[2023-03-19 05:19:33,645] [INFO] DFAST_QC pipeline started.
[2023-03-19 05:19:33,645] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 05:19:33,645] [INFO] DQC Reference Directory: /var/lib/cwl/stgcfea92d5-4fef-4f2b-a6c9-7a4ba03c2b3d/dqc_reference
[2023-03-19 05:19:34,866] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 05:19:34,867] [INFO] Task started: Prodigal
[2023-03-19 05:19:34,867] [INFO] Running command: cat /var/lib/cwl/stg55c82494-d834-456c-8e0b-55d8b0886145/OceanDNA-b3407.fa | prodigal -d OceanDNA-b3407/cds.fna -a OceanDNA-b3407/protein.faa -g 11 -q > /dev/null
[2023-03-19 05:19:45,344] [INFO] Task succeeded: Prodigal
[2023-03-19 05:19:45,345] [INFO] Task started: HMMsearch
[2023-03-19 05:19:45,345] [INFO] Running command: hmmsearch --tblout OceanDNA-b3407/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcfea92d5-4fef-4f2b-a6c9-7a4ba03c2b3d/dqc_reference/reference_markers.hmm OceanDNA-b3407/protein.faa > /dev/null
[2023-03-19 05:19:45,513] [INFO] Task succeeded: HMMsearch
[2023-03-19 05:19:45,514] [INFO] Found 6/6 markers.
[2023-03-19 05:19:45,529] [INFO] Query marker FASTA was written to OceanDNA-b3407/markers.fasta
[2023-03-19 05:19:45,529] [INFO] Task started: Blastn
[2023-03-19 05:19:45,529] [INFO] Running command: blastn -query OceanDNA-b3407/markers.fasta -db /var/lib/cwl/stgcfea92d5-4fef-4f2b-a6c9-7a4ba03c2b3d/dqc_reference/reference_markers.fasta -out OceanDNA-b3407/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:19:46,248] [INFO] Task succeeded: Blastn
[2023-03-19 05:19:46,249] [INFO] Selected 11 target genomes.
[2023-03-19 05:19:46,249] [INFO] Target genome list was writen to OceanDNA-b3407/target_genomes.txt
[2023-03-19 05:19:46,255] [INFO] Task started: fastANI
[2023-03-19 05:19:46,255] [INFO] Running command: fastANI --query /var/lib/cwl/stg55c82494-d834-456c-8e0b-55d8b0886145/OceanDNA-b3407.fa --refList OceanDNA-b3407/target_genomes.txt --output OceanDNA-b3407/fastani_result.tsv --threads 1
[2023-03-19 05:19:51,401] [INFO] Task succeeded: fastANI
[2023-03-19 05:19:51,401] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcfea92d5-4fef-4f2b-a6c9-7a4ba03c2b3d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 05:19:51,402] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcfea92d5-4fef-4f2b-a6c9-7a4ba03c2b3d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 05:19:51,407] [INFO] Found 6 fastANI hits (6 hits with ANI > threshold)
[2023-03-19 05:19:51,407] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-19 05:19:51,407] [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
Cutibacterium acnes	strain=ATCC 6919	GCA_008728435.1	1747	1747	type	True	98.8613	516	520	95	conclusive
Cutibacterium acnes	strain=DSM 1897	GCA_004136195.1	1747	1747	type	True	98.8608	519	520	95	conclusive
Cutibacterium acnes	strain=DSM 1897	GCA_000472405.1	1747	1747	type	True	98.8607	516	520	95	conclusive
Cutibacterium acnes	strain=ATCC 6919	GCA_003030305.1	1747	1747	type	True	98.8605	519	520	95	conclusive
Cutibacterium acnes	strain=ATCC 6919	GCA_000730485.1	1747	1747	type	True	98.753	506	520	95	conclusive
Cutibacterium acnes subsp. defendens	strain=ATCC 11828	GCA_000231215.1	1905725	1747	type	True	98.4969	518	520	95	conclusive
--------------------------------------------------------------------------------
[2023-03-19 05:19:51,407] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3407/tc_result.tsv
[2023-03-19 05:19:51,407] [INFO] ===== Taxonomy check completed =====
[2023-03-19 05:19:51,407] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 05:19:51,407] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcfea92d5-4fef-4f2b-a6c9-7a4ba03c2b3d/dqc_reference/checkm_data
[2023-03-19 05:19:51,408] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 05:19:51,411] [INFO] Task started: CheckM
[2023-03-19 05:19:51,411] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3407/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3407/checkm_input OceanDNA-b3407/checkm_result
[2023-03-19 05:20:21,918] [INFO] Task succeeded: CheckM
[2023-03-19 05:20:21,919] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 05:20:21,920] [INFO] ===== Completeness check finished =====
[2023-03-19 05:20:21,921] [INFO] ===== Start GTDB Search =====
[2023-03-19 05:20:21,921] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3407/markers.fasta)
[2023-03-19 05:20:21,921] [INFO] Task started: Blastn
[2023-03-19 05:20:21,921] [INFO] Running command: blastn -query OceanDNA-b3407/markers.fasta -db /var/lib/cwl/stgcfea92d5-4fef-4f2b-a6c9-7a4ba03c2b3d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3407/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:20:22,934] [INFO] Task succeeded: Blastn
[2023-03-19 05:20:22,935] [INFO] Selected 6 target genomes.
[2023-03-19 05:20:22,935] [INFO] Target genome list was writen to OceanDNA-b3407/target_genomes_gtdb.txt
[2023-03-19 05:20:22,940] [INFO] Task started: fastANI
[2023-03-19 05:20:22,940] [INFO] Running command: fastANI --query /var/lib/cwl/stg55c82494-d834-456c-8e0b-55d8b0886145/OceanDNA-b3407.fa --refList OceanDNA-b3407/target_genomes_gtdb.txt --output OceanDNA-b3407/fastani_result_gtdb.tsv --threads 1
[2023-03-19 05:20:26,157] [INFO] Task succeeded: fastANI
[2023-03-19 05:20:26,161] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 05:20:26,161] [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
GCF_003030305.1	s__Cutibacterium acnes	98.8605	519	520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Cutibacterium	95.0	99.06	96.60	0.98	0.92	326	conclusive
GCF_001642025.1	s__Cutibacterium namnetense	88.0045	472	520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Cutibacterium	95.0	99.52	99.43	0.97	0.94	5	-
GCF_008326345.1	s__Cutibacterium modestum	86.0447	487	520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Cutibacterium	95.0	99.93	99.74	1.00	0.99	9	-
GCF_009696315.1	s__Cutibacterium porci	82.5812	418	520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Cutibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000227295.1	s__Cutibacterium avidum	81.5546	392	520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Cutibacterium	95.0	97.99	95.78	0.94	0.87	29	-
GCF_001441165.1	s__Acidipropionibacterium acidipropionici	78.1752	144	520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Acidipropionibacterium	95.0	99.00	98.39	0.93	0.89	8	-
--------------------------------------------------------------------------------
[2023-03-19 05:20:26,162] [INFO] GTDB search result was written to OceanDNA-b3407/result_gtdb.tsv
[2023-03-19 05:20:26,162] [INFO] ===== GTDB Search completed =====
[2023-03-19 05:20:26,163] [INFO] DFAST_QC result json was written to OceanDNA-b3407/dqc_result.json
[2023-03-19 05:20:26,163] [INFO] DFAST_QC completed!
[2023-03-19 05:20:26,163] [INFO] Total running time: 0h0m53s