[2023-03-19 05:19:33,749] [INFO] DFAST_QC pipeline started.
[2023-03-19 05:19:33,749] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 05:19:33,749] [INFO] DQC Reference Directory: /var/lib/cwl/stgc59b9fb4-3d8e-4c39-b8b9-e69eb9d3d90e/dqc_reference
[2023-03-19 05:19:35,400] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 05:19:35,400] [INFO] Task started: Prodigal
[2023-03-19 05:19:35,400] [INFO] Running command: cat /var/lib/cwl/stgc0020b83-70bc-4317-aa37-20f4de3919c5/OceanDNA-b22101.fa | prodigal -d OceanDNA-b22101/cds.fna -a OceanDNA-b22101/protein.faa -g 11 -q > /dev/null
[2023-03-19 05:19:52,851] [INFO] Task succeeded: Prodigal
[2023-03-19 05:19:52,851] [INFO] Task started: HMMsearch
[2023-03-19 05:19:52,851] [INFO] Running command: hmmsearch --tblout OceanDNA-b22101/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc59b9fb4-3d8e-4c39-b8b9-e69eb9d3d90e/dqc_reference/reference_markers.hmm OceanDNA-b22101/protein.faa > /dev/null
[2023-03-19 05:19:53,097] [INFO] Task succeeded: HMMsearch
[2023-03-19 05:19:53,098] [INFO] Found 6/6 markers.
[2023-03-19 05:19:53,128] [INFO] Query marker FASTA was written to OceanDNA-b22101/markers.fasta
[2023-03-19 05:19:53,129] [INFO] Task started: Blastn
[2023-03-19 05:19:53,129] [INFO] Running command: blastn -query OceanDNA-b22101/markers.fasta -db /var/lib/cwl/stgc59b9fb4-3d8e-4c39-b8b9-e69eb9d3d90e/dqc_reference/reference_markers.fasta -out OceanDNA-b22101/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:19:53,730] [INFO] Task succeeded: Blastn
[2023-03-19 05:19:53,731] [INFO] Selected 35 target genomes.
[2023-03-19 05:19:53,732] [INFO] Target genome list was writen to OceanDNA-b22101/target_genomes.txt
[2023-03-19 05:19:53,749] [INFO] Task started: fastANI
[2023-03-19 05:19:53,749] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0020b83-70bc-4317-aa37-20f4de3919c5/OceanDNA-b22101.fa --refList OceanDNA-b22101/target_genomes.txt --output OceanDNA-b22101/fastani_result.tsv --threads 1
[2023-03-19 05:20:15,821] [INFO] Task succeeded: fastANI
[2023-03-19 05:20:15,822] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc59b9fb4-3d8e-4c39-b8b9-e69eb9d3d90e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 05:20:15,822] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc59b9fb4-3d8e-4c39-b8b9-e69eb9d3d90e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 05:20:15,822] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 05:20:15,822] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 05:20:15,822] [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
--------------------------------------------------------------------------------
[2023-03-19 05:20:15,822] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22101/tc_result.tsv
[2023-03-19 05:20:15,823] [INFO] ===== Taxonomy check completed =====
[2023-03-19 05:20:15,823] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 05:20:15,823] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc59b9fb4-3d8e-4c39-b8b9-e69eb9d3d90e/dqc_reference/checkm_data
[2023-03-19 05:20:15,826] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 05:20:15,851] [INFO] Task started: CheckM
[2023-03-19 05:20:15,852] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22101/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22101/checkm_input OceanDNA-b22101/checkm_result
[2023-03-19 05:21:04,085] [INFO] Task succeeded: CheckM
[2023-03-19 05:21:04,085] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.90%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 05:21:04,275] [INFO] ===== Completeness check finished =====
[2023-03-19 05:21:04,275] [INFO] ===== Start GTDB Search =====
[2023-03-19 05:21:04,275] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22101/markers.fasta)
[2023-03-19 05:21:04,277] [INFO] Task started: Blastn
[2023-03-19 05:21:04,277] [INFO] Running command: blastn -query OceanDNA-b22101/markers.fasta -db /var/lib/cwl/stgc59b9fb4-3d8e-4c39-b8b9-e69eb9d3d90e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22101/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:21:05,297] [INFO] Task succeeded: Blastn
[2023-03-19 05:21:05,298] [INFO] Selected 22 target genomes.
[2023-03-19 05:21:05,298] [INFO] Target genome list was writen to OceanDNA-b22101/target_genomes_gtdb.txt
[2023-03-19 05:21:05,402] [INFO] Task started: fastANI
[2023-03-19 05:21:05,402] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0020b83-70bc-4317-aa37-20f4de3919c5/OceanDNA-b22101.fa --refList OceanDNA-b22101/target_genomes_gtdb.txt --output OceanDNA-b22101/fastani_result_gtdb.tsv --threads 1
[2023-03-19 05:21:20,118] [INFO] Task succeeded: fastANI
[2023-03-19 05:21:20,121] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 05:21:20,121] [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_002704825.1	s__UBA7800 sp002704825	99.2345	599	641	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__Phycisphaeraceae;g__UBA7800	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002480565.1	s__UBA7800 sp002480565	79.6354	337	641	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__Phycisphaeraceae;g__UBA7800	95.0	99.91	99.88	0.96	0.96	5	-
GCA_016763955.1	s__UBA7800 sp016763955	76.035	69	641	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__Phycisphaeraceae;g__UBA7800	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 05:21:20,121] [INFO] GTDB search result was written to OceanDNA-b22101/result_gtdb.tsv
[2023-03-19 05:21:20,122] [INFO] ===== GTDB Search completed =====
[2023-03-19 05:21:20,122] [INFO] DFAST_QC result json was written to OceanDNA-b22101/dqc_result.json
[2023-03-19 05:21:20,122] [INFO] DFAST_QC completed!
[2023-03-19 05:21:20,122] [INFO] Total running time: 0h1m46s