[2023-03-15 10:52:57,301] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:52:57,301] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:52:57,301] [INFO] DQC Reference Directory: /var/lib/cwl/stg9a92f6a3-5238-4a1e-a8e1-a5dd6c4782c2/dqc_reference
[2023-03-15 10:52:58,864] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:52:58,864] [INFO] Task started: Prodigal
[2023-03-15 10:52:58,864] [INFO] Running command: cat /var/lib/cwl/stgdd6a5e8e-9811-42d0-aa27-7b327ff3237c/OceanDNA-b13590.fa | prodigal -d OceanDNA-b13590/cds.fna -a OceanDNA-b13590/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:53:19,858] [INFO] Task succeeded: Prodigal
[2023-03-15 10:53:19,858] [INFO] Task started: HMMsearch
[2023-03-15 10:53:19,858] [INFO] Running command: hmmsearch --tblout OceanDNA-b13590/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9a92f6a3-5238-4a1e-a8e1-a5dd6c4782c2/dqc_reference/reference_markers.hmm OceanDNA-b13590/protein.faa > /dev/null
[2023-03-15 10:53:20,039] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:53:20,039] [INFO] Found 6/6 markers.
[2023-03-15 10:53:20,060] [INFO] Query marker FASTA was written to OceanDNA-b13590/markers.fasta
[2023-03-15 10:53:20,061] [INFO] Task started: Blastn
[2023-03-15 10:53:20,061] [INFO] Running command: blastn -query OceanDNA-b13590/markers.fasta -db /var/lib/cwl/stg9a92f6a3-5238-4a1e-a8e1-a5dd6c4782c2/dqc_reference/reference_markers.fasta -out OceanDNA-b13590/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:53:20,589] [INFO] Task succeeded: Blastn
[2023-03-15 10:53:20,590] [INFO] Selected 14 target genomes.
[2023-03-15 10:53:20,590] [INFO] Target genome list was writen to OceanDNA-b13590/target_genomes.txt
[2023-03-15 10:53:20,600] [INFO] Task started: fastANI
[2023-03-15 10:53:20,600] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd6a5e8e-9811-42d0-aa27-7b327ff3237c/OceanDNA-b13590.fa --refList OceanDNA-b13590/target_genomes.txt --output OceanDNA-b13590/fastani_result.tsv --threads 1
[2023-03-15 10:53:30,644] [INFO] Task succeeded: fastANI
[2023-03-15 10:53:30,644] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9a92f6a3-5238-4a1e-a8e1-a5dd6c4782c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:53:30,644] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9a92f6a3-5238-4a1e-a8e1-a5dd6c4782c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:53:30,645] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:53:30,645] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 10:53:30,645] [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
--------------------------------------------------------------------------------
[2023-03-15 10:53:30,645] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13590/tc_result.tsv
[2023-03-15 10:53:30,645] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:53:30,645] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:53:30,645] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9a92f6a3-5238-4a1e-a8e1-a5dd6c4782c2/dqc_reference/checkm_data
[2023-03-15 10:53:30,648] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:53:30,718] [INFO] Task started: CheckM
[2023-03-15 10:53:30,718] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13590/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13590/checkm_input OceanDNA-b13590/checkm_result
[2023-03-15 10:54:22,053] [INFO] Task succeeded: CheckM
[2023-03-15 10:54:22,054] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 10:54:22,056] [INFO] ===== Completeness check finished =====
[2023-03-15 10:54:22,056] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:54:22,056] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13590/markers.fasta)
[2023-03-15 10:54:22,058] [INFO] Task started: Blastn
[2023-03-15 10:54:22,058] [INFO] Running command: blastn -query OceanDNA-b13590/markers.fasta -db /var/lib/cwl/stg9a92f6a3-5238-4a1e-a8e1-a5dd6c4782c2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13590/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:54:22,828] [INFO] Task succeeded: Blastn
[2023-03-15 10:54:22,829] [INFO] Selected 26 target genomes.
[2023-03-15 10:54:22,829] [INFO] Target genome list was writen to OceanDNA-b13590/target_genomes_gtdb.txt
[2023-03-15 10:54:22,958] [INFO] Task started: fastANI
[2023-03-15 10:54:22,958] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd6a5e8e-9811-42d0-aa27-7b327ff3237c/OceanDNA-b13590.fa --refList OceanDNA-b13590/target_genomes_gtdb.txt --output OceanDNA-b13590/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:54:37,161] [INFO] Task succeeded: fastANI
[2023-03-15 10:54:37,164] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 10:54:37,164] [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_003228175.2	s__TK10-74A sp003228175	78.0838	123	1095	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Bin125;f__Bin125;g__TK10-74A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002239025.1	s__Bin125 sp002239025	75.818	70	1095	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Bin125;f__Bin125;g__Bin125	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007571275.1	s__Bin125 sp007571275	75.6445	60	1095	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Bin125;f__Bin125;g__Bin125	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 10:54:37,164] [INFO] GTDB search result was written to OceanDNA-b13590/result_gtdb.tsv
[2023-03-15 10:54:37,164] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:54:37,164] [INFO] DFAST_QC result json was written to OceanDNA-b13590/dqc_result.json
[2023-03-15 10:54:37,165] [INFO] DFAST_QC completed!
[2023-03-15 10:54:37,165] [INFO] Total running time: 0h1m40s