[2024-01-24 12:05:26,612] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:05:26,616] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:05:26,616] [INFO] DQC Reference Directory: /var/lib/cwl/stg6f335a52-40dc-463d-84c1-056504808d3d/dqc_reference
[2024-01-24 12:05:30,677] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:05:30,678] [INFO] Task started: Prodigal
[2024-01-24 12:05:30,679] [INFO] Running command: gunzip -c /var/lib/cwl/stg47570b4c-3df7-40e2-8c32-60ea7f7057a0/GCF_004919685.1_ASM491968v1_genomic.fna.gz | prodigal -d GCF_004919685.1_ASM491968v1_genomic.fna/cds.fna -a GCF_004919685.1_ASM491968v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:05:56,050] [INFO] Task succeeded: Prodigal
[2024-01-24 12:05:56,050] [INFO] Task started: HMMsearch
[2024-01-24 12:05:56,051] [INFO] Running command: hmmsearch --tblout GCF_004919685.1_ASM491968v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6f335a52-40dc-463d-84c1-056504808d3d/dqc_reference/reference_markers.hmm GCF_004919685.1_ASM491968v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:05:56,390] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:05:56,392] [INFO] Found 6/6 markers.
[2024-01-24 12:05:56,459] [INFO] Query marker FASTA was written to GCF_004919685.1_ASM491968v1_genomic.fna/markers.fasta
[2024-01-24 12:05:56,460] [INFO] Task started: Blastn
[2024-01-24 12:05:56,460] [INFO] Running command: blastn -query GCF_004919685.1_ASM491968v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f335a52-40dc-463d-84c1-056504808d3d/dqc_reference/reference_markers.fasta -out GCF_004919685.1_ASM491968v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:05:57,525] [INFO] Task succeeded: Blastn
[2024-01-24 12:05:57,530] [INFO] Selected 14 target genomes.
[2024-01-24 12:05:57,530] [INFO] Target genome list was writen to GCF_004919685.1_ASM491968v1_genomic.fna/target_genomes.txt
[2024-01-24 12:05:57,536] [INFO] Task started: fastANI
[2024-01-24 12:05:57,536] [INFO] Running command: fastANI --query /var/lib/cwl/stg47570b4c-3df7-40e2-8c32-60ea7f7057a0/GCF_004919685.1_ASM491968v1_genomic.fna.gz --refList GCF_004919685.1_ASM491968v1_genomic.fna/target_genomes.txt --output GCF_004919685.1_ASM491968v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:23,984] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:23,984] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6f335a52-40dc-463d-84c1-056504808d3d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:23,985] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6f335a52-40dc-463d-84c1-056504808d3d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:23,996] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:23,996] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:23,997] [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
Mesorhizobium norvegicum	strain=10.2.2	GCA_004919685.1	1085774	1085774	type	True	100.0	2653	2662	95	conclusive
Mesorhizobium loti	strain=DSM 2626	GCA_003148495.1	381	381	suspected-type	True	93.7863	1909	2662	95	below_threshold
Mesorhizobium sangaii	strain=DSM 100039	GCA_014207355.1	505389	505389	type	True	89.7662	1694	2662	95	below_threshold
Mesorhizobium sophorae	strain=ICMP 19535	GCA_002270415.1	1300294	1300294	type	True	89.6868	1691	2662	95	below_threshold
Mesorhizobium qingshengii	strain=CGMCC 1.12097	GCA_900103325.1	1165689	1165689	type	True	89.3672	1624	2662	95	below_threshold
Mesorhizobium erdmanii	strain=USDA 3471	GCA_000472705.1	1777866	1777866	type	True	88.0563	1704	2662	95	below_threshold
Mesorhizobium carmichaelinearum	strain=ICMP 18942	GCA_900199455.1	1208188	1208188	type	True	88.0426	1836	2662	95	below_threshold
Mesorhizobium jarvisii	strain=LMG 28313	GCA_003601985.1	1777867	1777867	type	True	87.9905	1629	2662	95	below_threshold
Mesorhizobium opportunistum	strain=WSM2075	GCA_000176035.2	593909	593909	type	True	87.9107	1667	2662	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	86.432	1634	2662	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	85.4554	1398	2662	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	79.1347	662	2662	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	79.0604	737	2662	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	79.049	739	2662	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:23,998] [INFO] DFAST Taxonomy check result was written to GCF_004919685.1_ASM491968v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:23,999] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:23,999] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:23,999] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6f335a52-40dc-463d-84c1-056504808d3d/dqc_reference/checkm_data
[2024-01-24 12:06:24,000] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:24,073] [INFO] Task started: CheckM
[2024-01-24 12:06:24,073] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004919685.1_ASM491968v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004919685.1_ASM491968v1_genomic.fna/checkm_input GCF_004919685.1_ASM491968v1_genomic.fna/checkm_result
[2024-01-24 12:07:34,703] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:34,704] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:34,733] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:34,734] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:34,734] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004919685.1_ASM491968v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:34,734] [INFO] Task started: Blastn
[2024-01-24 12:07:34,735] [INFO] Running command: blastn -query GCF_004919685.1_ASM491968v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f335a52-40dc-463d-84c1-056504808d3d/dqc_reference/reference_markers_gtdb.fasta -out GCF_004919685.1_ASM491968v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:36,798] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:36,805] [INFO] Selected 10 target genomes.
[2024-01-24 12:07:36,805] [INFO] Target genome list was writen to GCF_004919685.1_ASM491968v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:36,815] [INFO] Task started: fastANI
[2024-01-24 12:07:36,815] [INFO] Running command: fastANI --query /var/lib/cwl/stg47570b4c-3df7-40e2-8c32-60ea7f7057a0/GCF_004919685.1_ASM491968v1_genomic.fna.gz --refList GCF_004919685.1_ASM491968v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004919685.1_ASM491968v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:56,369] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:56,382] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:56,382] [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_004919685.1	s__Mesorhizobium norvegicum	100.0	2653	2662	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.97	99.97	0.98	0.98	2	conclusive
GCA_014189435.1	s__Mesorhizobium loti_G	93.7826	2055	2662	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148495.1	s__Mesorhizobium loti	93.7761	1910	2662	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.10	97.93	0.88	0.86	3	-
GCF_001425625.1	s__Mesorhizobium sp001425625	93.1729	1658	2662	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.21	99.21	0.90	0.90	2	-
GCF_000519305.1	s__Mesorhizobium ciceri_B	91.6577	1730	2662	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003997495.1	s__Mesorhizobium sp003997495	91.5976	1740	2662	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000502875.1	s__Mesorhizobium sp000502875	91.446	1745	2662	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.15	96.47	0.88	0.87	3	-
GCF_000185905.1	s__Mesorhizobium ciceri	91.2897	1738	2662	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.42	98.05	0.90	0.85	36	-
GCA_004017275.1	s__Mesorhizobium sp004017275	91.2805	1660	2662	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.13	97.50	0.90	0.85	4	-
GCF_003996995.1	s__Mesorhizobium sp003996995	91.0625	1399	2662	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.83	97.35	0.87	0.74	32	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:56,384] [INFO] GTDB search result was written to GCF_004919685.1_ASM491968v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:56,385] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:56,388] [INFO] DFAST_QC result json was written to GCF_004919685.1_ASM491968v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:56,388] [INFO] DFAST_QC completed!
[2024-01-24 12:07:56,389] [INFO] Total running time: 0h2m30s