[2024-01-25 20:02:50,476] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:02:50,478] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:02:50,479] [INFO] DQC Reference Directory: /var/lib/cwl/stg33cd445d-2e58-47ed-8340-57f1687e5e8b/dqc_reference
[2024-01-25 20:02:51,630] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:02:51,631] [INFO] Task started: Prodigal
[2024-01-25 20:02:51,631] [INFO] Running command: gunzip -c /var/lib/cwl/stg451abd31-f8f3-4c10-a189-06da48208a8c/GCF_000512205.2_ASM51220v2_genomic.fna.gz | prodigal -d GCF_000512205.2_ASM51220v2_genomic.fna/cds.fna -a GCF_000512205.2_ASM51220v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:03:09,222] [INFO] Task succeeded: Prodigal
[2024-01-25 20:03:09,222] [INFO] Task started: HMMsearch
[2024-01-25 20:03:09,223] [INFO] Running command: hmmsearch --tblout GCF_000512205.2_ASM51220v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg33cd445d-2e58-47ed-8340-57f1687e5e8b/dqc_reference/reference_markers.hmm GCF_000512205.2_ASM51220v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:03:09,549] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:03:09,550] [INFO] Found 6/6 markers.
[2024-01-25 20:03:09,604] [INFO] Query marker FASTA was written to GCF_000512205.2_ASM51220v2_genomic.fna/markers.fasta
[2024-01-25 20:03:09,605] [INFO] Task started: Blastn
[2024-01-25 20:03:09,605] [INFO] Running command: blastn -query GCF_000512205.2_ASM51220v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg33cd445d-2e58-47ed-8340-57f1687e5e8b/dqc_reference/reference_markers.fasta -out GCF_000512205.2_ASM51220v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:03:10,476] [INFO] Task succeeded: Blastn
[2024-01-25 20:03:10,480] [INFO] Selected 26 target genomes.
[2024-01-25 20:03:10,480] [INFO] Target genome list was writen to GCF_000512205.2_ASM51220v2_genomic.fna/target_genomes.txt
[2024-01-25 20:03:10,512] [INFO] Task started: fastANI
[2024-01-25 20:03:10,512] [INFO] Running command: fastANI --query /var/lib/cwl/stg451abd31-f8f3-4c10-a189-06da48208a8c/GCF_000512205.2_ASM51220v2_genomic.fna.gz --refList GCF_000512205.2_ASM51220v2_genomic.fna/target_genomes.txt --output GCF_000512205.2_ASM51220v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:03:34,197] [INFO] Task succeeded: fastANI
[2024-01-25 20:03:34,198] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg33cd445d-2e58-47ed-8340-57f1687e5e8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:03:34,198] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg33cd445d-2e58-47ed-8340-57f1687e5e8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:03:34,212] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:03:34,213] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:03:34,213] [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
Sphingomonas sanxanigenens	strain=NX02	GCA_000512205.2	397260	397260	type	True	100.0	2190	2192	95	conclusive
Sphingobium scionense	strain=DSM 19371	GCA_014197035.1	1404341	1404341	type	True	79.6217	629	2192	95	below_threshold
Sphingomonas fennica	strain=K101	GCA_003034225.1	114404	114404	type	True	79.5846	620	2192	95	below_threshold
Sphingomonas gilva	strain=ZDH117	GCA_003515075.1	2305907	2305907	type	True	79.5279	563	2192	95	below_threshold
Sphingobium chungbukense	strain=DJ77	GCA_001005725.1	56193	56193	type	True	79.508	472	2192	95	below_threshold
Rhizorhabdus histidinilytica	strain=UM2	GCA_900167915.1	439228	439228	type	True	79.4452	628	2192	95	below_threshold
Sphingomonas desiccabilis	strain=CP1D	GCA_004135605.1	429134	429134	type	True	79.3692	500	2192	95	below_threshold
Sphingomonas desiccabilis	strain=DSM 16792	GCA_014196135.1	429134	429134	type	True	79.3622	495	2192	95	below_threshold
Sphingobium ummariense	strain=RL-3	GCA_000447205.1	420994	420994	type	True	79.2984	520	2192	95	below_threshold
Sphingomonas formosensis	strain=CC-Nfb-2	GCA_009755815.1	861534	861534	type	True	79.1864	658	2192	95	below_threshold
Sphingomonas metalli	strain=CGMCC 1.15330	GCA_014641735.1	1779358	1779358	type	True	79.1559	553	2192	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	79.1171	522	2192	95	below_threshold
Sphingomonas oleivorans	strain=FW-11	GCA_003050615.1	1735121	1735121	type	True	79.0835	515	2192	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	79.0727	504	2192	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	79.0707	617	2192	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	79.0552	479	2192	95	below_threshold
Sphingomonas jatrophae	strain=S5-249	GCA_900113315.1	1166337	1166337	type	True	79.0462	565	2192	95	below_threshold
Sphingomonas solaris	strain=R4DWN	GCA_007785815.1	2529389	2529389	type	True	78.9929	536	2192	95	below_threshold
Sphingomonas laterariae	strain=LNB2	GCA_900188165.1	861865	861865	type	True	78.9892	602	2192	95	below_threshold
Sphingomonas horti	strain=MAH-20	GCA_009753715.1	2682842	2682842	type	True	78.9892	463	2192	95	below_threshold
Sphingomonas changbaiensis	strain=NBRC 104936	GCA_000974765.1	529705	529705	type	True	78.8906	423	2192	95	below_threshold
Sphingomonas baiyangensis	strain=L-1-4 w-11	GCA_005144715.1	2572576	2572576	type	True	78.7887	501	2192	95	below_threshold
Sphingosinicella ginsenosidimutans	strain=BS-11	GCA_007995055.1	1176539	1176539	type	True	78.6308	417	2192	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	78.5058	597	2192	95	below_threshold
Sphingomonas panacisoli	strain=HKS19	GCA_007859635.1	1813879	1813879	type	True	78.4641	427	2192	95	below_threshold
Sphingomonas prati	strain=DSM 103336	GCA_014199405.1	1843237	1843237	type	True	78.1414	465	2192	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:03:34,214] [INFO] DFAST Taxonomy check result was written to GCF_000512205.2_ASM51220v2_genomic.fna/tc_result.tsv
[2024-01-25 20:03:34,215] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:03:34,215] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:03:34,215] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg33cd445d-2e58-47ed-8340-57f1687e5e8b/dqc_reference/checkm_data
