[2023-03-17 08:39:27,396] [INFO] DFAST_QC pipeline started.
[2023-03-17 08:39:27,396] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 08:39:27,396] [INFO] DQC Reference Directory: /var/lib/cwl/stg12326c38-44c4-477c-a35a-8fd04bcf66db/dqc_reference
[2023-03-17 08:39:28,533] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 08:39:28,534] [INFO] Task started: Prodigal
[2023-03-17 08:39:28,534] [INFO] Running command: cat /var/lib/cwl/stge6945ee8-092e-4694-b0c0-68f305d0fa82/OceanDNA-b35965.fa | prodigal -d OceanDNA-b35965/cds.fna -a OceanDNA-b35965/protein.faa -g 11 -q > /dev/null
[2023-03-17 08:39:37,203] [INFO] Task succeeded: Prodigal
[2023-03-17 08:39:37,203] [INFO] Task started: HMMsearch
[2023-03-17 08:39:37,203] [INFO] Running command: hmmsearch --tblout OceanDNA-b35965/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg12326c38-44c4-477c-a35a-8fd04bcf66db/dqc_reference/reference_markers.hmm OceanDNA-b35965/protein.faa > /dev/null
[2023-03-17 08:39:37,397] [INFO] Task succeeded: HMMsearch
[2023-03-17 08:39:37,397] [WARNING] Found 4/6 markers. [/var/lib/cwl/stge6945ee8-092e-4694-b0c0-68f305d0fa82/OceanDNA-b35965.fa]
[2023-03-17 08:39:37,419] [INFO] Query marker FASTA was written to OceanDNA-b35965/markers.fasta
[2023-03-17 08:39:37,420] [INFO] Task started: Blastn
[2023-03-17 08:39:37,420] [INFO] Running command: blastn -query OceanDNA-b35965/markers.fasta -db /var/lib/cwl/stg12326c38-44c4-477c-a35a-8fd04bcf66db/dqc_reference/reference_markers.fasta -out OceanDNA-b35965/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:39:37,924] [INFO] Task succeeded: Blastn
[2023-03-17 08:39:37,924] [INFO] Selected 16 target genomes.
[2023-03-17 08:39:37,925] [INFO] Target genome list was writen to OceanDNA-b35965/target_genomes.txt
[2023-03-17 08:39:38,218] [INFO] Task started: fastANI
[2023-03-17 08:39:38,218] [INFO] Running command: fastANI --query /var/lib/cwl/stge6945ee8-092e-4694-b0c0-68f305d0fa82/OceanDNA-b35965.fa --refList OceanDNA-b35965/target_genomes.txt --output OceanDNA-b35965/fastani_result.tsv --threads 1
[2023-03-17 08:39:45,850] [INFO] Task succeeded: fastANI
[2023-03-17 08:39:45,851] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg12326c38-44c4-477c-a35a-8fd04bcf66db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 08:39:45,851] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg12326c38-44c4-477c-a35a-8fd04bcf66db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 08:39:45,851] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 08:39:45,851] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 08:39:45,851] [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
--------------------------------------------------------------------------------
[2023-03-17 08:39:45,851] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35965/tc_result.tsv
[2023-03-17 08:39:45,851] [INFO] ===== Taxonomy check completed =====
[2023-03-17 08:39:45,852] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 08:39:45,852] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg12326c38-44c4-477c-a35a-8fd04bcf66db/dqc_reference/checkm_data
[2023-03-17 08:39:45,854] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 08:39:45,859] [INFO] Task started: CheckM
[2023-03-17 08:39:45,859] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35965/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35965/checkm_input OceanDNA-b35965/checkm_result
[2023-03-17 08:40:14,492] [INFO] Task succeeded: CheckM
[2023-03-17 08:40:14,493] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.37%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 08:40:14,495] [INFO] ===== Completeness check finished =====
[2023-03-17 08:40:14,495] [INFO] ===== Start GTDB Search =====
[2023-03-17 08:40:14,495] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35965/markers.fasta)
[2023-03-17 08:40:14,497] [INFO] Task started: Blastn
[2023-03-17 08:40:14,497] [INFO] Running command: blastn -query OceanDNA-b35965/markers.fasta -db /var/lib/cwl/stg12326c38-44c4-477c-a35a-8fd04bcf66db/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35965/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:40:15,122] [INFO] Task succeeded: Blastn
[2023-03-17 08:40:15,133] [INFO] Selected 22 target genomes.
[2023-03-17 08:40:15,133] [INFO] Target genome list was writen to OceanDNA-b35965/target_genomes_gtdb.txt
[2023-03-17 08:40:15,940] [INFO] Task started: fastANI
[2023-03-17 08:40:15,940] [INFO] Running command: fastANI --query /var/lib/cwl/stge6945ee8-092e-4694-b0c0-68f305d0fa82/OceanDNA-b35965.fa --refList OceanDNA-b35965/target_genomes_gtdb.txt --output OceanDNA-b35965/fastani_result_gtdb.tsv --threads 1
[2023-03-17 08:40:28,159] [INFO] Task succeeded: fastANI
[2023-03-17 08:40:28,160] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 08:40:28,161] [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_018672285.1	s__JABHGC01 sp018672285	99.6783	286	296	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__JABHGC01;f__JABHGC01;g__JABHGC01	95.0	99.85	99.85	0.95	0.95	2	conclusive
--------------------------------------------------------------------------------
[2023-03-17 08:40:28,161] [INFO] GTDB search result was written to OceanDNA-b35965/result_gtdb.tsv
[2023-03-17 08:40:28,161] [INFO] ===== GTDB Search completed =====
[2023-03-17 08:40:28,161] [INFO] DFAST_QC result json was written to OceanDNA-b35965/dqc_result.json
[2023-03-17 08:40:28,161] [INFO] DFAST_QC completed!
[2023-03-17 08:40:28,161] [INFO] Total running time: 0h1m1s