[2024-01-25 18:48:35,449] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:48:35,452] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:48:35,452] [INFO] DQC Reference Directory: /var/lib/cwl/stgef9b536a-4165-4c90-b4f6-6783dac645e2/dqc_reference
[2024-01-25 18:48:36,751] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:48:36,752] [INFO] Task started: Prodigal
[2024-01-25 18:48:36,752] [INFO] Running command: gunzip -c /var/lib/cwl/stga70357a1-d66c-43d2-8a62-87484d6e4b83/GCF_014640215.1_ASM1464021v1_genomic.fna.gz | prodigal -d GCF_014640215.1_ASM1464021v1_genomic.fna/cds.fna -a GCF_014640215.1_ASM1464021v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:48:55,508] [INFO] Task succeeded: Prodigal
[2024-01-25 18:48:55,508] [INFO] Task started: HMMsearch
[2024-01-25 18:48:55,508] [INFO] Running command: hmmsearch --tblout GCF_014640215.1_ASM1464021v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgef9b536a-4165-4c90-b4f6-6783dac645e2/dqc_reference/reference_markers.hmm GCF_014640215.1_ASM1464021v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:48:55,777] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:48:55,781] [INFO] Found 6/6 markers.
[2024-01-25 18:48:55,830] [INFO] Query marker FASTA was written to GCF_014640215.1_ASM1464021v1_genomic.fna/markers.fasta
[2024-01-25 18:48:55,831] [INFO] Task started: Blastn
[2024-01-25 18:48:55,831] [INFO] Running command: blastn -query GCF_014640215.1_ASM1464021v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgef9b536a-4165-4c90-b4f6-6783dac645e2/dqc_reference/reference_markers.fasta -out GCF_014640215.1_ASM1464021v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:48:56,631] [INFO] Task succeeded: Blastn
[2024-01-25 18:48:56,634] [INFO] Selected 12 target genomes.
[2024-01-25 18:48:56,634] [INFO] Target genome list was writen to GCF_014640215.1_ASM1464021v1_genomic.fna/target_genomes.txt
[2024-01-25 18:48:56,666] [INFO] Task started: fastANI
[2024-01-25 18:48:56,666] [INFO] Running command: fastANI --query /var/lib/cwl/stga70357a1-d66c-43d2-8a62-87484d6e4b83/GCF_014640215.1_ASM1464021v1_genomic.fna.gz --refList GCF_014640215.1_ASM1464021v1_genomic.fna/target_genomes.txt --output GCF_014640215.1_ASM1464021v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:49:09,081] [INFO] Task succeeded: fastANI
[2024-01-25 18:49:09,081] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgef9b536a-4165-4c90-b4f6-6783dac645e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:49:09,081] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgef9b536a-4165-4c90-b4f6-6783dac645e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:49:09,090] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:49:09,090] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:49:09,090] [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
Niveispirillum cyanobacteriorum	strain=CGMCC 1.12958	GCA_014640215.1	1612173	1612173	type	True	100.0	1980	1980	95	conclusive
Niveispirillum cyanobacteriorum	strain=TH16	GCA_002868735.1	1612173	1612173	type	True	99.9982	1972	1980	95	conclusive
Niveispirillum lacus	strain=1-14	GCA_002251795.1	1981099	1981099	type	True	84.8442	1178	1980	95	below_threshold
Niveispirillum irakense	strain=DSM 11586	GCA_000429645.1	34011	34011	type	True	81.027	901	1980	95	below_threshold
Nitrospirillum iridis	strain=DSM 22198	GCA_014205765.1	765888	765888	type	True	77.8528	502	1980	95	below_threshold
Azospirillum melinis	strain=TMCY 0552	GCA_017876055.1	328839	328839	type	True	77.073	380	1980	95	below_threshold
Roseomonas ludipueritiae	strain=DSM 14915	GCA_014490445.1	198093	198093	type	True	76.4539	191	1980	95	below_threshold
Xanthobacter agilis	strain=LMG 16336	GCA_021730435.1	47492	47492	type	True	76.2005	148	1980	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	76.0996	81	1980	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	76.0732	203	1980	95	below_threshold
Sphingomicrobium aestuariivivum	strain=KCTC 42286	GCA_024721585.1	1582356	1582356	type	True	75.9159	66	1980	95	below_threshold
Sphingomicrobium aestuariivivum	strain=KCTC 42286	GCA_022953075.1	1582356	1582356	type	True	75.9081	68	1980	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:49:09,092] [INFO] DFAST Taxonomy check result was written to GCF_014640215.1_ASM1464021v1_genomic.fna/tc_result.tsv
[2024-01-25 18:49:09,092] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:49:09,093] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:49:09,093] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgef9b536a-4165-4c90-b4f6-6783dac645e2/dqc_reference/checkm_data
[2024-01-25 18:49:09,094] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:49:09,151] [INFO] Task started: CheckM
[2024-01-25 18:49:09,151] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014640215.1_ASM1464021v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014640215.1_ASM1464021v1_genomic.fna/checkm_input GCF_014640215.1_ASM1464021v1_genomic.fna/checkm_result
[2024-01-25 18:50:03,349] [INFO] Task succeeded: CheckM
[2024-01-25 18:50:03,350] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:50:03,377] [INFO] ===== Completeness check finished =====
[2024-01-25 18:50:03,377] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:50:03,378] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014640215.1_ASM1464021v1_genomic.fna/markers.fasta)
[2024-01-25 18:50:03,378] [INFO] Task started: Blastn
[2024-01-25 18:50:03,378] [INFO] Running command: blastn -query GCF_014640215.1_ASM1464021v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgef9b536a-4165-4c90-b4f6-6783dac645e2/dqc_reference/reference_markers_gtdb.fasta -out GCF_014640215.1_ASM1464021v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:50:04,928] [INFO] Task succeeded: Blastn
[2024-01-25 18:50:04,931] [INFO] Selected 7 target genomes.
[2024-01-25 18:50:04,931] [INFO] Target genome list was writen to GCF_014640215.1_ASM1464021v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:50:04,941] [INFO] Task started: fastANI
[2024-01-25 18:50:04,941] [INFO] Running command: fastANI --query /var/lib/cwl/stga70357a1-d66c-43d2-8a62-87484d6e4b83/GCF_014640215.1_ASM1464021v1_genomic.fna.gz --refList GCF_014640215.1_ASM1464021v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014640215.1_ASM1464021v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:50:15,290] [INFO] Task succeeded: fastANI
[2024-01-25 18:50:15,301] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:50:15,302] [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_002868735.1	s__Niveispirillum cyanobacteriorum	99.9982	1972	1980	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Niveispirillum	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_001296005.1	s__Niveispirillum sp001296005	92.1582	1655	1980	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Niveispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017996735.1	s__Niveispirillum sp017996735	86.1183	1330	1980	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Niveispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002251795.1	s__Niveispirillum lacus	84.8488	1177	1980	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Niveispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188385.1	s__Niveispirillum sp900188385	81.047	952	1980	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Niveispirillum	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000429645.1	s__Niveispirillum irakense	81.01	903	1980	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Niveispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009495745.1	s__Niveispirillum sp009495745	80.8583	920	1980	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Niveispirillum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:50:15,303] [INFO] GTDB search result was written to GCF_014640215.1_ASM1464021v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:50:15,303] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:50:15,306] [INFO] DFAST_QC result json was written to GCF_014640215.1_ASM1464021v1_genomic.fna/dqc_result.json
[2024-01-25 18:50:15,306] [INFO] DFAST_QC completed!
[2024-01-25 18:50:15,306] [INFO] Total running time: 0h1m40s