[2023-03-18 09:02:27,084] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:02:27,084] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:02:27,084] [INFO] DQC Reference Directory: /var/lib/cwl/stg2b789bdb-a7fc-4bd1-9bf0-977d590a7858/dqc_reference
[2023-03-18 09:02:28,200] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:02:28,201] [INFO] Task started: Prodigal
[2023-03-18 09:02:28,201] [INFO] Running command: cat /var/lib/cwl/stgaf5b37f9-4578-4b25-8f2b-40e632c577c2/OceanDNA-a1187.fa | prodigal -d OceanDNA-a1187/cds.fna -a OceanDNA-a1187/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:02:33,092] [INFO] Task succeeded: Prodigal
[2023-03-18 09:02:33,092] [INFO] Task started: HMMsearch
[2023-03-18 09:02:33,092] [INFO] Running command: hmmsearch --tblout OceanDNA-a1187/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2b789bdb-a7fc-4bd1-9bf0-977d590a7858/dqc_reference/reference_markers.hmm OceanDNA-a1187/protein.faa > /dev/null
[2023-03-18 09:02:33,238] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:02:33,239] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgaf5b37f9-4578-4b25-8f2b-40e632c577c2/OceanDNA-a1187.fa]
[2023-03-18 09:02:33,246] [INFO] Query marker FASTA was written to OceanDNA-a1187/markers.fasta
[2023-03-18 09:02:33,248] [INFO] Task started: Blastn
[2023-03-18 09:02:33,248] [INFO] Running command: blastn -query OceanDNA-a1187/markers.fasta -db /var/lib/cwl/stg2b789bdb-a7fc-4bd1-9bf0-977d590a7858/dqc_reference/reference_markers.fasta -out OceanDNA-a1187/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:02:33,961] [INFO] Task succeeded: Blastn
[2023-03-18 09:02:33,961] [INFO] Selected 5 target genomes.
[2023-03-18 09:02:33,962] [INFO] Target genome list was writen to OceanDNA-a1187/target_genomes.txt
[2023-03-18 09:02:33,993] [INFO] Task started: fastANI
[2023-03-18 09:02:33,993] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf5b37f9-4578-4b25-8f2b-40e632c577c2/OceanDNA-a1187.fa --refList OceanDNA-a1187/target_genomes.txt --output OceanDNA-a1187/fastani_result.tsv --threads 1
[2023-03-18 09:02:35,545] [INFO] Task succeeded: fastANI
[2023-03-18 09:02:35,546] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2b789bdb-a7fc-4bd1-9bf0-977d590a7858/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:02:35,546] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2b789bdb-a7fc-4bd1-9bf0-977d590a7858/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:02:35,546] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:02:35,546] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 09:02:35,546] [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 09:02:35,546] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1187/tc_result.tsv
[2023-03-18 09:02:35,546] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:02:35,546] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:02:35,547] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2b789bdb-a7fc-4bd1-9bf0-977d590a7858/dqc_reference/checkm_data
[2023-03-18 09:02:35,673] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:02:35,675] [INFO] Task started: CheckM
[2023-03-18 09:02:35,676] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1187/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1187/checkm_input OceanDNA-a1187/checkm_result
[2023-03-18 09:02:55,082] [INFO] Task succeeded: CheckM
[2023-03-18 09:02:55,083] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 09:02:55,084] [INFO] ===== Completeness check finished =====
[2023-03-18 09:02:55,084] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:02:55,084] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1187/markers.fasta)
[2023-03-18 09:02:55,087] [INFO] Task started: Blastn
[2023-03-18 09:02:55,087] [INFO] Running command: blastn -query OceanDNA-a1187/markers.fasta -db /var/lib/cwl/stg2b789bdb-a7fc-4bd1-9bf0-977d590a7858/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1187/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:02:56,138] [INFO] Task succeeded: Blastn
[2023-03-18 09:02:56,139] [INFO] Selected 7 target genomes.
[2023-03-18 09:02:56,139] [INFO] Target genome list was writen to OceanDNA-a1187/target_genomes_gtdb.txt
[2023-03-18 09:02:56,184] [INFO] Task started: fastANI
[2023-03-18 09:02:56,184] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf5b37f9-4578-4b25-8f2b-40e632c577c2/OceanDNA-a1187.fa --refList OceanDNA-a1187/target_genomes_gtdb.txt --output OceanDNA-a1187/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:02:57,184] [INFO] Task succeeded: fastANI
[2023-03-18 09:02:57,186] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 09:02:57,186] [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_018692925.1	s__BS150m-G60 sp018692925	99.9344	308	326	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__SCGC-AAA011-G17;f__GW2011-AR17;g__BS150m-G60	95.0	99.90	99.76	0.95	0.92	8	conclusive
GCA_016784245.1	s__BS150m-G60 sp016784245	88.0103	122	326	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__SCGC-AAA011-G17;f__GW2011-AR17;g__BS150m-G60	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 09:02:57,187] [INFO] GTDB search result was written to OceanDNA-a1187/result_gtdb.tsv
[2023-03-18 09:02:57,187] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:02:57,187] [INFO] DFAST_QC result json was written to OceanDNA-a1187/dqc_result.json
[2023-03-18 09:02:57,187] [INFO] DFAST_QC completed!
[2023-03-18 09:02:57,187] [INFO] Total running time: 0h0m30s