[2024-01-24 13:58:10,248] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:10,250] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:10,250] [INFO] DQC Reference Directory: /var/lib/cwl/stg2644c73c-716c-4bc6-84bf-1886b029c807/dqc_reference
[2024-01-24 13:58:11,583] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:11,584] [INFO] Task started: Prodigal
[2024-01-24 13:58:11,584] [INFO] Running command: gunzip -c /var/lib/cwl/stg704939d3-2b36-4bb7-b17b-b37cc2a10887/GCF_006475605.1_ASM647560v1_genomic.fna.gz | prodigal -d GCF_006475605.1_ASM647560v1_genomic.fna/cds.fna -a GCF_006475605.1_ASM647560v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:20,683] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:20,684] [INFO] Task started: HMMsearch
[2024-01-24 13:58:20,684] [INFO] Running command: hmmsearch --tblout GCF_006475605.1_ASM647560v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2644c73c-716c-4bc6-84bf-1886b029c807/dqc_reference/reference_markers.hmm GCF_006475605.1_ASM647560v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:20,939] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:20,940] [INFO] Found 6/6 markers.
[2024-01-24 13:58:20,969] [INFO] Query marker FASTA was written to GCF_006475605.1_ASM647560v1_genomic.fna/markers.fasta
[2024-01-24 13:58:20,969] [INFO] Task started: Blastn
[2024-01-24 13:58:20,970] [INFO] Running command: blastn -query GCF_006475605.1_ASM647560v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2644c73c-716c-4bc6-84bf-1886b029c807/dqc_reference/reference_markers.fasta -out GCF_006475605.1_ASM647560v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:21,779] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:21,782] [INFO] Selected 23 target genomes.
[2024-01-24 13:58:21,782] [INFO] Target genome list was writen to GCF_006475605.1_ASM647560v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:21,821] [INFO] Task started: fastANI
[2024-01-24 13:58:21,821] [INFO] Running command: fastANI --query /var/lib/cwl/stg704939d3-2b36-4bb7-b17b-b37cc2a10887/GCF_006475605.1_ASM647560v1_genomic.fna.gz --refList GCF_006475605.1_ASM647560v1_genomic.fna/target_genomes.txt --output GCF_006475605.1_ASM647560v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:40,639] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:40,639] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2644c73c-716c-4bc6-84bf-1886b029c807/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:40,640] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2644c73c-716c-4bc6-84bf-1886b029c807/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:40,652] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:40,653] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:40,653] [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
Asticcacaulis tiandongensis	strain=3.1105	GCA_006475605.1	2565365	2565365	type	True	100.0	1063	1064	95	conclusive
Asticcacaulis excentricus	strain=CB 48	GCA_000175215.2	78587	78587	type	True	78.187	345	1064	95	below_threshold
Asticcacaulis endophyticus	strain=KCTC 32296	GCA_014652575.1	1395890	1395890	type	True	78.0607	336	1064	95	below_threshold
Asticcacaulis benevestitus	strain=DSM 16100	GCA_000376105.1	347481	347481	type	True	77.5802	253	1064	95	below_threshold
Asticcacaulis benevestitus	strain=DSM 16100	GCA_000495775.1	347481	347481	type	True	77.5263	255	1064	95	below_threshold
Asticcacaulis taihuensis	strain=CGMCC 1.3431	GCA_900100255.1	260084	260084	type	True	77.4085	262	1064	95	below_threshold
Asticcacaulis biprosthecium	strain=C19	GCA_000204015.1	76891	76891	type	True	77.1182	224	1064	95	below_threshold
Caulobacter flavus	strain=RHGG3	GCA_003722335.1	1679497	1679497	type	True	76.6241	99	1064	95	below_threshold
Brevundimonas bullata	strain=HAMBI_262	GCA_003350205.1	13160	13160	type	True	76.3338	94	1064	95	below_threshold
Caulobacter zeae	strain=410	GCA_002858925.1	2055137	2055137	type	True	76.1432	111	1064	95	below_threshold
Roseibium suaedae	strain=DSM 22153	GCA_900142725.1	735517	735517	type	True	75.9458	52	1064	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:40,654] [INFO] DFAST Taxonomy check result was written to GCF_006475605.1_ASM647560v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:40,655] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:40,655] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:40,655] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2644c73c-716c-4bc6-84bf-1886b029c807/dqc_reference/checkm_data
[2024-01-24 13:58:40,656] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:40,695] [INFO] Task started: CheckM
[2024-01-24 13:58:40,695] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006475605.1_ASM647560v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006475605.1_ASM647560v1_genomic.fna/checkm_input GCF_006475605.1_ASM647560v1_genomic.fna/checkm_result
[2024-01-24 13:59:12,382] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:12,384] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:12,411] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:12,411] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:12,412] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006475605.1_ASM647560v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:12,413] [INFO] Task started: Blastn
[2024-01-24 13:59:12,413] [INFO] Running command: blastn -query GCF_006475605.1_ASM647560v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2644c73c-716c-4bc6-84bf-1886b029c807/dqc_reference/reference_markers_gtdb.fasta -out GCF_006475605.1_ASM647560v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:13,697] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:13,700] [INFO] Selected 13 target genomes.
[2024-01-24 13:59:13,700] [INFO] Target genome list was writen to GCF_006475605.1_ASM647560v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:13,753] [INFO] Task started: fastANI
[2024-01-24 13:59:13,753] [INFO] Running command: fastANI --query /var/lib/cwl/stg704939d3-2b36-4bb7-b17b-b37cc2a10887/GCF_006475605.1_ASM647560v1_genomic.fna.gz --refList GCF_006475605.1_ASM647560v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006475605.1_ASM647560v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:22,912] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:22,927] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:22,927] [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_006475605.1	s__Asticcacaulis tiandongensis	100.0	1063	1064	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Asticcacaulis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003966695.1	s__Asticcacaulis excentricus_A	78.3568	399	1064	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Asticcacaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003053985.1	s__Asticcacaulis sp003053985	78.3009	415	1064	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Asticcacaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000495855.1	s__Asticcacaulis sp000495855	78.1875	406	1064	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Asticcacaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000175215.2	s__Asticcacaulis excentricus	78.1594	347	1064	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Asticcacaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652575.1	s__Asticcacaulis endophyticus	78.0607	336	1064	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Asticcacaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002342035.1	s__Asticcacaulis sp002342035	77.9164	329	1064	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Asticcacaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000376105.1	s__Asticcacaulis benevestitus	77.5799	253	1064	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Asticcacaulis	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900100255.1	s__Asticcacaulis taihuensis	77.3971	263	1064	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Asticcacaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873225.1	s__Asticcacaulis sp014873225	77.3554	242	1064	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Asticcacaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017875235.1	s__Asticcacaulis solisilvae	77.2261	240	1064	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Asticcacaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000495835.1	s__Asticcacaulis sp000495835	76.9482	191	1064	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Asticcacaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018826885.1	s__Brevundimonas sp018826885	76.1446	71	1064	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:22,929] [INFO] GTDB search result was written to GCF_006475605.1_ASM647560v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:22,929] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:22,933] [INFO] DFAST_QC result json was written to GCF_006475605.1_ASM647560v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:22,933] [INFO] DFAST_QC completed!
[2024-01-24 13:59:22,933] [INFO] Total running time: 0h1m13s