[2023-03-16 07:01:29,793] [INFO] DFAST_QC pipeline started.
[2023-03-16 07:01:29,793] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 07:01:29,793] [INFO] DQC Reference Directory: /var/lib/cwl/stgc550b804-f532-4b10-a689-fc425c3e0bb2/dqc_reference
[2023-03-16 07:01:30,900] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 07:01:30,901] [INFO] Task started: Prodigal
[2023-03-16 07:01:30,901] [INFO] Running command: cat /var/lib/cwl/stg92e3d754-ad0f-4b74-b76c-97cea453a6aa/OceanDNA-b17829.fa | prodigal -d OceanDNA-b17829/cds.fna -a OceanDNA-b17829/protein.faa -g 11 -q > /dev/null
[2023-03-16 07:01:49,200] [INFO] Task succeeded: Prodigal
[2023-03-16 07:01:49,201] [INFO] Task started: HMMsearch
[2023-03-16 07:01:49,201] [INFO] Running command: hmmsearch --tblout OceanDNA-b17829/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc550b804-f532-4b10-a689-fc425c3e0bb2/dqc_reference/reference_markers.hmm OceanDNA-b17829/protein.faa > /dev/null
[2023-03-16 07:01:49,385] [INFO] Task succeeded: HMMsearch
[2023-03-16 07:01:49,385] [INFO] Found 6/6 markers.
[2023-03-16 07:01:49,409] [INFO] Query marker FASTA was written to OceanDNA-b17829/markers.fasta
[2023-03-16 07:01:49,410] [INFO] Task started: Blastn
[2023-03-16 07:01:49,411] [INFO] Running command: blastn -query OceanDNA-b17829/markers.fasta -db /var/lib/cwl/stgc550b804-f532-4b10-a689-fc425c3e0bb2/dqc_reference/reference_markers.fasta -out OceanDNA-b17829/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:01:49,922] [INFO] Task succeeded: Blastn
[2023-03-16 07:01:49,925] [INFO] Selected 17 target genomes.
[2023-03-16 07:01:49,925] [INFO] Target genome list was writen to OceanDNA-b17829/target_genomes.txt
[2023-03-16 07:01:49,984] [INFO] Task started: fastANI
[2023-03-16 07:01:49,984] [INFO] Running command: fastANI --query /var/lib/cwl/stg92e3d754-ad0f-4b74-b76c-97cea453a6aa/OceanDNA-b17829.fa --refList OceanDNA-b17829/target_genomes.txt --output OceanDNA-b17829/fastani_result.tsv --threads 1
[2023-03-16 07:01:57,717] [INFO] Task succeeded: fastANI
[2023-03-16 07:01:57,717] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc550b804-f532-4b10-a689-fc425c3e0bb2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 07:01:57,718] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc550b804-f532-4b10-a689-fc425c3e0bb2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 07:01:57,718] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 07:01:57,718] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 07:01:57,718] [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
--------------------------------------------------------------------------------
[2023-03-16 07:01:57,718] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17829/tc_result.tsv
[2023-03-16 07:01:57,718] [INFO] ===== Taxonomy check completed =====
[2023-03-16 07:01:57,718] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 07:01:57,718] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc550b804-f532-4b10-a689-fc425c3e0bb2/dqc_reference/checkm_data
[2023-03-16 07:01:57,721] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 07:01:57,745] [INFO] Task started: CheckM
[2023-03-16 07:01:57,745] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17829/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17829/checkm_input OceanDNA-b17829/checkm_result
[2023-03-16 07:02:45,889] [INFO] Task succeeded: CheckM
[2023-03-16 07:02:45,890] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 07:02:45,910] [INFO] ===== Completeness check finished =====
[2023-03-16 07:02:45,910] [INFO] ===== Start GTDB Search =====
[2023-03-16 07:02:45,910] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17829/markers.fasta)
[2023-03-16 07:02:45,912] [INFO] Task started: Blastn
[2023-03-16 07:02:45,912] [INFO] Running command: blastn -query OceanDNA-b17829/markers.fasta -db /var/lib/cwl/stgc550b804-f532-4b10-a689-fc425c3e0bb2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17829/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:02:46,919] [INFO] Task succeeded: Blastn
[2023-03-16 07:02:46,921] [INFO] Selected 26 target genomes.
[2023-03-16 07:02:46,922] [INFO] Target genome list was writen to OceanDNA-b17829/target_genomes_gtdb.txt
[2023-03-16 07:02:46,979] [INFO] Task started: fastANI
[2023-03-16 07:02:46,979] [INFO] Running command: fastANI --query /var/lib/cwl/stg92e3d754-ad0f-4b74-b76c-97cea453a6aa/OceanDNA-b17829.fa --refList OceanDNA-b17829/target_genomes_gtdb.txt --output OceanDNA-b17829/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:02:58,678] [INFO] Task succeeded: fastANI
[2023-03-16 07:02:58,680] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 07:02:58,681] [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_018657495.1	s__JABHXA01 sp018657495	99.9445	993	1083	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__JACNLC01;g__JABHXA01	95.0	99.97	99.94	0.97	0.96	15	conclusive
--------------------------------------------------------------------------------
[2023-03-16 07:02:58,682] [INFO] GTDB search result was written to OceanDNA-b17829/result_gtdb.tsv
[2023-03-16 07:02:58,683] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:02:58,684] [INFO] DFAST_QC result json was written to OceanDNA-b17829/dqc_result.json
[2023-03-16 07:02:58,684] [INFO] DFAST_QC completed!
[2023-03-16 07:02:58,684] [INFO] Total running time: 0h1m29s