[2024-01-24 13:09:27,802] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:27,804] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:27,804] [INFO] DQC Reference Directory: /var/lib/cwl/stgcea4de81-5e2b-4aee-8b83-0a672bf6d47f/dqc_reference
[2024-01-24 13:09:29,037] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:29,038] [INFO] Task started: Prodigal
[2024-01-24 13:09:29,038] [INFO] Running command: gunzip -c /var/lib/cwl/stg3ac3ee90-31f6-4220-bd71-d378b8ff1932/GCF_000472705.1_ASM47270v1_genomic.fna.gz | prodigal -d GCF_000472705.1_ASM47270v1_genomic.fna/cds.fna -a GCF_000472705.1_ASM47270v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:50,736] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:50,737] [INFO] Task started: HMMsearch
[2024-01-24 13:09:50,737] [INFO] Running command: hmmsearch --tblout GCF_000472705.1_ASM47270v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcea4de81-5e2b-4aee-8b83-0a672bf6d47f/dqc_reference/reference_markers.hmm GCF_000472705.1_ASM47270v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:51,151] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:51,152] [INFO] Found 6/6 markers.
[2024-01-24 13:09:51,208] [INFO] Query marker FASTA was written to GCF_000472705.1_ASM47270v1_genomic.fna/markers.fasta
[2024-01-24 13:09:51,208] [INFO] Task started: Blastn
[2024-01-24 13:09:51,208] [INFO] Running command: blastn -query GCF_000472705.1_ASM47270v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcea4de81-5e2b-4aee-8b83-0a672bf6d47f/dqc_reference/reference_markers.fasta -out GCF_000472705.1_ASM47270v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:52,225] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:52,228] [INFO] Selected 13 target genomes.
[2024-01-24 13:09:52,229] [INFO] Target genome list was writen to GCF_000472705.1_ASM47270v1_genomic.fna/target_genomes.txt
[2024-01-24 13:09:52,235] [INFO] Task started: fastANI
[2024-01-24 13:09:52,235] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ac3ee90-31f6-4220-bd71-d378b8ff1932/GCF_000472705.1_ASM47270v1_genomic.fna.gz --refList GCF_000472705.1_ASM47270v1_genomic.fna/target_genomes.txt --output GCF_000472705.1_ASM47270v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:12,947] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:12,947] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcea4de81-5e2b-4aee-8b83-0a672bf6d47f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:12,948] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcea4de81-5e2b-4aee-8b83-0a672bf6d47f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:12,959] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:10:12,959] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:12,959] [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 erdmanii	strain=USDA 3471	GCA_000472705.1	1777866	1777866	type	True	100.0	2311	2320	95	conclusive
Mesorhizobium japonicum	strain=MAFF 303099	GCA_000009625.1	2066070	2066070	type	True	90.2987	1803	2320	95	below_threshold
Mesorhizobium jarvisii	strain=ATCC 33669	GCA_013170785.1	1777867	1777867	type	True	90.2239	1796	2320	95	below_threshold
Mesorhizobium carmichaelinearum	strain=ICMP 18942	GCA_900199455.1	1208188	1208188	type	True	90.115	1816	2320	95	below_threshold
Mesorhizobium jarvisii	strain=LMG 28313	GCA_003601985.1	1777867	1777867	type	True	90.0923	1689	2320	95	below_threshold
Mesorhizobium intechi	strain=BD68	GCA_002879535.2	537601	537601	type	True	89.9158	1619	2320	95	below_threshold
Mesorhizobium opportunistum	strain=WSM2075	GCA_000176035.2	593909	593909	type	True	88.4951	1681	2320	95	below_threshold
Mesorhizobium loti	strain=DSM 2626	GCA_003148495.1	381	381	suspected-type	True	87.9799	1713	2320	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	87.4177	1607	2320	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	84.4162	1383	2320	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	79.0161	699	2320	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	79.0147	699	2320	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	78.82	675	2320	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:12,961] [INFO] DFAST Taxonomy check result was written to GCF_000472705.1_ASM47270v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:12,961] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:12,961] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:12,962] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcea4de81-5e2b-4aee-8b83-0a672bf6d47f/dqc_reference/checkm_data
