[2023-03-14 11:33:34,952] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:33:34,952] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:33:34,952] [INFO] DQC Reference Directory: /var/lib/cwl/stg211831ca-1086-4e95-8d98-21f135c79a82/dqc_reference
[2023-03-14 11:33:36,169] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:33:36,170] [INFO] Task started: Prodigal
[2023-03-14 11:33:36,170] [INFO] Running command: cat /var/lib/cwl/stg0d77b874-290d-46ae-86f9-f11889ac1e2b/OceanDNA-b13206.fa | prodigal -d OceanDNA-b13206/cds.fna -a OceanDNA-b13206/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:33:55,122] [INFO] Task succeeded: Prodigal
[2023-03-14 11:33:55,123] [INFO] Task started: HMMsearch
[2023-03-14 11:33:55,123] [INFO] Running command: hmmsearch --tblout OceanDNA-b13206/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg211831ca-1086-4e95-8d98-21f135c79a82/dqc_reference/reference_markers.hmm OceanDNA-b13206/protein.faa > /dev/null
[2023-03-14 11:33:55,369] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:33:55,369] [INFO] Found 6/6 markers.
[2023-03-14 11:33:55,391] [INFO] Query marker FASTA was written to OceanDNA-b13206/markers.fasta
[2023-03-14 11:33:55,391] [INFO] Task started: Blastn
[2023-03-14 11:33:55,391] [INFO] Running command: blastn -query OceanDNA-b13206/markers.fasta -db /var/lib/cwl/stg211831ca-1086-4e95-8d98-21f135c79a82/dqc_reference/reference_markers.fasta -out OceanDNA-b13206/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:33:55,929] [INFO] Task succeeded: Blastn
[2023-03-14 11:33:55,930] [INFO] Selected 20 target genomes.
[2023-03-14 11:33:55,930] [INFO] Target genome list was writen to OceanDNA-b13206/target_genomes.txt
[2023-03-14 11:33:55,941] [INFO] Task started: fastANI
[2023-03-14 11:33:55,941] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d77b874-290d-46ae-86f9-f11889ac1e2b/OceanDNA-b13206.fa --refList OceanDNA-b13206/target_genomes.txt --output OceanDNA-b13206/fastani_result.tsv --threads 1
[2023-03-14 11:34:08,238] [INFO] Task succeeded: fastANI
[2023-03-14 11:34:08,239] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg211831ca-1086-4e95-8d98-21f135c79a82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:34:08,239] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg211831ca-1086-4e95-8d98-21f135c79a82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:34:08,239] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:34:08,239] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 11:34:08,239] [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 11:34:08,239] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13206/tc_result.tsv
[2023-03-14 11:34:08,240] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:34:08,240] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:34:08,240] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg211831ca-1086-4e95-8d98-21f135c79a82/dqc_reference/checkm_data
[2023-03-14 11:34:08,242] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:34:08,327] [INFO] Task started: CheckM
[2023-03-14 11:34:08,327] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13206/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13206/checkm_input OceanDNA-b13206/checkm_result
[2023-03-14 11:34:56,435] [INFO] Task succeeded: CheckM
[2023-03-14 11:34:56,435] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:34:56,438] [INFO] ===== Completeness check finished =====
[2023-03-14 11:34:56,438] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:34:56,438] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13206/markers.fasta)
[2023-03-14 11:34:56,438] [INFO] Task started: Blastn
[2023-03-14 11:34:56,438] [INFO] Running command: blastn -query OceanDNA-b13206/markers.fasta -db /var/lib/cwl/stg211831ca-1086-4e95-8d98-21f135c79a82/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13206/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:34:57,183] [INFO] Task succeeded: Blastn
[2023-03-14 11:34:57,184] [INFO] Selected 21 target genomes.
[2023-03-14 11:34:57,184] [INFO] Target genome list was writen to OceanDNA-b13206/target_genomes_gtdb.txt
[2023-03-14 11:34:57,215] [INFO] Task started: fastANI
[2023-03-14 11:34:57,215] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d77b874-290d-46ae-86f9-f11889ac1e2b/OceanDNA-b13206.fa --refList OceanDNA-b13206/target_genomes_gtdb.txt --output OceanDNA-b13206/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:35:07,651] [INFO] Task succeeded: fastANI
[2023-03-14 11:35:07,653] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 11:35:07,653] [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_002321895.1	s__UBA1609 sp002321895	99.9932	1082	1094	d__Bacteria;p__Bdellovibrionota;c__Bdellovibrionia;o__Bdellovibrionales;f__UBA1609;g__UBA1609	95.0	99.93	99.93	0.99	0.99	2	conclusive
--------------------------------------------------------------------------------
[2023-03-14 11:35:07,653] [INFO] GTDB search result was written to OceanDNA-b13206/result_gtdb.tsv
[2023-03-14 11:35:07,653] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:35:07,653] [INFO] DFAST_QC result json was written to OceanDNA-b13206/dqc_result.json
[2023-03-14 11:35:07,654] [INFO] DFAST_QC completed!
[2023-03-14 11:35:07,654] [INFO] Total running time: 0h1m33s