[2023-03-16 16:50:08,751] [INFO] DFAST_QC pipeline started.
[2023-03-16 16:50:08,751] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 16:50:08,751] [INFO] DQC Reference Directory: /var/lib/cwl/stg253b2e77-3d4d-4f0e-80ef-5eb24dd2faf1/dqc_reference
[2023-03-16 16:50:10,424] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 16:50:10,425] [INFO] Task started: Prodigal
[2023-03-16 16:50:10,425] [INFO] Running command: cat /var/lib/cwl/stgc317f63f-3a3d-44e4-ad80-53189b3c2167/OceanDNA-b22253.fa | prodigal -d OceanDNA-b22253/cds.fna -a OceanDNA-b22253/protein.faa -g 11 -q > /dev/null
[2023-03-16 16:50:16,567] [INFO] Task succeeded: Prodigal
[2023-03-16 16:50:16,567] [INFO] Task started: HMMsearch
[2023-03-16 16:50:16,567] [INFO] Running command: hmmsearch --tblout OceanDNA-b22253/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg253b2e77-3d4d-4f0e-80ef-5eb24dd2faf1/dqc_reference/reference_markers.hmm OceanDNA-b22253/protein.faa > /dev/null
[2023-03-16 16:50:16,776] [INFO] Task succeeded: HMMsearch
[2023-03-16 16:50:16,777] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc317f63f-3a3d-44e4-ad80-53189b3c2167/OceanDNA-b22253.fa]
[2023-03-16 16:50:16,795] [INFO] Query marker FASTA was written to OceanDNA-b22253/markers.fasta
[2023-03-16 16:50:16,797] [INFO] Task started: Blastn
[2023-03-16 16:50:16,797] [INFO] Running command: blastn -query OceanDNA-b22253/markers.fasta -db /var/lib/cwl/stg253b2e77-3d4d-4f0e-80ef-5eb24dd2faf1/dqc_reference/reference_markers.fasta -out OceanDNA-b22253/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:50:19,820] [INFO] Task succeeded: Blastn
[2023-03-16 16:50:19,822] [INFO] Selected 24 target genomes.
[2023-03-16 16:50:19,823] [INFO] Target genome list was writen to OceanDNA-b22253/target_genomes.txt
[2023-03-16 16:50:19,870] [INFO] Task started: fastANI
[2023-03-16 16:50:19,870] [INFO] Running command: fastANI --query /var/lib/cwl/stgc317f63f-3a3d-44e4-ad80-53189b3c2167/OceanDNA-b22253.fa --refList OceanDNA-b22253/target_genomes.txt --output OceanDNA-b22253/fastani_result.tsv --threads 1
[2023-03-16 16:50:46,269] [INFO] Task succeeded: fastANI
[2023-03-16 16:50:46,269] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg253b2e77-3d4d-4f0e-80ef-5eb24dd2faf1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 16:50:46,269] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg253b2e77-3d4d-4f0e-80ef-5eb24dd2faf1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 16:50:46,269] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 16:50:46,269] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 16:50:46,269] [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 16:50:46,271] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22253/tc_result.tsv
[2023-03-16 16:50:46,272] [INFO] ===== Taxonomy check completed =====
[2023-03-16 16:50:46,272] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 16:50:46,272] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg253b2e77-3d4d-4f0e-80ef-5eb24dd2faf1/dqc_reference/checkm_data
[2023-03-16 16:50:46,319] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 16:50:46,323] [INFO] Task started: CheckM
[2023-03-16 16:50:46,323] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22253/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22253/checkm_input OceanDNA-b22253/checkm_result
[2023-03-16 16:51:17,275] [INFO] Task succeeded: CheckM
[2023-03-16 16:51:17,276] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 55.18%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 16:51:17,279] [INFO] ===== Completeness check finished =====
[2023-03-16 16:51:17,279] [INFO] ===== Start GTDB Search =====
[2023-03-16 16:51:17,279] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22253/markers.fasta)
[2023-03-16 16:51:17,286] [INFO] Task started: Blastn
[2023-03-16 16:51:17,286] [INFO] Running command: blastn -query OceanDNA-b22253/markers.fasta -db /var/lib/cwl/stg253b2e77-3d4d-4f0e-80ef-5eb24dd2faf1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22253/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:51:18,691] [INFO] Task succeeded: Blastn
[2023-03-16 16:51:18,692] [INFO] Selected 16 target genomes.
[2023-03-16 16:51:18,693] [INFO] Target genome list was writen to OceanDNA-b22253/target_genomes_gtdb.txt
[2023-03-16 16:51:19,068] [INFO] Task started: fastANI
[2023-03-16 16:51:19,068] [INFO] Running command: fastANI --query /var/lib/cwl/stgc317f63f-3a3d-44e4-ad80-53189b3c2167/OceanDNA-b22253.fa --refList OceanDNA-b22253/target_genomes_gtdb.txt --output OceanDNA-b22253/fastani_result_gtdb.tsv --threads 1
[2023-03-16 16:51:30,380] [INFO] Task succeeded: fastANI
[2023-03-16 16:51:30,383] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 16:51:30,383] [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_002862305.1	s__UBA8087 sp002862305	93.4389	193	195	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA8087	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002171655.1	s__UBA8087 sp002171655	77.3548	66	195	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA8087	95.0	100.00	100.00	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2023-03-16 16:51:30,384] [INFO] GTDB search result was written to OceanDNA-b22253/result_gtdb.tsv
[2023-03-16 16:51:30,385] [INFO] ===== GTDB Search completed =====
[2023-03-16 16:51:30,545] [INFO] DFAST_QC result json was written to OceanDNA-b22253/dqc_result.json
[2023-03-16 16:51:30,545] [INFO] DFAST_QC completed!
[2023-03-16 16:51:30,545] [INFO] Total running time: 0h1m22s