[2024-01-24 12:22:13,280] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:13,282] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:13,282] [INFO] DQC Reference Directory: /var/lib/cwl/stg14e3aa4a-c340-46d1-8017-f25fe439becb/dqc_reference
[2024-01-24 12:22:14,783] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:14,784] [INFO] Task started: Prodigal
[2024-01-24 12:22:14,784] [INFO] Running command: gunzip -c /var/lib/cwl/stg155d43df-b451-4bfb-a8b2-c9e3f9c2c60d/GCF_007830545.1_ASM783054v1_genomic.fna.gz | prodigal -d GCF_007830545.1_ASM783054v1_genomic.fna/cds.fna -a GCF_007830545.1_ASM783054v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:30,202] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:30,202] [INFO] Task started: HMMsearch
[2024-01-24 12:22:30,202] [INFO] Running command: hmmsearch --tblout GCF_007830545.1_ASM783054v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg14e3aa4a-c340-46d1-8017-f25fe439becb/dqc_reference/reference_markers.hmm GCF_007830545.1_ASM783054v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:30,600] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:30,601] [INFO] Found 6/6 markers.
[2024-01-24 12:22:30,667] [INFO] Query marker FASTA was written to GCF_007830545.1_ASM783054v1_genomic.fna/markers.fasta
[2024-01-24 12:22:30,668] [INFO] Task started: Blastn
[2024-01-24 12:22:30,668] [INFO] Running command: blastn -query GCF_007830545.1_ASM783054v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg14e3aa4a-c340-46d1-8017-f25fe439becb/dqc_reference/reference_markers.fasta -out GCF_007830545.1_ASM783054v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:31,559] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:31,562] [INFO] Selected 20 target genomes.
[2024-01-24 12:22:31,562] [INFO] Target genome list was writen to GCF_007830545.1_ASM783054v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:31,571] [INFO] Task started: fastANI
[2024-01-24 12:22:31,572] [INFO] Running command: fastANI --query /var/lib/cwl/stg155d43df-b451-4bfb-a8b2-c9e3f9c2c60d/GCF_007830545.1_ASM783054v1_genomic.fna.gz --refList GCF_007830545.1_ASM783054v1_genomic.fna/target_genomes.txt --output GCF_007830545.1_ASM783054v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:47,873] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:47,874] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg14e3aa4a-c340-46d1-8017-f25fe439becb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:47,875] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg14e3aa4a-c340-46d1-8017-f25fe439becb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:47,888] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:22:47,888] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:47,888] [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
Roseibium hamelinense	strain=ATCC BAA-252	GCA_007830545.1	150831	150831	type	True	100.0	1559	1559	95	conclusive
Roseibium hamelinense	strain=NBRC 16783	GCA_009711505.1	150831	150831	type	True	99.9609	1521	1559	95	conclusive
Roseibium denhamense	strain=JCM 10543	GCA_009711415.1	76305	76305	type	True	79.3753	341	1559	95	below_threshold
Roseibium alexandrii	strain=DFL-11	GCA_000158095.2	388408	388408	type	True	78.5257	323	1559	95	below_threshold
Roseibium aestuarii	strain=SYSU M00256-3	GCA_008477545.1	2600299	2600299	type	True	78.0134	244	1559	95	below_threshold
Roseibium aggregatum	strain=IAM 12614	GCA_000168975.1	187304	187304	suspected-type	True	77.9458	322	1559	95	below_threshold
Roseibium sediminis	strain=KCTC 52373	GCA_008711325.1	1775174	1775174	type	True	77.8271	270	1559	95	below_threshold
Roseibium limicola	strain=CAU 1637	GCA_017313085.1	2816037	2816037	type	True	77.7451	208	1559	95	below_threshold
Roseibium polysiphoniae	strain=KACC 19711	GCA_014842925.1	2571221	2571221	type	True	77.7381	260	1559	95	below_threshold
Roseibium marinum	strain=DSM 17023	GCA_002906165.1	281252	281252	type	True	77.6797	293	1559	95	below_threshold
Pannonibacter phragmitetus	strain=NCTC13350	GCA_900454465.1	121719	121719	suspected-type	True	77.4303	205	1559	95	below_threshold
Pannonibacter indicus	strain=DSM 23407	GCA_001418225.1	466044	466044	type	True	77.4278	195	1559	95	below_threshold
Pannonibacter phragmitetus	strain=DSM 14782	GCA_000382365.1	121719	121719	suspected-type	True	77.3626	203	1559	95	below_threshold
Neorhizobium galegae	strain=HAMBI 540	GCA_000731315.1	399	399	suspected-type	True	76.5171	84	1559	95	below_threshold
Rhizobium populisoli	strain=XQZ8	GCA_019430945.1	2859785	2859785	type	True	76.3829	82	1559	95	below_threshold
Kaustia mangrovi	strain=R1DC25	GCA_015482775.1	2593653	2593653	type	True	75.9449	97	1559	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:47,891] [INFO] DFAST Taxonomy check result was written to GCF_007830545.1_ASM783054v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:47,892] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:47,892] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:47,892] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg14e3aa4a-c340-46d1-8017-f25fe439becb/dqc_reference/checkm_data
