[2023-03-16 18:27:01,714] [INFO] DFAST_QC pipeline started.
[2023-03-16 18:27:01,715] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 18:27:01,715] [INFO] DQC Reference Directory: /var/lib/cwl/stgaa508826-2617-4414-bf21-12d014a8ca68/dqc_reference
[2023-03-16 18:27:02,831] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 18:27:02,832] [INFO] Task started: Prodigal
[2023-03-16 18:27:02,832] [INFO] Running command: cat /var/lib/cwl/stgeccc064b-0d92-45ae-bdbf-5401151ace89/OceanDNA-b14379.fa | prodigal -d OceanDNA-b14379/cds.fna -a OceanDNA-b14379/protein.faa -g 11 -q > /dev/null
[2023-03-16 18:27:14,866] [INFO] Task succeeded: Prodigal
[2023-03-16 18:27:14,866] [INFO] Task started: HMMsearch
[2023-03-16 18:27:14,866] [INFO] Running command: hmmsearch --tblout OceanDNA-b14379/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaa508826-2617-4414-bf21-12d014a8ca68/dqc_reference/reference_markers.hmm OceanDNA-b14379/protein.faa > /dev/null
[2023-03-16 18:27:15,042] [INFO] Task succeeded: HMMsearch
[2023-03-16 18:27:15,043] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgeccc064b-0d92-45ae-bdbf-5401151ace89/OceanDNA-b14379.fa]
[2023-03-16 18:27:15,060] [INFO] Query marker FASTA was written to OceanDNA-b14379/markers.fasta
[2023-03-16 18:27:15,062] [INFO] Task started: Blastn
[2023-03-16 18:27:15,062] [INFO] Running command: blastn -query OceanDNA-b14379/markers.fasta -db /var/lib/cwl/stgaa508826-2617-4414-bf21-12d014a8ca68/dqc_reference/reference_markers.fasta -out OceanDNA-b14379/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:27:15,925] [INFO] Task succeeded: Blastn
[2023-03-16 18:27:15,925] [INFO] Selected 9 target genomes.
[2023-03-16 18:27:15,926] [INFO] Target genome list was writen to OceanDNA-b14379/target_genomes.txt
[2023-03-16 18:27:15,930] [INFO] Task started: fastANI
[2023-03-16 18:27:15,930] [INFO] Running command: fastANI --query /var/lib/cwl/stgeccc064b-0d92-45ae-bdbf-5401151ace89/OceanDNA-b14379.fa --refList OceanDNA-b14379/target_genomes.txt --output OceanDNA-b14379/fastani_result.tsv --threads 1
[2023-03-16 18:27:25,488] [INFO] Task succeeded: fastANI
[2023-03-16 18:27:25,488] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaa508826-2617-4414-bf21-12d014a8ca68/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 18:27:25,489] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaa508826-2617-4414-bf21-12d014a8ca68/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 18:27:25,489] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 18:27:25,489] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 18:27:25,489] [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 18:27:25,489] [INFO] DFAST Taxonomy check result was written to OceanDNA-b14379/tc_result.tsv
[2023-03-16 18:27:25,489] [INFO] ===== Taxonomy check completed =====
[2023-03-16 18:27:25,489] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 18:27:25,489] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaa508826-2617-4414-bf21-12d014a8ca68/dqc_reference/checkm_data
[2023-03-16 18:27:25,547] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 18:27:25,551] [INFO] Task started: CheckM
[2023-03-16 18:27:25,551] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b14379/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b14379/checkm_input OceanDNA-b14379/checkm_result
[2023-03-16 18:28:03,961] [INFO] Task succeeded: CheckM
[2023-03-16 18:28:03,961] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.21%
Contamintation: 1.39%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 18:28:03,963] [INFO] ===== Completeness check finished =====
[2023-03-16 18:28:03,963] [INFO] ===== Start GTDB Search =====
[2023-03-16 18:28:03,964] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b14379/markers.fasta)
[2023-03-16 18:28:03,965] [INFO] Task started: Blastn
[2023-03-16 18:28:03,965] [INFO] Running command: blastn -query OceanDNA-b14379/markers.fasta -db /var/lib/cwl/stgaa508826-2617-4414-bf21-12d014a8ca68/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b14379/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:28:05,941] [INFO] Task succeeded: Blastn
[2023-03-16 18:28:05,942] [INFO] Selected 13 target genomes.
[2023-03-16 18:28:05,942] [INFO] Target genome list was writen to OceanDNA-b14379/target_genomes_gtdb.txt
[2023-03-16 18:28:05,959] [INFO] Task started: fastANI
[2023-03-16 18:28:05,959] [INFO] Running command: fastANI --query /var/lib/cwl/stgeccc064b-0d92-45ae-bdbf-5401151ace89/OceanDNA-b14379.fa --refList OceanDNA-b14379/target_genomes_gtdb.txt --output OceanDNA-b14379/fastani_result_gtdb.tsv --threads 1
[2023-03-16 18:28:15,942] [INFO] Task succeeded: fastANI
[2023-03-16 18:28:15,945] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 18:28:15,945] [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_018657655.1	s__JABMQN01 sp018657655	99.4294	356	428	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SZUA-161;f__SpSt-899;g__JABMQN01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013203045.1	s__JABMQN01 sp013203045	79.4294	128	428	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SZUA-161;f__SpSt-899;g__JABMQN01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 18:28:15,946] [INFO] GTDB search result was written to OceanDNA-b14379/result_gtdb.tsv
[2023-03-16 18:28:15,946] [INFO] ===== GTDB Search completed =====
[2023-03-16 18:28:15,946] [INFO] DFAST_QC result json was written to OceanDNA-b14379/dqc_result.json
[2023-03-16 18:28:15,946] [INFO] DFAST_QC completed!
[2023-03-16 18:28:15,946] [INFO] Total running time: 0h1m14s