[2023-03-16 15:11:23,504] [INFO] DFAST_QC pipeline started.
[2023-03-16 15:11:23,504] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 15:11:23,504] [INFO] DQC Reference Directory: /var/lib/cwl/stg5998143b-03b1-476f-b5f2-0022e25d3d05/dqc_reference
[2023-03-16 15:11:24,899] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 15:11:24,899] [INFO] Task started: Prodigal
[2023-03-16 15:11:24,899] [INFO] Running command: cat /var/lib/cwl/stgf75faa74-9b42-416d-82dc-5d0341b3a145/OceanDNA-b525.fa | prodigal -d OceanDNA-b525/cds.fna -a OceanDNA-b525/protein.faa -g 11 -q > /dev/null
[2023-03-16 15:11:33,323] [INFO] Task succeeded: Prodigal
[2023-03-16 15:11:33,323] [INFO] Task started: HMMsearch
[2023-03-16 15:11:33,323] [INFO] Running command: hmmsearch --tblout OceanDNA-b525/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5998143b-03b1-476f-b5f2-0022e25d3d05/dqc_reference/reference_markers.hmm OceanDNA-b525/protein.faa > /dev/null
[2023-03-16 15:11:33,464] [INFO] Task succeeded: HMMsearch
[2023-03-16 15:11:33,465] [INFO] Found 6/6 markers.
[2023-03-16 15:11:33,476] [INFO] Query marker FASTA was written to OceanDNA-b525/markers.fasta
[2023-03-16 15:11:33,477] [INFO] Task started: Blastn
[2023-03-16 15:11:33,477] [INFO] Running command: blastn -query OceanDNA-b525/markers.fasta -db /var/lib/cwl/stg5998143b-03b1-476f-b5f2-0022e25d3d05/dqc_reference/reference_markers.fasta -out OceanDNA-b525/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 15:11:33,998] [INFO] Task succeeded: Blastn
[2023-03-16 15:11:33,999] [INFO] Selected 22 target genomes.
[2023-03-16 15:11:33,999] [INFO] Target genome list was writen to OceanDNA-b525/target_genomes.txt
[2023-03-16 15:11:34,017] [INFO] Task started: fastANI
[2023-03-16 15:11:34,018] [INFO] Running command: fastANI --query /var/lib/cwl/stgf75faa74-9b42-416d-82dc-5d0341b3a145/OceanDNA-b525.fa --refList OceanDNA-b525/target_genomes.txt --output OceanDNA-b525/fastani_result.tsv --threads 1
[2023-03-16 15:11:47,756] [INFO] Task succeeded: fastANI
[2023-03-16 15:11:47,756] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5998143b-03b1-476f-b5f2-0022e25d3d05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 15:11:47,757] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5998143b-03b1-476f-b5f2-0022e25d3d05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 15:11:47,757] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 15:11:47,757] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 15:11:47,757] [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 15:11:47,757] [INFO] DFAST Taxonomy check result was written to OceanDNA-b525/tc_result.tsv
[2023-03-16 15:11:47,757] [INFO] ===== Taxonomy check completed =====
[2023-03-16 15:11:47,757] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 15:11:47,757] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5998143b-03b1-476f-b5f2-0022e25d3d05/dqc_reference/checkm_data
[2023-03-16 15:11:47,760] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 15:11:47,763] [INFO] Task started: CheckM
[2023-03-16 15:11:47,763] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b525/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b525/checkm_input OceanDNA-b525/checkm_result
[2023-03-16 15:12:24,599] [INFO] Task succeeded: CheckM
[2023-03-16 15:12:24,600] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.98%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 15:12:24,602] [INFO] ===== Completeness check finished =====
[2023-03-16 15:12:24,602] [INFO] ===== Start GTDB Search =====
[2023-03-16 15:12:24,602] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b525/markers.fasta)
[2023-03-16 15:12:24,602] [INFO] Task started: Blastn
[2023-03-16 15:12:24,602] [INFO] Running command: blastn -query OceanDNA-b525/markers.fasta -db /var/lib/cwl/stg5998143b-03b1-476f-b5f2-0022e25d3d05/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b525/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 15:12:25,518] [INFO] Task succeeded: Blastn
[2023-03-16 15:12:25,519] [INFO] Selected 19 target genomes.
[2023-03-16 15:12:25,519] [INFO] Target genome list was writen to OceanDNA-b525/target_genomes_gtdb.txt
[2023-03-16 15:12:26,430] [INFO] Task started: fastANI
[2023-03-16 15:12:26,430] [INFO] Running command: fastANI --query /var/lib/cwl/stgf75faa74-9b42-416d-82dc-5d0341b3a145/OceanDNA-b525.fa --refList OceanDNA-b525/target_genomes_gtdb.txt --output OceanDNA-b525/fastani_result_gtdb.tsv --threads 1
[2023-03-16 15:12:34,813] [INFO] Task succeeded: fastANI
[2023-03-16 15:12:34,819] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 15:12:34,819] [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_903850275.1	s__UBA3006 sp903850275	89.4184	230	389	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA3006	95.0	96.61	96.61	0.70	0.70	2	-
GCA_001438985.1	s__UBA3006 sp001438985	79.7964	87	389	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA3006	95.0	98.19	98.19	0.91	0.91	2	-
GCA_903895515.1	s__UBA3006 sp903895515	78.8995	108	389	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA3006	95.0	98.23	97.46	0.84	0.83	3	-
GCA_014190095.1	s__UBA3006 sp014190095	78.3635	123	389	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA3006	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002367695.1	s__UBA3006 sp002367695	77.9343	107	389	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA3006	95.0	99.47	99.24	0.90	0.87	7	-
GCA_017853385.1	s__UBA3006 sp017853385	77.7767	88	389	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA3006	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903853285.1	s__UBA3006 sp903853285	77.5928	84	389	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA3006	95.0	97.79	97.42	0.77	0.73	4	-
GCA_009698745.1	s__UBA3006 sp009698745	76.7209	71	389	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA3006	95.0	99.77	99.77	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2023-03-16 15:12:34,819] [INFO] GTDB search result was written to OceanDNA-b525/result_gtdb.tsv
[2023-03-16 15:12:34,819] [INFO] ===== GTDB Search completed =====
[2023-03-16 15:12:34,820] [INFO] DFAST_QC result json was written to OceanDNA-b525/dqc_result.json
[2023-03-16 15:12:34,820] [INFO] DFAST_QC completed!
[2023-03-16 15:12:34,820] [INFO] Total running time: 0h1m11s