[2024-01-24 12:05:26,619] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:05:26,622] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:05:26,622] [INFO] DQC Reference Directory: /var/lib/cwl/stgd92384a0-f26b-472b-8cab-733525452796/dqc_reference
[2024-01-24 12:05:30,678] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:05:30,679] [INFO] Task started: Prodigal
[2024-01-24 12:05:30,679] [INFO] Running command: gunzip -c /var/lib/cwl/stg0f7fafaa-b9cf-47e2-b53b-d096b1af954a/GCF_012720095.1_ASM1272009v1_genomic.fna.gz | prodigal -d GCF_012720095.1_ASM1272009v1_genomic.fna/cds.fna -a GCF_012720095.1_ASM1272009v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:05:41,595] [INFO] Task succeeded: Prodigal
[2024-01-24 12:05:41,595] [INFO] Task started: HMMsearch
[2024-01-24 12:05:41,595] [INFO] Running command: hmmsearch --tblout GCF_012720095.1_ASM1272009v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd92384a0-f26b-472b-8cab-733525452796/dqc_reference/reference_markers.hmm GCF_012720095.1_ASM1272009v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:05:41,869] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:05:41,871] [INFO] Found 6/6 markers.
[2024-01-24 12:05:41,908] [INFO] Query marker FASTA was written to GCF_012720095.1_ASM1272009v1_genomic.fna/markers.fasta
[2024-01-24 12:05:41,909] [INFO] Task started: Blastn
[2024-01-24 12:05:41,909] [INFO] Running command: blastn -query GCF_012720095.1_ASM1272009v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd92384a0-f26b-472b-8cab-733525452796/dqc_reference/reference_markers.fasta -out GCF_012720095.1_ASM1272009v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:05:42,594] [INFO] Task succeeded: Blastn
[2024-01-24 12:05:42,599] [INFO] Selected 18 target genomes.
[2024-01-24 12:05:42,599] [INFO] Target genome list was writen to GCF_012720095.1_ASM1272009v1_genomic.fna/target_genomes.txt
[2024-01-24 12:05:42,609] [INFO] Task started: fastANI
[2024-01-24 12:05:42,609] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f7fafaa-b9cf-47e2-b53b-d096b1af954a/GCF_012720095.1_ASM1272009v1_genomic.fna.gz --refList GCF_012720095.1_ASM1272009v1_genomic.fna/target_genomes.txt --output GCF_012720095.1_ASM1272009v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:05:54,473] [INFO] Task succeeded: fastANI
[2024-01-24 12:05:54,473] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd92384a0-f26b-472b-8cab-733525452796/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:05:54,474] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd92384a0-f26b-472b-8cab-733525452796/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:05:54,484] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:05:54,484] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:05:54,484] [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 aquimaris	strain=216LB-ZA1-12	GCA_012720095.1	2599305	2599305	type	True	100.0	1294	1294	95	conclusive
Sneathiella limimaris	strain=KCTC 52846	GCA_012932565.1	1964213	1964213	type	True	77.2245	157	1294	95	below_threshold
Sneathiella glossodoripedis	strain=JCM 23214	GCA_000616095.1	418853	418853	type	True	77.0757	154	1294	95	below_threshold
Sneathiella chinensis	strain=LMG23452	GCA_012720115.1	349750	349750	type	True	76.8154	164	1294	95	below_threshold
Sneathiella sedimenti	strain=CAU 1612	GCA_017313765.1	2816034	2816034	type	True	76.375	86	1294	95	below_threshold
Sneathiella litorea	strain=DP05	GCA_009882915.1	2606216	2606216	type	True	76.3647	79	1294	95	below_threshold
Sneathiella chungangensis	strain=KCTC 32476	GCA_009882935.1	1418234	1418234	type	True	76.3281	79	1294	95	below_threshold
Sneathiella chungangensis	strain=KCTC32476	GCA_012720125.1	1418234	1418234	type	True	76.2614	78	1294	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:05:54,486] [INFO] DFAST Taxonomy check result was written to GCF_012720095.1_ASM1272009v1_genomic.fna/tc_result.tsv
[2024-01-24 12:05:54,487] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:05:54,487] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:05:54,487] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd92384a0-f26b-472b-8cab-733525452796/dqc_reference/checkm_data
[2024-01-24 12:05:54,489] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:05:54,533] [INFO] Task started: CheckM
[2024-01-24 12:05:54,534] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012720095.1_ASM1272009v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012720095.1_ASM1272009v1_genomic.fna/checkm_input GCF_012720095.1_ASM1272009v1_genomic.fna/checkm_result
[2024-01-24 12:06:31,377] [INFO] Task succeeded: CheckM
[2024-01-24 12:06:31,378] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:06:31,398] [INFO] ===== Completeness check finished =====
[2024-01-24 12:06:31,398] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:06:31,399] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012720095.1_ASM1272009v1_genomic.fna/markers.fasta)
[2024-01-24 12:06:31,399] [INFO] Task started: Blastn
[2024-01-24 12:06:31,399] [INFO] Running command: blastn -query GCF_012720095.1_ASM1272009v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd92384a0-f26b-472b-8cab-733525452796/dqc_reference/reference_markers_gtdb.fasta -out GCF_012720095.1_ASM1272009v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:32,475] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:32,478] [INFO] Selected 15 target genomes.
[2024-01-24 12:06:32,478] [INFO] Target genome list was writen to GCF_012720095.1_ASM1272009v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:06:32,490] [INFO] Task started: fastANI
[2024-01-24 12:06:32,491] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f7fafaa-b9cf-47e2-b53b-d096b1af954a/GCF_012720095.1_ASM1272009v1_genomic.fna.gz --refList GCF_012720095.1_ASM1272009v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012720095.1_ASM1272009v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:06:41,177] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:41,187] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:06:41,187] [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_012720095.1	s__Sneathiella aquimaris	100.0	1294	1294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002428885.1	s__Sneathiella sp002428885	77.425	226	1294	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	77.2384	150	1294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932565.1	s__Sneathiella limimaris	77.2069	158	1294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000616095.1	s__Sneathiella glossodoripedis	77.0628	154	1294	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	76.9362	155	1294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012720115.1	s__Sneathiella chinensis	76.8305	163	1294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016765515.1	s__Sneathiella sp016765515	76.6573	91	1294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017313765.1	s__Sneathiella sp017313765	76.3753	86	1294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009882915.1	s__Sneathiella litorea	76.3647	79	1294	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	76.3281	79	1294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:06:41,189] [INFO] GTDB search result was written to GCF_012720095.1_ASM1272009v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:06:41,190] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:06:41,193] [INFO] DFAST_QC result json was written to GCF_012720095.1_ASM1272009v1_genomic.fna/dqc_result.json
[2024-01-24 12:06:41,193] [INFO] DFAST_QC completed!
[2024-01-24 12:06:41,193] [INFO] Total running time: 0h1m15s