[2023-03-18 10:15:15,038] [INFO] DFAST_QC pipeline started.
[2023-03-18 10:15:15,038] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 10:15:15,038] [INFO] DQC Reference Directory: /var/lib/cwl/stgb140524c-2fc6-452c-b0b2-c09bf99b1988/dqc_reference
[2023-03-18 10:15:16,173] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 10:15:16,173] [INFO] Task started: Prodigal
[2023-03-18 10:15:16,173] [INFO] Running command: cat /var/lib/cwl/stg6c9743db-5d80-409f-8747-28b276573027/OceanDNA-b35803.fa | prodigal -d OceanDNA-b35803/cds.fna -a OceanDNA-b35803/protein.faa -g 11 -q > /dev/null
[2023-03-18 10:15:34,366] [INFO] Task succeeded: Prodigal
[2023-03-18 10:15:34,366] [INFO] Task started: HMMsearch
[2023-03-18 10:15:34,366] [INFO] Running command: hmmsearch --tblout OceanDNA-b35803/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb140524c-2fc6-452c-b0b2-c09bf99b1988/dqc_reference/reference_markers.hmm OceanDNA-b35803/protein.faa > /dev/null
[2023-03-18 10:15:34,593] [INFO] Task succeeded: HMMsearch
[2023-03-18 10:15:34,594] [INFO] Found 6/6 markers.
[2023-03-18 10:15:34,614] [INFO] Query marker FASTA was written to OceanDNA-b35803/markers.fasta
[2023-03-18 10:15:34,615] [INFO] Task started: Blastn
[2023-03-18 10:15:34,615] [INFO] Running command: blastn -query OceanDNA-b35803/markers.fasta -db /var/lib/cwl/stgb140524c-2fc6-452c-b0b2-c09bf99b1988/dqc_reference/reference_markers.fasta -out OceanDNA-b35803/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:15:35,226] [INFO] Task succeeded: Blastn
[2023-03-18 10:15:35,227] [INFO] Selected 33 target genomes.
[2023-03-18 10:15:35,227] [INFO] Target genome list was writen to OceanDNA-b35803/target_genomes.txt
[2023-03-18 10:15:35,253] [INFO] Task started: fastANI
[2023-03-18 10:15:35,253] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c9743db-5d80-409f-8747-28b276573027/OceanDNA-b35803.fa --refList OceanDNA-b35803/target_genomes.txt --output OceanDNA-b35803/fastani_result.tsv --threads 1
[2023-03-18 10:15:59,363] [INFO] Task succeeded: fastANI
[2023-03-18 10:15:59,363] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb140524c-2fc6-452c-b0b2-c09bf99b1988/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 10:15:59,363] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb140524c-2fc6-452c-b0b2-c09bf99b1988/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 10:15:59,364] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 10:15:59,364] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 10:15:59,364] [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
--------------------------------------------------------------------------------
[2023-03-18 10:15:59,365] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35803/tc_result.tsv
[2023-03-18 10:15:59,366] [INFO] ===== Taxonomy check completed =====
[2023-03-18 10:15:59,366] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 10:15:59,366] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb140524c-2fc6-452c-b0b2-c09bf99b1988/dqc_reference/checkm_data
[2023-03-18 10:15:59,369] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 10:15:59,374] [INFO] Task started: CheckM
[2023-03-18 10:15:59,374] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35803/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35803/checkm_input OceanDNA-b35803/checkm_result
[2023-03-18 10:16:44,996] [INFO] Task succeeded: CheckM
[2023-03-18 10:16:44,996] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 10:16:45,001] [INFO] ===== Completeness check finished =====
[2023-03-18 10:16:45,001] [INFO] ===== Start GTDB Search =====
[2023-03-18 10:16:45,002] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35803/markers.fasta)
[2023-03-18 10:16:45,003] [INFO] Task started: Blastn
[2023-03-18 10:16:45,003] [INFO] Running command: blastn -query OceanDNA-b35803/markers.fasta -db /var/lib/cwl/stgb140524c-2fc6-452c-b0b2-c09bf99b1988/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35803/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:16:46,109] [INFO] Task succeeded: Blastn
[2023-03-18 10:16:46,120] [INFO] Selected 32 target genomes.
[2023-03-18 10:16:46,120] [INFO] Target genome list was writen to OceanDNA-b35803/target_genomes_gtdb.txt
[2023-03-18 10:16:46,171] [INFO] Task started: fastANI
[2023-03-18 10:16:46,171] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c9743db-5d80-409f-8747-28b276573027/OceanDNA-b35803.fa --refList OceanDNA-b35803/target_genomes_gtdb.txt --output OceanDNA-b35803/fastani_result_gtdb.tsv --threads 1
[2023-03-18 10:17:04,584] [INFO] Task succeeded: fastANI
[2023-03-18 10:17:04,586] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 10:17:04,586] [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_016719885.1	s__JADJYF01 sp016719885	76.7828	113	976	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ga0077536;f__Ga0077536;g__JADJYF01	95.0	97.68	97.68	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-03-18 10:17:04,587] [INFO] GTDB search result was written to OceanDNA-b35803/result_gtdb.tsv
[2023-03-18 10:17:04,587] [INFO] ===== GTDB Search completed =====
[2023-03-18 10:17:04,587] [INFO] DFAST_QC result json was written to OceanDNA-b35803/dqc_result.json
[2023-03-18 10:17:04,587] [INFO] DFAST_QC completed!
[2023-03-18 10:17:04,587] [INFO] Total running time: 0h1m50s