[2024-01-24 13:10:12,963] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:13,026] [INFO] Task started: CheckM
[2024-01-24 13:10:13,027] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000472705.1_ASM47270v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000472705.1_ASM47270v1_genomic.fna/checkm_input GCF_000472705.1_ASM47270v1_genomic.fna/checkm_result
[2024-01-24 13:11:15,361] [INFO] Task succeeded: CheckM
[2024-01-24 13:11:15,362] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:11:15,387] [INFO] ===== Completeness check finished =====
[2024-01-24 13:11:15,387] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:11:15,387] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000472705.1_ASM47270v1_genomic.fna/markers.fasta)
[2024-01-24 13:11:15,388] [INFO] Task started: Blastn
[2024-01-24 13:11:15,388] [INFO] Running command: blastn -query GCF_000472705.1_ASM47270v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcea4de81-5e2b-4aee-8b83-0a672bf6d47f/dqc_reference/reference_markers_gtdb.fasta -out GCF_000472705.1_ASM47270v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:11:17,403] [INFO] Task succeeded: Blastn
[2024-01-24 13:11:17,407] [INFO] Selected 16 target genomes.
[2024-01-24 13:11:17,407] [INFO] Target genome list was writen to GCF_000472705.1_ASM47270v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:11:17,421] [INFO] Task started: fastANI
[2024-01-24 13:11:17,421] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ac3ee90-31f6-4220-bd71-d378b8ff1932/GCF_000472705.1_ASM47270v1_genomic.fna.gz --refList GCF_000472705.1_ASM47270v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000472705.1_ASM47270v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:11:46,494] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:46,510] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:11:46,510] [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_000472705.1	s__Mesorhizobium erdmanii	100.0	2312	2320	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.40	97.39	0.90	0.90	3	conclusive
GCF_002356515.1	s__Mesorhizobium loti_C	90.5894	1881	2320	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.70	98.70	0.94	0.94	2	-
GCF_003353565.1	s__Mesorhizobium sp003353565	90.4001	1699	2320	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000688075.1	s__Mesorhizobium sp000688075	90.3907	1731	2320	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016756495.1	s__Mesorhizobium sp016756495	90.3684	1835	2320	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013170805.1	s__Mesorhizobium sp013170805	90.3308	1840	2320	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000009625.1	s__Mesorhizobium japonicum	90.3097	1801	2320	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.35	97.93	0.93	0.85	23	-
GCF_014189455.1	s__Mesorhizobium huakuii_A	90.2033	1801	2320	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900199455.1	s__Mesorhizobium carmichaelinearum	90.1144	1816	2320	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003601985.1	s__Mesorhizobium jarvisii	90.0936	1687	2320	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.40	98.93	0.96	0.91	10	-
GCF_013170825.1	s__Mesorhizobium sp013170825	90.0835	1744	2320	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	95.36	95.35	0.82	0.81	3	-
GCF_013170845.1	s__Mesorhizobium loti_B	89.704	1811	2320	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000472785.1	s__Mesorhizobium loti_E	89.6981	1792	2320	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018588885.1	s__Mesorhizobium sp018588885	88.8613	1634	2320	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000176035.2	s__Mesorhizobium opportunistum	88.4941	1683	2320	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	96.26	95.55	0.85	0.80	10	-
GCF_006658505.1	s__Mesorhizobium sp006658505	87.9842	1517	2320	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	95.84	95.17	0.86	0.81	6	-
--------------------------------------------------------------------------------
[2024-01-24 13:11:46,512] [INFO] GTDB search result was written to GCF_000472705.1_ASM47270v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:11:46,513] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:11:46,527] [INFO] DFAST_QC result json was written to GCF_000472705.1_ASM47270v1_genomic.fna/dqc_result.json
[2024-01-24 13:11:46,527] [INFO] DFAST_QC completed!
[2024-01-24 13:11:46,527] [INFO] Total running time: 0h2m19s