[2023-03-16 04:54:07,043] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:54:07,043] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:54:07,043] [INFO] DQC Reference Directory: /var/lib/cwl/stgc70fc650-7162-427e-9937-9f30db4fc2b2/dqc_reference
[2023-03-16 04:54:08,382] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:54:08,383] [INFO] Task started: Prodigal
[2023-03-16 04:54:08,383] [INFO] Running command: cat /var/lib/cwl/stgf5d5f0d7-bbda-4a9f-a905-75a4f73c6953/OceanDNA-b3242.fa | prodigal -d OceanDNA-b3242/cds.fna -a OceanDNA-b3242/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:54:20,661] [INFO] Task succeeded: Prodigal
[2023-03-16 04:54:20,661] [INFO] Task started: HMMsearch
[2023-03-16 04:54:20,661] [INFO] Running command: hmmsearch --tblout OceanDNA-b3242/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc70fc650-7162-427e-9937-9f30db4fc2b2/dqc_reference/reference_markers.hmm OceanDNA-b3242/protein.faa > /dev/null
[2023-03-16 04:54:20,882] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:54:20,883] [INFO] Found 6/6 markers.
[2023-03-16 04:54:20,897] [INFO] Query marker FASTA was written to OceanDNA-b3242/markers.fasta
[2023-03-16 04:54:20,898] [INFO] Task started: Blastn
[2023-03-16 04:54:20,898] [INFO] Running command: blastn -query OceanDNA-b3242/markers.fasta -db /var/lib/cwl/stgc70fc650-7162-427e-9937-9f30db4fc2b2/dqc_reference/reference_markers.fasta -out OceanDNA-b3242/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:54:21,460] [INFO] Task succeeded: Blastn
[2023-03-16 04:54:21,461] [INFO] Selected 23 target genomes.
[2023-03-16 04:54:21,462] [INFO] Target genome list was writen to OceanDNA-b3242/target_genomes.txt
[2023-03-16 04:54:21,474] [INFO] Task started: fastANI
[2023-03-16 04:54:21,474] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5d5f0d7-bbda-4a9f-a905-75a4f73c6953/OceanDNA-b3242.fa --refList OceanDNA-b3242/target_genomes.txt --output OceanDNA-b3242/fastani_result.tsv --threads 1
[2023-03-16 04:54:39,019] [INFO] Task succeeded: fastANI
[2023-03-16 04:54:39,020] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc70fc650-7162-427e-9937-9f30db4fc2b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:54:39,020] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc70fc650-7162-427e-9937-9f30db4fc2b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:54:39,020] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:54:39,020] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 04:54:39,020] [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 04:54:39,020] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3242/tc_result.tsv
[2023-03-16 04:54:39,020] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:54:39,021] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:54:39,021] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc70fc650-7162-427e-9937-9f30db4fc2b2/dqc_reference/checkm_data
[2023-03-16 04:54:39,024] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:54:39,087] [INFO] Task started: CheckM
[2023-03-16 04:54:39,088] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3242/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3242/checkm_input OceanDNA-b3242/checkm_result
[2023-03-16 04:55:15,569] [INFO] Task succeeded: CheckM
[2023-03-16 04:55:15,570] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:55:15,572] [INFO] ===== Completeness check finished =====
[2023-03-16 04:55:15,572] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:55:15,572] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3242/markers.fasta)
[2023-03-16 04:55:15,573] [INFO] Task started: Blastn
[2023-03-16 04:55:15,573] [INFO] Running command: blastn -query OceanDNA-b3242/markers.fasta -db /var/lib/cwl/stgc70fc650-7162-427e-9937-9f30db4fc2b2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3242/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:55:16,302] [INFO] Task succeeded: Blastn
[2023-03-16 04:55:16,303] [INFO] Selected 16 target genomes.
[2023-03-16 04:55:16,303] [INFO] Target genome list was writen to OceanDNA-b3242/target_genomes_gtdb.txt
[2023-03-16 04:55:16,366] [INFO] Task started: fastANI
[2023-03-16 04:55:16,367] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5d5f0d7-bbda-4a9f-a905-75a4f73c6953/OceanDNA-b3242.fa --refList OceanDNA-b3242/target_genomes_gtdb.txt --output OceanDNA-b3242/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:55:24,671] [INFO] Task succeeded: fastANI
[2023-03-16 04:55:24,675] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 04:55:24,675] [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_002390705.1	s__UBA4592 sp002390705	99.8224	615	648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA4592	95.0	99.34	99.13	0.94	0.92	9	conclusive
GCA_905181745.1	s__UBA4592 sp905181745	93.786	308	648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA4592	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002365735.1	s__UBA4592 sp002365735	88.0116	467	648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA4592	95.0	97.71	97.71	0.84	0.84	2	-
GCA_903896585.1	s__UBA6154 sp903896585	77.5876	55	648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA6154	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017857175.1	s__UBA6154 sp017857175	77.1798	59	648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA6154	95.0	99.75	99.69	0.94	0.93	4	-
--------------------------------------------------------------------------------
[2023-03-16 04:55:24,676] [INFO] GTDB search result was written to OceanDNA-b3242/result_gtdb.tsv
[2023-03-16 04:55:24,676] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:55:24,676] [INFO] DFAST_QC result json was written to OceanDNA-b3242/dqc_result.json
[2023-03-16 04:55:24,676] [INFO] DFAST_QC completed!
[2023-03-16 04:55:24,676] [INFO] Total running time: 0h1m18s