[2024-01-24 13:28:44,479] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:44,481] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:44,481] [INFO] DQC Reference Directory: /var/lib/cwl/stg2b7dc78a-dfd2-48cf-a594-9007544f23d4/dqc_reference
[2024-01-24 13:28:45,840] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:45,841] [INFO] Task started: Prodigal
[2024-01-24 13:28:45,842] [INFO] Running command: gunzip -c /var/lib/cwl/stg79ab187b-c431-4572-8803-3f91b1ef1c09/GCF_000616095.1_ASM61609v1_genomic.fna.gz | prodigal -d GCF_000616095.1_ASM61609v1_genomic.fna/cds.fna -a GCF_000616095.1_ASM61609v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:55,808] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:55,808] [INFO] Task started: HMMsearch
[2024-01-24 13:28:55,809] [INFO] Running command: hmmsearch --tblout GCF_000616095.1_ASM61609v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2b7dc78a-dfd2-48cf-a594-9007544f23d4/dqc_reference/reference_markers.hmm GCF_000616095.1_ASM61609v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:56,096] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:56,098] [INFO] Found 6/6 markers.
[2024-01-24 13:28:56,135] [INFO] Query marker FASTA was written to GCF_000616095.1_ASM61609v1_genomic.fna/markers.fasta
[2024-01-24 13:28:56,135] [INFO] Task started: Blastn
[2024-01-24 13:28:56,135] [INFO] Running command: blastn -query GCF_000616095.1_ASM61609v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b7dc78a-dfd2-48cf-a594-9007544f23d4/dqc_reference/reference_markers.fasta -out GCF_000616095.1_ASM61609v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:56,938] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:56,942] [INFO] Selected 22 target genomes.
[2024-01-24 13:28:56,943] [INFO] Target genome list was writen to GCF_000616095.1_ASM61609v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:56,959] [INFO] Task started: fastANI
[2024-01-24 13:28:56,959] [INFO] Running command: fastANI --query /var/lib/cwl/stg79ab187b-c431-4572-8803-3f91b1ef1c09/GCF_000616095.1_ASM61609v1_genomic.fna.gz --refList GCF_000616095.1_ASM61609v1_genomic.fna/target_genomes.txt --output GCF_000616095.1_ASM61609v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:29:12,316] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:12,317] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2b7dc78a-dfd2-48cf-a594-9007544f23d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:29:12,317] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2b7dc78a-dfd2-48cf-a594-9007544f23d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:29:12,323] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:29:12,323] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:29:12,323] [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 glossodoripedis	strain=JCM 23214	GCA_000616095.1	418853	418853	type	True	100.0	1204	1205	95	conclusive
Sneathiella limimaris	strain=KCTC 52846	GCA_012932565.1	1964213	1964213	type	True	77.8493	226	1205	95	below_threshold
Sneathiella aquimaris	strain=216LB-ZA1-12	GCA_012720095.1	2599305	2599305	type	True	76.9086	158	1205	95	below_threshold
Sneathiella litorea	strain=DP05	GCA_009882915.1	2606216	2606216	type	True	76.4355	69	1205	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:29:12,325] [INFO] DFAST Taxonomy check result was written to GCF_000616095.1_ASM61609v1_genomic.fna/tc_result.tsv
[2024-01-24 13:29:12,326] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:29:12,326] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:29:12,326] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2b7dc78a-dfd2-48cf-a594-9007544f23d4/dqc_reference/checkm_data
[2024-01-24 13:29:12,327] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:29:12,370] [INFO] Task started: CheckM
[2024-01-24 13:29:12,370] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000616095.1_ASM61609v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000616095.1_ASM61609v1_genomic.fna/checkm_input GCF_000616095.1_ASM61609v1_genomic.fna/checkm_result
[2024-01-24 13:29:48,037] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:48,038] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.48%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:48,070] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:48,070] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:48,071] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000616095.1_ASM61609v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:48,071] [INFO] Task started: Blastn
[2024-01-24 13:29:48,071] [INFO] Running command: blastn -query GCF_000616095.1_ASM61609v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b7dc78a-dfd2-48cf-a594-9007544f23d4/dqc_reference/reference_markers_gtdb.fasta -out GCF_000616095.1_ASM61609v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:49,108] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:49,112] [INFO] Selected 20 target genomes.
[2024-01-24 13:29:49,112] [INFO] Target genome list was writen to GCF_000616095.1_ASM61609v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:49,155] [INFO] Task started: fastANI
[2024-01-24 13:29:49,155] [INFO] Running command: fastANI --query /var/lib/cwl/stg79ab187b-c431-4572-8803-3f91b1ef1c09/GCF_000616095.1_ASM61609v1_genomic.fna.gz --refList GCF_000616095.1_ASM61609v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000616095.1_ASM61609v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:30:02,175] [INFO] Task succeeded: fastANI
[2024-01-24 13:30:02,188] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:30:02,188] [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_000616095.1	s__Sneathiella glossodoripedis	100.0	1204	1205	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_012932565.1	s__Sneathiella limimaris	77.8492	226	1205	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015143595.1	s__Sneathiella sp015143595	77.0906	158	1205	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002163135.1	s__Sneathiella sp002163135	77.0672	160	1205	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012720095.1	s__Sneathiella aquimaris	76.9086	158	1205	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002428885.1	s__Sneathiella sp002428885	76.6241	113	1205	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002706985.1	s__Sneathiella sp002706985	76.5484	59	1205	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	99.70	99.70	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:30:02,190] [INFO] GTDB search result was written to GCF_000616095.1_ASM61609v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:30:02,190] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:30:02,193] [INFO] DFAST_QC result json was written to GCF_000616095.1_ASM61609v1_genomic.fna/dqc_result.json
[2024-01-24 13:30:02,193] [INFO] DFAST_QC completed!
[2024-01-24 13:30:02,193] [INFO] Total running time: 0h1m18s