[2024-01-25 19:50:05,760] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:50:05,764] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:50:05,764] [INFO] DQC Reference Directory: /var/lib/cwl/stgcde71b45-b9ea-44ee-8bf4-7514929a0ede/dqc_reference
[2024-01-25 19:50:06,942] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:50:06,942] [INFO] Task started: Prodigal
[2024-01-25 19:50:06,942] [INFO] Running command: gunzip -c /var/lib/cwl/stga949073f-9d1c-49f4-b632-103de2d5e046/GCF_000381065.1_ASM38106v1_genomic.fna.gz | prodigal -d GCF_000381065.1_ASM38106v1_genomic.fna/cds.fna -a GCF_000381065.1_ASM38106v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:50:15,033] [INFO] Task succeeded: Prodigal
[2024-01-25 19:50:15,034] [INFO] Task started: HMMsearch
[2024-01-25 19:50:15,034] [INFO] Running command: hmmsearch --tblout GCF_000381065.1_ASM38106v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcde71b45-b9ea-44ee-8bf4-7514929a0ede/dqc_reference/reference_markers.hmm GCF_000381065.1_ASM38106v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:50:15,276] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:50:15,277] [INFO] Found 6/6 markers.
[2024-01-25 19:50:15,310] [INFO] Query marker FASTA was written to GCF_000381065.1_ASM38106v1_genomic.fna/markers.fasta
[2024-01-25 19:50:15,310] [INFO] Task started: Blastn
[2024-01-25 19:50:15,310] [INFO] Running command: blastn -query GCF_000381065.1_ASM38106v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcde71b45-b9ea-44ee-8bf4-7514929a0ede/dqc_reference/reference_markers.fasta -out GCF_000381065.1_ASM38106v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:50:15,851] [INFO] Task succeeded: Blastn
[2024-01-25 19:50:15,853] [INFO] Selected 21 target genomes.
[2024-01-25 19:50:15,854] [INFO] Target genome list was writen to GCF_000381065.1_ASM38106v1_genomic.fna/target_genomes.txt
[2024-01-25 19:50:15,873] [INFO] Task started: fastANI
[2024-01-25 19:50:15,873] [INFO] Running command: fastANI --query /var/lib/cwl/stga949073f-9d1c-49f4-b632-103de2d5e046/GCF_000381065.1_ASM38106v1_genomic.fna.gz --refList GCF_000381065.1_ASM38106v1_genomic.fna/target_genomes.txt --output GCF_000381065.1_ASM38106v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:50:28,416] [INFO] Task succeeded: fastANI
[2024-01-25 19:50:28,417] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcde71b45-b9ea-44ee-8bf4-7514929a0ede/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:50:28,417] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcde71b45-b9ea-44ee-8bf4-7514929a0ede/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:50:28,422] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:50:28,422] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 19:50:28,423] [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
Propionispira raffinosivorans	strain=DSM 20765	GCA_000381065.1	86959	86959	type	True	100.0	1342	1348	95	inconclusive
Propionispira arboris	strain=DSM 2179	GCA_900109225.1	84035	84035	type	True	96.356	1151	1348	95	inconclusive
Pelosinus propionicus	strain=DSM 13327	GCA_900114615.1	380084	380084	type	True	76.6772	62	1348	95	below_threshold
Pectinatus brassicae	strain=DSM 24661	GCA_014201835.1	862415	862415	type	True	76.5886	69	1348	95	below_threshold
Pectinatus brassicae	strain=MB591	GCA_015732205.1	862415	862415	type	True	76.5485	75	1348	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:50:28,425] [INFO] DFAST Taxonomy check result was written to GCF_000381065.1_ASM38106v1_genomic.fna/tc_result.tsv
[2024-01-25 19:50:28,426] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:50:28,426] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:50:28,426] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcde71b45-b9ea-44ee-8bf4-7514929a0ede/dqc_reference/checkm_data
[2024-01-25 19:50:28,427] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:50:28,468] [INFO] Task started: CheckM
[2024-01-25 19:50:28,468] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000381065.1_ASM38106v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000381065.1_ASM38106v1_genomic.fna/checkm_input GCF_000381065.1_ASM38106v1_genomic.fna/checkm_result
[2024-01-25 19:50:55,941] [INFO] Task succeeded: CheckM
[2024-01-25 19:50:55,942] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:50:55,962] [INFO] ===== Completeness check finished =====
[2024-01-25 19:50:55,962] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:50:55,962] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000381065.1_ASM38106v1_genomic.fna/markers.fasta)
[2024-01-25 19:50:55,963] [INFO] Task started: Blastn
[2024-01-25 19:50:55,963] [INFO] Running command: blastn -query GCF_000381065.1_ASM38106v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcde71b45-b9ea-44ee-8bf4-7514929a0ede/dqc_reference/reference_markers_gtdb.fasta -out GCF_000381065.1_ASM38106v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:50:56,699] [INFO] Task succeeded: Blastn
[2024-01-25 19:50:56,702] [INFO] Selected 19 target genomes.
[2024-01-25 19:50:56,702] [INFO] Target genome list was writen to GCF_000381065.1_ASM38106v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:50:56,713] [INFO] Task started: fastANI
[2024-01-25 19:50:56,714] [INFO] Running command: fastANI --query /var/lib/cwl/stga949073f-9d1c-49f4-b632-103de2d5e046/GCF_000381065.1_ASM38106v1_genomic.fna.gz --refList GCF_000381065.1_ASM38106v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000381065.1_ASM38106v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:51:08,896] [INFO] Task succeeded: fastANI
[2024-01-25 19:51:08,901] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:51:08,901] [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_000381065.1	s__Propionispira raffinosivorans	100.0	1344	1348	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Propionispira	96.4486	N/A	N/A	N/A	N/A	1	conclusive
GCF_900109225.1	s__Propionispira arboris	96.3746	1149	1348	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Propionispira	96.4486	N/A	N/A	N/A	N/A	1	-
GCA_902363205.1	s__CABIZH01 sp902363205	77.2572	104	1348	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Massilibacillaceae;g__CABIZH01	95.0	97.61	97.54	0.87	0.81	4	-
GCF_000725345.1	s__Pelosinus sp000725345	76.8456	85	1348	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Propionisporales;f__Propionisporaceae;g__Pelosinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114615.1	s__Pelosinus propionicus	76.7185	62	1348	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Propionisporales;f__Propionisporaceae;g__Pelosinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201835.1	s__Pectinatus brassicae	76.5886	69	1348	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Pectinatus	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:51:08,902] [INFO] GTDB search result was written to GCF_000381065.1_ASM38106v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:51:08,903] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:51:08,905] [INFO] DFAST_QC result json was written to GCF_000381065.1_ASM38106v1_genomic.fna/dqc_result.json
[2024-01-25 19:51:08,905] [INFO] DFAST_QC completed!
[2024-01-25 19:51:08,905] [INFO] Total running time: 0h1m3s