[2024-01-25 20:03:34,216] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:03:34,276] [INFO] Task started: CheckM
[2024-01-25 20:03:34,276] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000512205.2_ASM51220v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000512205.2_ASM51220v2_genomic.fna/checkm_input GCF_000512205.2_ASM51220v2_genomic.fna/checkm_result
[2024-01-25 20:04:45,645] [INFO] Task succeeded: CheckM
[2024-01-25 20:04:45,646] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:04:45,665] [INFO] ===== Completeness check finished =====
[2024-01-25 20:04:45,665] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:04:45,666] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000512205.2_ASM51220v2_genomic.fna/markers.fasta)
[2024-01-25 20:04:45,666] [INFO] Task started: Blastn
[2024-01-25 20:04:45,666] [INFO] Running command: blastn -query GCF_000512205.2_ASM51220v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg33cd445d-2e58-47ed-8340-57f1687e5e8b/dqc_reference/reference_markers_gtdb.fasta -out GCF_000512205.2_ASM51220v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:04:47,281] [INFO] Task succeeded: Blastn
[2024-01-25 20:04:47,284] [INFO] Selected 29 target genomes.
[2024-01-25 20:04:47,284] [INFO] Target genome list was writen to GCF_000512205.2_ASM51220v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:04:47,306] [INFO] Task started: fastANI
[2024-01-25 20:04:47,306] [INFO] Running command: fastANI --query /var/lib/cwl/stg451abd31-f8f3-4c10-a189-06da48208a8c/GCF_000512205.2_ASM51220v2_genomic.fna.gz --refList GCF_000512205.2_ASM51220v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000512205.2_ASM51220v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:05:13,642] [INFO] Task succeeded: fastANI
[2024-01-25 20:05:13,658] [INFO] Found 29 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:05:13,659] [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_000512205.2	s__Sphingomonas_D sanxanigenens	100.0	2191	2192	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_D	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014197035.1	s__Sphingobium scionense	79.665	623	2192	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000016765.1	s__Rhizorhabdus wittichii	79.6406	689	2192	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	98.56	98.46	0.83	0.82	5	-
GCF_003034225.1	s__Sphingomonas_E fennica	79.5499	625	2192	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_E	95.0	98.08	97.94	0.82	0.81	3	-
GCF_003515075.1	s__Sphingomonas gilva	79.5407	561	2192	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167915.1	s__Rhizorhabdus histidinilytica	79.457	625	2192	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	99.24	99.18	0.90	0.89	3	-
GCA_003240855.1	s__Sphingomonas_L sanxanigenens_A	79.4248	468	2192	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_L	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001724715.1	s__SCN-67-18 sp001724715	79.3603	493	2192	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__SCN-67-18	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000447205.1	s__Sphingobium ummariense	79.2618	523	2192	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409985.1	s__Sphingomonas melonis_A	79.2612	590	2192	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014641735.1	s__Sphingomonas metalli	79.1738	551	2192	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009755815.1	s__Sphingomonas_M formosensis	79.1651	662	2192	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_M	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013113735.1	s__Sphingomonas_I sp013113735	79.1339	610	2192	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114095.1	s__Sphingomonas sp900114095	79.1088	625	2192	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003050615.1	s__Sphingomonas_H oleivorans	79.0751	516	2192	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_H	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003590775.1	s__Sphingobium_A sp003590775	79.0718	522	2192	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008274695.1	s__Rhizorhabdus montanisoli	79.0686	482	2192	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113315.1	s__Sphingomonas_G jatrophae	79.0346	565	2192	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188165.1	s__Sphingomonas_E laterariae	78.997	601	2192	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013044515.1	s__Sphingomonas_B sp013044515	78.9913	461	2192	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177405.1	s__Allosphingosinicella indica	78.9682	453	2192	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000974765.1	s__Sphingomonas_B changbaiensis	78.8394	428	2192	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007995055.1	s__Allosphingosinicella ginsenosidimutans	78.6819	411	2192	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002457415.1	s__Sphingobium sp002457415	78.648	475	2192	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000281715.1	s__Sphingobium sp000281715	78.6087	509	2192	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240865.1	s__Sphingomonas_B sp018240865	78.4768	471	2192	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013328205.1	s__Sphingomonas hominis	78.2439	464	2192	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826325.1	s__Sphingomonas sp902826325	78.2355	366	2192	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.74	97.74	0.84	0.84	2	-
GCA_001899715.1	s__Sphingobium sp001899715	78.1685	407	2192	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:05:13,665] [INFO] GTDB search result was written to GCF_000512205.2_ASM51220v2_genomic.fna/result_gtdb.tsv
[2024-01-25 20:05:13,666] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:05:13,670] [INFO] DFAST_QC result json was written to GCF_000512205.2_ASM51220v2_genomic.fna/dqc_result.json
[2024-01-25 20:05:13,671] [INFO] DFAST_QC completed!
[2024-01-25 20:05:13,671] [INFO] Total running time: 0h2m23s