:23:23,390] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 13:23:23,390] [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
--------------------------------------------------------------------------------
[2023-03-14 13:23:23,391] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41945/tc_result.tsv
[2023-03-14 13:23:23,391] [INFO] ===== Taxonomy check completed =====
[2023-03-14 13:23:23,391] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 13:23:23,391] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg16b0059c-6002-457a-ba7b-477592252b06/dqc_reference/checkm_data
[2023-03-14 13:23:23,442] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 13:23:23,444] [INFO] Task started: CheckM
[2023-03-14 13:23:23,445] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41945/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41945/checkm_input OceanDNA-b41945/checkm_result
[2023-03-14 13:23:49,511] [INFO] Task succeeded: CheckM
[2023-03-14 13:23:49,511] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.97%
Contamintation: 5.09%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 13:23:49,513] [INFO] ===== Completeness check finished =====
[2023-03-14 13:23:49,513] [INFO] ===== Start GTDB Search =====
[2023-03-14 13:23:49,513] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41945/markers.fasta)
[2023-03-14 13:23:49,515] [INFO] Task started: Blastn
[2023-03-14 13:23:49,515] [INFO] Running command: blastn -query OceanDNA-b41945/markers.fasta -db /var/lib/cwl/stg16b0059c-6002-457a-ba7b-477592252b06/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41945/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:23:51,176] [INFO] Task succeeded: Blastn
[2023-03-14 13:23:51,177] [INFO] Selected 13 target genomes.
[2023-03-14 13:23:51,177] [INFO] Target genome list was writen to OceanDNA-b41945/target_genomes_gtdb.txt
[2023-03-14 13:23:51,192] [INFO] Task started: fastANI
[2023-03-14 13:23:51,192] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b92c40f-7ab4-44cb-90d6-ca6ae4309195/OceanDNA-b41945.fa --refList OceanDNA-b41945/target_genomes_gtdb.txt --output OceanDNA-b41945/fastani_result_gtdb.tsv --threads 1
[2023-03-14 13:23:54,333] [INFO] Task succeeded: fastANI
[2023-03-14 13:23:54,336] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 13:23:54,336] [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_902509965.1	s__MED-G78 sp902509965	98.436	156	210	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__MED-G78	95.0	96.76	96.76	0.83	0.83	2	conclusive
GCA_905181645.1	s__MED-G78 sp905181645	83.9472	188	210	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__MED-G78	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181955.1	s__MED-G78 sp905181955	81.6707	178	210	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__MED-G78	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 13:23:54,336] [INFO] GTDB search result was written to OceanDNA-b41945/result_gtdb.tsv
[2023-03-14 13:23:54,337] [INFO] ===== GTDB Search completed =====
[2023-03-14 13:23:54,337] [INFO] DFAST_QC result json was written to OceanDNA-b41945/dqc_result.json
[2023-03-14 13:23:54,337] [INFO] DFAST_QC completed!
[2023-03-14 13:23:54,337] [INFO] Total running time: 0h0m40s