[2024-01-24 13:18:29,117] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:29,121] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:29,121] [INFO] DQC Reference Directory: /var/lib/cwl/stg0f3177cd-fe35-47be-85d1-cf054ba14e25/dqc_reference
[2024-01-24 13:18:30,399] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:30,400] [INFO] Task started: Prodigal
[2024-01-24 13:18:30,400] [INFO] Running command: gunzip -c /var/lib/cwl/stgdb032a42-6e11-43c3-8e42-08426793006f/GCF_009696315.1_ASM969631v1_genomic.fna.gz | prodigal -d GCF_009696315.1_ASM969631v1_genomic.fna/cds.fna -a GCF_009696315.1_ASM969631v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:38,887] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:38,888] [INFO] Task started: HMMsearch
[2024-01-24 13:18:38,888] [INFO] Running command: hmmsearch --tblout GCF_009696315.1_ASM969631v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0f3177cd-fe35-47be-85d1-cf054ba14e25/dqc_reference/reference_markers.hmm GCF_009696315.1_ASM969631v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:39,178] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:39,179] [INFO] Found 6/6 markers.
[2024-01-24 13:18:39,213] [INFO] Query marker FASTA was written to GCF_009696315.1_ASM969631v1_genomic.fna/markers.fasta
[2024-01-24 13:18:39,213] [INFO] Task started: Blastn
[2024-01-24 13:18:39,214] [INFO] Running command: blastn -query GCF_009696315.1_ASM969631v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f3177cd-fe35-47be-85d1-cf054ba14e25/dqc_reference/reference_markers.fasta -out GCF_009696315.1_ASM969631v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:40,019] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:40,022] [INFO] Selected 17 target genomes.
[2024-01-24 13:18:40,023] [INFO] Target genome list was writen to GCF_009696315.1_ASM969631v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:40,034] [INFO] Task started: fastANI
[2024-01-24 13:18:40,034] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb032a42-6e11-43c3-8e42-08426793006f/GCF_009696315.1_ASM969631v1_genomic.fna.gz --refList GCF_009696315.1_ASM969631v1_genomic.fna/target_genomes.txt --output GCF_009696315.1_ASM969631v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:52,063] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:52,063] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0f3177cd-fe35-47be-85d1-cf054ba14e25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:52,064] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0f3177cd-fe35-47be-85d1-cf054ba14e25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:52,074] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:18:52,074] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:52,075] [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 porci	strain=WCA-380-WT-3A	GCA_009696315.1	2605781	2605781	type	True	100.0	860	861	95	conclusive
Cutibacterium acnes	strain=ATCC 6919	GCA_003030305.1	1747	1747	type	True	82.6775	609	861	95	below_threshold
Cutibacterium acnes	strain=ATCC 6919	GCA_000730485.1	1747	1747	type	True	82.6364	590	861	95	below_threshold
Cutibacterium acnes	strain=DSM 1897	GCA_000472405.1	1747	1747	type	True	82.6181	608	861	95	below_threshold
Cutibacterium acnes	strain=ATCC 6919	GCA_008728435.1	1747	1747	type	True	82.5982	624	861	95	below_threshold
Cutibacterium acnes subsp. defendens	strain=ATCC 11828	GCA_000231215.1	1905725	1747	type	True	82.5398	620	861	95	below_threshold
Cutibacterium modestum	strain=M12	GCA_008326345.1	2559073	2559073	type	True	82.4849	632	861	95	below_threshold
Cutibacterium namnetense	strain=NTS 31307302	GCA_001642025.1	1574624	1574624	type	True	82.2932	591	861	95	below_threshold
Cutibacterium avidum	strain=ATCC 25577	GCA_000227295.1	33010	33010	type	True	80.7806	502	861	95	below_threshold
Cutibacterium granulosum	strain=NCTC11865	GCA_900186975.1	33011	33011	type	True	78.0536	160	861	95	below_threshold
Cutibacterium granulosum	strain=DSM 20700	GCA_000463665.1	33011	33011	type	True	78.0444	135	861	95	below_threshold
Acidipropionibacterium thoenii	strain=DSM 20276	GCA_000423445.1	1751	1751	type	True	77.7227	158	861	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:52,080] [INFO] DFAST Taxonomy check result was written to GCF_009696315.1_ASM969631v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:52,081] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:52,081] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:52,082] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0f3177cd-fe35-47be-85d1-cf054ba14e25/dqc_reference/checkm_data
[2024-01-24 13:18:52,083] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:52,115] [INFO] Task started: CheckM
[2024-01-24 13:18:52,115] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009696315.1_ASM969631v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009696315.1_ASM969631v1_genomic.fna/checkm_input GCF_009696315.1_ASM969631v1_genomic.fna/checkm_result
[2024-01-24 13:19:22,363] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:22,365] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:22,394] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:22,394] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:22,395] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009696315.1_ASM969631v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:22,395] [INFO] Task started: Blastn
[2024-01-24 13:19:22,395] [INFO] Running command: blastn -query GCF_009696315.1_ASM969631v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f3177cd-fe35-47be-85d1-cf054ba14e25/dqc_reference/reference_markers_gtdb.fasta -out GCF_009696315.1_ASM969631v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:23,634] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:23,638] [INFO] Selected 11 target genomes.
[2024-01-24 13:19:23,638] [INFO] Target genome list was writen to GCF_009696315.1_ASM969631v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:23,652] [INFO] Task started: fastANI
[2024-01-24 13:19:23,652] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb032a42-6e11-43c3-8e42-08426793006f/GCF_009696315.1_ASM969631v1_genomic.fna.gz --refList GCF_009696315.1_ASM969631v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009696315.1_ASM969631v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:30,351] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:30,360] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:30,361] [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_009696315.1	s__Cutibacterium porci	100.0	860	861	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Cutibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003030305.1	s__Cutibacterium acnes	82.6775	609	861	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Cutibacterium	95.0	99.06	96.60	0.98	0.92	326	-
GCF_008326345.1	s__Cutibacterium modestum	82.4723	633	861	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Cutibacterium	95.0	99.93	99.74	1.00	0.99	9	-
GCF_001642025.1	s__Cutibacterium namnetense	82.3065	590	861	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Cutibacterium	95.0	99.52	99.43	0.97	0.94	5	-
GCF_000227295.1	s__Cutibacterium avidum	80.768	503	861	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Cutibacterium	95.0	97.99	95.78	0.94	0.87	29	-
GCF_900186975.1	s__Cutibacterium granulosum	78.0756	159	861	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Cutibacterium	95.0	98.45	97.35	0.97	0.94	5	-
GCF_900605005.1	s__Cutibacterium timonense	78.0123	200	861	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Cutibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423445.1	s__Acidipropionibacterium thoenii	77.7015	159	861	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Acidipropionibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017355265.1	s__Aestuariimicrobium sp017355265	76.0941	61	861	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Aestuariimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:30,364] [INFO] GTDB search result was written to GCF_009696315.1_ASM969631v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:30,365] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:30,370] [INFO] DFAST_QC result json was written to GCF_009696315.1_ASM969631v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:30,370] [INFO] DFAST_QC completed!
[2024-01-24 13:19:30,371] [INFO] Total running time: 0h1m1s