[2024-01-24 15:06:36,789] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:06:36,791] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:06:36,791] [INFO] DQC Reference Directory: /var/lib/cwl/stg01ef99e4-4bb9-4c3f-bc4d-2193b0f6053d/dqc_reference
[2024-01-24 15:06:38,237] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:06:38,238] [INFO] Task started: Prodigal
[2024-01-24 15:06:38,238] [INFO] Running command: gunzip -c /var/lib/cwl/stgf3fb32f6-f548-40d5-b534-1675450e192e/GCF_008326345.1_ASM832634v1_genomic.fna.gz | prodigal -d GCF_008326345.1_ASM832634v1_genomic.fna/cds.fna -a GCF_008326345.1_ASM832634v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:06:46,904] [INFO] Task succeeded: Prodigal
[2024-01-24 15:06:46,904] [INFO] Task started: HMMsearch
[2024-01-24 15:06:46,904] [INFO] Running command: hmmsearch --tblout GCF_008326345.1_ASM832634v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg01ef99e4-4bb9-4c3f-bc4d-2193b0f6053d/dqc_reference/reference_markers.hmm GCF_008326345.1_ASM832634v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:06:47,185] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:06:47,186] [INFO] Found 6/6 markers.
[2024-01-24 15:06:47,210] [INFO] Query marker FASTA was written to GCF_008326345.1_ASM832634v1_genomic.fna/markers.fasta
[2024-01-24 15:06:47,211] [INFO] Task started: Blastn
[2024-01-24 15:06:47,211] [INFO] Running command: blastn -query GCF_008326345.1_ASM832634v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg01ef99e4-4bb9-4c3f-bc4d-2193b0f6053d/dqc_reference/reference_markers.fasta -out GCF_008326345.1_ASM832634v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:06:48,112] [INFO] Task succeeded: Blastn
[2024-01-24 15:06:48,116] [INFO] Selected 12 target genomes.
[2024-01-24 15:06:48,116] [INFO] Target genome list was writen to GCF_008326345.1_ASM832634v1_genomic.fna/target_genomes.txt
[2024-01-24 15:06:48,121] [INFO] Task started: fastANI
[2024-01-24 15:06:48,122] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3fb32f6-f548-40d5-b534-1675450e192e/GCF_008326345.1_ASM832634v1_genomic.fna.gz --refList GCF_008326345.1_ASM832634v1_genomic.fna/target_genomes.txt --output GCF_008326345.1_ASM832634v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:06:55,034] [INFO] Task succeeded: fastANI
[2024-01-24 15:06:55,034] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg01ef99e4-4bb9-4c3f-bc4d-2193b0f6053d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:06:55,035] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg01ef99e4-4bb9-4c3f-bc4d-2193b0f6053d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:06:55,043] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:06:55,043] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:06:55,043] [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 modestum	strain=M12	GCA_008326345.1	2559073	2559073	type	True	100.0	870	871	95	conclusive
Cutibacterium acnes subsp. defendens	strain=ATCC 11828	GCA_000231215.1	1905725	1747	type	True	86.1758	732	871	95	below_threshold
Cutibacterium acnes	strain=ATCC 6919	GCA_008728435.1	1747	1747	type	True	85.8554	726	871	95	below_threshold
Cutibacterium acnes	strain=DSM 1897	GCA_000472405.1	1747	1747	type	True	85.8299	725	871	95	below_threshold
Cutibacterium acnes	strain=ATCC 6919	GCA_003030305.1	1747	1747	type	True	85.7861	735	871	95	below_threshold
Cutibacterium acnes	strain=ATCC 6919	GCA_000730485.1	1747	1747	type	True	85.7279	688	871	95	below_threshold
Cutibacterium namnetense	strain=NTS 31307302	GCA_001642025.1	1574624	1574624	type	True	85.1941	685	871	95	below_threshold
Propioniciclava sinopodophylli	strain=KCTC 33808	GCA_004324755.1	1837344	1837344	type	True	76.3844	78	871	95	below_threshold
Nocardioides yefusunii	strain=HY056	GCA_004014875.1	2500546	2500546	type	True	76.3091	50	871	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:06:55,045] [INFO] DFAST Taxonomy check result was written to GCF_008326345.1_ASM832634v1_genomic.fna/tc_result.tsv
[2024-01-24 15:06:55,046] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:06:55,046] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:06:55,046] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg01ef99e4-4bb9-4c3f-bc4d-2193b0f6053d/dqc_reference/checkm_data
[2024-01-24 15:06:55,048] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:06:55,079] [INFO] Task started: CheckM
[2024-01-24 15:06:55,079] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008326345.1_ASM832634v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008326345.1_ASM832634v1_genomic.fna/checkm_input GCF_008326345.1_ASM832634v1_genomic.fna/checkm_result
[2024-01-24 15:07:25,148] [INFO] Task succeeded: CheckM
[2024-01-24 15:07:25,150] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:07:25,172] [INFO] ===== Completeness check finished =====
[2024-01-24 15:07:25,172] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:07:25,173] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008326345.1_ASM832634v1_genomic.fna/markers.fasta)
[2024-01-24 15:07:25,173] [INFO] Task started: Blastn
[2024-01-24 15:07:25,173] [INFO] Running command: blastn -query GCF_008326345.1_ASM832634v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg01ef99e4-4bb9-4c3f-bc4d-2193b0f6053d/dqc_reference/reference_markers_gtdb.fasta -out GCF_008326345.1_ASM832634v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:07:26,386] [INFO] Task succeeded: Blastn
[2024-01-24 15:07:26,390] [INFO] Selected 10 target genomes.
[2024-01-24 15:07:26,391] [INFO] Target genome list was writen to GCF_008326345.1_ASM832634v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:07:26,403] [INFO] Task started: fastANI
[2024-01-24 15:07:26,403] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3fb32f6-f548-40d5-b534-1675450e192e/GCF_008326345.1_ASM832634v1_genomic.fna.gz --refList GCF_008326345.1_ASM832634v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008326345.1_ASM832634v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:07:33,493] [INFO] Task succeeded: fastANI
[2024-01-24 15:07:33,508] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:07:33,508] [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_008326345.1	s__Cutibacterium modestum	100.0	870	871	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Cutibacterium	95.0	99.93	99.74	1.00	0.99	9	conclusive
GCF_003030305.1	s__Cutibacterium acnes	85.7581	737	871	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Cutibacterium	95.0	99.06	96.60	0.98	0.92	326	-
GCF_001642025.1	s__Cutibacterium namnetense	85.1941	685	871	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Cutibacterium	95.0	99.52	99.43	0.97	0.94	5	-
GCF_009696315.1	s__Cutibacterium porci	82.4143	645	871	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	81.3376	551	871	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	78.14	213	871	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Acidipropionibacterium	95.0	99.00	98.39	0.93	0.89	8	-
GCF_003859805.1	s__Arachnia propionica_C	76.6242	66	871	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002387005.1	s__Luteococcus avicola	76.5297	65	871	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Luteococcus	95.0	96.77	96.77	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:07:33,513] [INFO] GTDB search result was written to GCF_008326345.1_ASM832634v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:07:33,513] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:07:33,516] [INFO] DFAST_QC result json was written to GCF_008326345.1_ASM832634v1_genomic.fna/dqc_result.json
[2024-01-24 15:07:33,517] [INFO] DFAST_QC completed!
[2024-01-24 15:07:33,517] [INFO] Total running time: 0h0m57s