[2024-01-24 12:22:47,894] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:47,943] [INFO] Task started: CheckM
[2024-01-24 12:22:47,943] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007830545.1_ASM783054v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007830545.1_ASM783054v1_genomic.fna/checkm_input GCF_007830545.1_ASM783054v1_genomic.fna/checkm_result
[2024-01-24 12:23:35,603] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:35,604] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:35,627] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:35,627] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:35,628] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007830545.1_ASM783054v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:35,628] [INFO] Task started: Blastn
[2024-01-24 12:23:35,628] [INFO] Running command: blastn -query GCF_007830545.1_ASM783054v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg14e3aa4a-c340-46d1-8017-f25fe439becb/dqc_reference/reference_markers_gtdb.fasta -out GCF_007830545.1_ASM783054v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:37,100] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:37,104] [INFO] Selected 19 target genomes.
[2024-01-24 12:23:37,104] [INFO] Target genome list was writen to GCF_007830545.1_ASM783054v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:37,119] [INFO] Task started: fastANI
[2024-01-24 12:23:37,119] [INFO] Running command: fastANI --query /var/lib/cwl/stg155d43df-b451-4bfb-a8b2-c9e3f9c2c60d/GCF_007830545.1_ASM783054v1_genomic.fna.gz --refList GCF_007830545.1_ASM783054v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007830545.1_ASM783054v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:54,002] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:54,021] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:54,022] [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_007830545.1	s__Roseibium hamelinense	100.0	1559	1559	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_009711415.1	s__Roseibium denhamense	79.3753	341	1559	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142725.1	s__Roseibium suaedae	78.0626	267	1559	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002237595.1	s__Roseibium sp002237595	78.0169	365	1559	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000168975.1	s__Roseibium aggregatum	77.9458	322	1559	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008107755.1	s__Roseibium sp008107755	77.8207	264	1559	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001999245.1	s__Roseibium aggregatum_A	77.8066	315	1559	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	97.61	96.85	0.93	0.89	16	-
GCF_008107695.1	s__Roseibium sp008107695	77.7872	296	1559	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014692675.1	s__Roseibium aggregatum_C	77.7516	328	1559	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017643925.1	s__Roseibium sp017643925	77.7302	272	1559	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_017309185.1	s__Roseibium aggregatum_B	77.7153	310	1559	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009915765.1	s__Pannonibacter sp009915765	77.5049	208	1559	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pannonibacter	95.0	98.76	98.76	0.96	0.96	2	-
GCF_001418225.1	s__Pannonibacter indicus	77.4278	195	1559	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pannonibacter	95.0	96.01	95.55	0.94	0.89	12	-
GCF_000382365.1	s__Pannonibacter phragmitetus	77.3626	203	1559	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pannonibacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001404055.1	s__Roseibium album_A	77.2324	228	1559	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424065.1	s__Pararhizobium sp001424065	76.6143	67	1559	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium	95.0	99.05	98.24	0.93	0.91	3	-
GCF_014237835.1	s__Allorhizobium sp014237835	76.4473	85	1559	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003425685.1	s__Neorhizobium sp003425685	76.1247	86	1559	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007693435.1	s__Salinarimonas sp007693435	75.9193	54	1559	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Salinarimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:54,024] [INFO] GTDB search result was written to GCF_007830545.1_ASM783054v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:54,025] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:54,029] [INFO] DFAST_QC result json was written to GCF_007830545.1_ASM783054v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:54,029] [INFO] DFAST_QC completed!
[2024-01-24 12:23:54,029] [INFO] Total running time: 0h1m41s