[2023-03-15 06:28:21,334] [INFO] DFAST_QC pipeline started.
[2023-03-15 06:28:21,334] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 06:28:21,334] [INFO] DQC Reference Directory: /var/lib/cwl/stge600d423-c616-46aa-8cd0-fbc291a32136/dqc_reference
[2023-03-15 06:28:22,450] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 06:28:22,450] [INFO] Task started: Prodigal
[2023-03-15 06:28:22,450] [INFO] Running command: cat /var/lib/cwl/stga2b9cfbb-fe9c-43fb-8300-facc2400f4ab/OceanDNA-b21346.fa | prodigal -d OceanDNA-b21346/cds.fna -a OceanDNA-b21346/protein.faa -g 11 -q > /dev/null
[2023-03-15 06:28:30,118] [INFO] Task succeeded: Prodigal
[2023-03-15 06:28:30,118] [INFO] Task started: HMMsearch
[2023-03-15 06:28:30,118] [INFO] Running command: hmmsearch --tblout OceanDNA-b21346/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge600d423-c616-46aa-8cd0-fbc291a32136/dqc_reference/reference_markers.hmm OceanDNA-b21346/protein.faa > /dev/null
[2023-03-15 06:28:30,310] [INFO] Task succeeded: HMMsearch
[2023-03-15 06:28:30,311] [INFO] Found 6/6 markers.
[2023-03-15 06:28:30,325] [INFO] Query marker FASTA was written to OceanDNA-b21346/markers.fasta
[2023-03-15 06:28:30,325] [INFO] Task started: Blastn
[2023-03-15 06:28:30,325] [INFO] Running command: blastn -query OceanDNA-b21346/markers.fasta -db /var/lib/cwl/stge600d423-c616-46aa-8cd0-fbc291a32136/dqc_reference/reference_markers.fasta -out OceanDNA-b21346/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 06:28:30,887] [INFO] Task succeeded: Blastn
[2023-03-15 06:28:30,887] [INFO] Selected 20 target genomes.
[2023-03-15 06:28:30,888] [INFO] Target genome list was writen to OceanDNA-b21346/target_genomes.txt
[2023-03-15 06:28:30,897] [INFO] Task started: fastANI
[2023-03-15 06:28:30,897] [INFO] Running command: fastANI --query /var/lib/cwl/stga2b9cfbb-fe9c-43fb-8300-facc2400f4ab/OceanDNA-b21346.fa --refList OceanDNA-b21346/target_genomes.txt --output OceanDNA-b21346/fastani_result.tsv --threads 1
[2023-03-15 06:28:41,926] [INFO] Task succeeded: fastANI
[2023-03-15 06:28:41,926] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge600d423-c616-46aa-8cd0-fbc291a32136/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 06:28:41,927] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge600d423-c616-46aa-8cd0-fbc291a32136/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 06:28:41,927] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 06:28:41,927] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 06:28:41,927] [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 06:28:41,929] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21346/tc_result.tsv
[2023-03-15 06:28:41,931] [INFO] ===== Taxonomy check completed =====
[2023-03-15 06:28:41,931] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 06:28:41,931] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge600d423-c616-46aa-8cd0-fbc291a32136/dqc_reference/checkm_data
[2023-03-15 06:28:41,934] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 06:28:41,938] [INFO] Task started: CheckM
[2023-03-15 06:28:41,938] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21346/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21346/checkm_input OceanDNA-b21346/checkm_result
[2023-03-15 06:29:06,527] [INFO] Task succeeded: CheckM
[2023-03-15 06:29:06,527] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.19%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 06:29:06,533] [INFO] ===== Completeness check finished =====
[2023-03-15 06:29:06,534] [INFO] ===== Start GTDB Search =====
[2023-03-15 06:29:06,534] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21346/markers.fasta)
[2023-03-15 06:29:06,534] [INFO] Task started: Blastn
[2023-03-15 06:29:06,534] [INFO] Running command: blastn -query OceanDNA-b21346/markers.fasta -db /var/lib/cwl/stge600d423-c616-46aa-8cd0-fbc291a32136/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21346/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 06:29:07,458] [INFO] Task succeeded: Blastn
[2023-03-15 06:29:07,466] [INFO] Selected 23 target genomes.
[2023-03-15 06:29:07,466] [INFO] Target genome list was writen to OceanDNA-b21346/target_genomes_gtdb.txt
[2023-03-15 06:29:07,479] [INFO] Task started: fastANI
[2023-03-15 06:29:07,479] [INFO] Running command: fastANI --query /var/lib/cwl/stga2b9cfbb-fe9c-43fb-8300-facc2400f4ab/OceanDNA-b21346.fa --refList OceanDNA-b21346/target_genomes_gtdb.txt --output OceanDNA-b21346/fastani_result_gtdb.tsv --threads 1
[2023-03-15 06:29:15,167] [INFO] Task succeeded: fastANI
[2023-03-15 06:29:15,171] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 06:29:15,171] [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_002697825.1	s__UBA8687 sp002697825	98.1714	323	456	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__UBA8687	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002721515.1	s__UBA8687 sp002721515	81.0772	240	456	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__UBA8687	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018665625.1	s__UBA8687 sp018665625	77.3844	173	456	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__UBA8687	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009873655.1	s__UBA8687 sp009873655	77.2564	153	456	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__UBA8687	95.0	99.50	99.47	0.94	0.93	3	-
GCA_013349585.1	s__UBA8687 sp013349585	77.2282	128	456	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__UBA8687	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 06:29:15,171] [INFO] GTDB search result was written to OceanDNA-b21346/result_gtdb.tsv
[2023-03-15 06:29:15,171] [INFO] ===== GTDB Search completed =====
[2023-03-15 06:29:15,172] [INFO] DFAST_QC result json was written to OceanDNA-b21346/dqc_result.json
[2023-03-15 06:29:15,172] [INFO] DFAST_QC completed!
[2023-03-15 06:29:15,172] [INFO] Total running time: 0h0m54s