[2024-01-24 14:30:30,170] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:30,173] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:30,174] [INFO] DQC Reference Directory: /var/lib/cwl/stg7db3038f-8c4c-47da-9264-4bbf21674d66/dqc_reference
[2024-01-24 14:30:33,671] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:33,672] [INFO] Task started: Prodigal
[2024-01-24 14:30:33,672] [INFO] Running command: gunzip -c /var/lib/cwl/stga76b0f0c-2b65-414c-9c8a-81a01ff5bf28/GCF_009882915.1_ASM988291v1_genomic.fna.gz | prodigal -d GCF_009882915.1_ASM988291v1_genomic.fna/cds.fna -a GCF_009882915.1_ASM988291v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:30:44,471] [INFO] Task succeeded: Prodigal
[2024-01-24 14:30:44,471] [INFO] Task started: HMMsearch
[2024-01-24 14:30:44,471] [INFO] Running command: hmmsearch --tblout GCF_009882915.1_ASM988291v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7db3038f-8c4c-47da-9264-4bbf21674d66/dqc_reference/reference_markers.hmm GCF_009882915.1_ASM988291v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:30:44,759] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:30:44,760] [INFO] Found 6/6 markers.
[2024-01-24 14:30:44,795] [INFO] Query marker FASTA was written to GCF_009882915.1_ASM988291v1_genomic.fna/markers.fasta
[2024-01-24 14:30:44,796] [INFO] Task started: Blastn
[2024-01-24 14:30:44,796] [INFO] Running command: blastn -query GCF_009882915.1_ASM988291v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7db3038f-8c4c-47da-9264-4bbf21674d66/dqc_reference/reference_markers.fasta -out GCF_009882915.1_ASM988291v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:45,574] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:45,578] [INFO] Selected 15 target genomes.
[2024-01-24 14:30:45,579] [INFO] Target genome list was writen to GCF_009882915.1_ASM988291v1_genomic.fna/target_genomes.txt
[2024-01-24 14:30:45,596] [INFO] Task started: fastANI
[2024-01-24 14:30:45,596] [INFO] Running command: fastANI --query /var/lib/cwl/stga76b0f0c-2b65-414c-9c8a-81a01ff5bf28/GCF_009882915.1_ASM988291v1_genomic.fna.gz --refList GCF_009882915.1_ASM988291v1_genomic.fna/target_genomes.txt --output GCF_009882915.1_ASM988291v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:30:56,129] [INFO] Task succeeded: fastANI
[2024-01-24 14:30:56,130] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7db3038f-8c4c-47da-9264-4bbf21674d66/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:30:56,130] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7db3038f-8c4c-47da-9264-4bbf21674d66/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:30:56,136] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:30:56,137] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:30:56,137] [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
Sneathiella litorea	strain=DP05	GCA_009882915.1	2606216	2606216	type	True	100.0	1242	1242	95	conclusive
Sneathiella sedimenti	strain=CAU 1612	GCA_017313765.1	2816034	2816034	type	True	83.4379	862	1242	95	below_threshold
Sneathiella chungangensis	strain=KCTC32476	GCA_012720125.1	1418234	1418234	type	True	80.1432	568	1242	95	below_threshold
Sneathiella chungangensis	strain=KCTC 32476	GCA_009882935.1	1418234	1418234	type	True	80.1144	586	1242	95	below_threshold
Sneathiella chinensis	strain=LMG23452	GCA_012720115.1	349750	349750	type	True	76.8742	152	1242	95	below_threshold
Sneathiella aquimaris	strain=216LB-ZA1-12	GCA_012720095.1	2599305	2599305	type	True	76.2043	84	1242	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:30:56,138] [INFO] DFAST Taxonomy check result was written to GCF_009882915.1_ASM988291v1_genomic.fna/tc_result.tsv
[2024-01-24 14:30:56,139] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:30:56,139] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:30:56,139] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7db3038f-8c4c-47da-9264-4bbf21674d66/dqc_reference/checkm_data
[2024-01-24 14:30:56,140] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:30:56,177] [INFO] Task started: CheckM
[2024-01-24 14:30:56,177] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009882915.1_ASM988291v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009882915.1_ASM988291v1_genomic.fna/checkm_input GCF_009882915.1_ASM988291v1_genomic.fna/checkm_result
[2024-01-24 14:31:33,911] [INFO] Task succeeded: CheckM
[2024-01-24 14:31:33,912] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:31:33,949] [INFO] ===== Completeness check finished =====
[2024-01-24 14:31:33,950] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:31:33,950] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009882915.1_ASM988291v1_genomic.fna/markers.fasta)
[2024-01-24 14:31:33,951] [INFO] Task started: Blastn
[2024-01-24 14:31:33,951] [INFO] Running command: blastn -query GCF_009882915.1_ASM988291v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7db3038f-8c4c-47da-9264-4bbf21674d66/dqc_reference/reference_markers_gtdb.fasta -out GCF_009882915.1_ASM988291v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:35,268] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:35,272] [INFO] Selected 10 target genomes.
[2024-01-24 14:31:35,272] [INFO] Target genome list was writen to GCF_009882915.1_ASM988291v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:31:35,298] [INFO] Task started: fastANI
[2024-01-24 14:31:35,298] [INFO] Running command: fastANI --query /var/lib/cwl/stga76b0f0c-2b65-414c-9c8a-81a01ff5bf28/GCF_009882915.1_ASM988291v1_genomic.fna.gz --refList GCF_009882915.1_ASM988291v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009882915.1_ASM988291v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:31:42,359] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:42,367] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:31:42,367] [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_009882915.1	s__Sneathiella litorea	100.0	1242	1242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017313765.1	s__Sneathiella sp017313765	83.4301	863	1242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009882935.1	s__Sneathiella chungangensis	80.1202	586	1242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	99.99	99.99	1.00	1.00	2	-
GCA_002706985.1	s__Sneathiella sp002706985	79.53	453	1242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	99.70	99.70	0.85	0.85	2	-
GCA_002694385.1	s__Sneathiella sp002694385	78.1623	407	1242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	95.34	95.31	0.92	0.91	3	-
GCA_006226265.1	s__Sneathiella sp006226265	77.5635	226	1242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002732675.1	s__Sneathiella sp002732675	77.0951	123	1242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017643685.1	s__Sneathiella sp017643685	76.2353	68	1242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:31:42,369] [INFO] GTDB search result was written to GCF_009882915.1_ASM988291v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:31:42,370] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:31:42,374] [INFO] DFAST_QC result json was written to GCF_009882915.1_ASM988291v1_genomic.fna/dqc_result.json
[2024-01-24 14:31:42,375] [INFO] DFAST_QC completed!
[2024-01-24 14:31:42,375] [INFO] Total running time: 0h1m12s