[2024-01-25 19:03:35,514] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:03:35,520] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:03:35,520] [INFO] DQC Reference Directory: /var/lib/cwl/stg5db21171-6d47-48b9-8b57-feee35834e07/dqc_reference
[2024-01-25 19:03:36,702] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:03:36,703] [INFO] Task started: Prodigal
[2024-01-25 19:03:36,704] [INFO] Running command: gunzip -c /var/lib/cwl/stgb0db50c2-96b0-46ad-8b16-22b3fd7616a1/GCF_003012735.1_ASM301273v1_genomic.fna.gz | prodigal -d GCF_003012735.1_ASM301273v1_genomic.fna/cds.fna -a GCF_003012735.1_ASM301273v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:03:52,201] [INFO] Task succeeded: Prodigal
[2024-01-25 19:03:52,201] [INFO] Task started: HMMsearch
[2024-01-25 19:03:52,201] [INFO] Running command: hmmsearch --tblout GCF_003012735.1_ASM301273v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5db21171-6d47-48b9-8b57-feee35834e07/dqc_reference/reference_markers.hmm GCF_003012735.1_ASM301273v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:03:52,487] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:03:52,488] [INFO] Found 6/6 markers.
[2024-01-25 19:03:52,533] [INFO] Query marker FASTA was written to GCF_003012735.1_ASM301273v1_genomic.fna/markers.fasta
[2024-01-25 19:03:52,534] [INFO] Task started: Blastn
[2024-01-25 19:03:52,534] [INFO] Running command: blastn -query GCF_003012735.1_ASM301273v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5db21171-6d47-48b9-8b57-feee35834e07/dqc_reference/reference_markers.fasta -out GCF_003012735.1_ASM301273v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:03:53,473] [INFO] Task succeeded: Blastn
[2024-01-25 19:03:53,476] [INFO] Selected 21 target genomes.
[2024-01-25 19:03:53,477] [INFO] Target genome list was writen to GCF_003012735.1_ASM301273v1_genomic.fna/target_genomes.txt
[2024-01-25 19:03:53,502] [INFO] Task started: fastANI
[2024-01-25 19:03:53,502] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0db50c2-96b0-46ad-8b16-22b3fd7616a1/GCF_003012735.1_ASM301273v1_genomic.fna.gz --refList GCF_003012735.1_ASM301273v1_genomic.fna/target_genomes.txt --output GCF_003012735.1_ASM301273v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:04:09,475] [INFO] Task succeeded: fastANI
[2024-01-25 19:04:09,476] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5db21171-6d47-48b9-8b57-feee35834e07/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:04:09,477] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5db21171-6d47-48b9-8b57-feee35834e07/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:04:09,491] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:04:09,491] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:04:09,491] [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 deserti	strain=GL-C-18	GCA_003012735.1	2116704	2116704	type	True	100.0	2016	2019	95	conclusive
Sphingomonas parva	strain=17J27-24	GCA_004564275.1	2555898	2555898	type	True	82.1711	840	2019	95	below_threshold
Sphingosinicella humi	strain=QZX222	GCA_003129465.1	2068657	2068657	type	True	79.2135	482	2019	95	below_threshold
Sphingosinicella ginsenosidimutans	strain=BS-11	GCA_007995055.1	1176539	1176539	type	True	78.8083	511	2019	95	below_threshold
Sphingomonas ginsengisoli An et al. 2013	strain=KACC 16858	GCA_009363895.1	363835	363835	type	True	78.201	361	2019	95	below_threshold
Sphingomonas desiccabilis	strain=DSM 16792	GCA_014196135.1	429134	429134	type	True	78.1786	395	2019	95	below_threshold
Sphingomonas desiccabilis	strain=CP1D	GCA_004135605.1	429134	429134	type	True	78.17	397	2019	95	below_threshold
Sphingomonas laterariae	strain=LNB2	GCA_900188165.1	861865	861865	type	True	78.0968	393	2019	95	below_threshold
Sphingomonas changbaiensis	strain=NBRC 104936	GCA_000974765.1	529705	529705	type	True	78.091	372	2019	95	below_threshold
Sphingomonas jatrophae	strain=S5-249	GCA_900113315.1	1166337	1166337	type	True	78.0369	414	2019	95	below_threshold
Sphingomonas horti	strain=MAH-20	GCA_009753715.1	2682842	2682842	type	True	77.9983	412	2019	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	77.9886	436	2019	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	77.8566	376	2019	95	below_threshold
Sphingomonas solaris	strain=R4DWN	GCA_007785815.1	2529389	2529389	type	True	77.8394	357	2019	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	77.7982	439	2019	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	77.7676	368	2019	95	below_threshold
Rhizorhabdus phycosphaerae	strain=MK52	GCA_011044255.1	2711156	2711156	type	True	77.7375	368	2019	95	below_threshold
Sphingomonas hengshuiensis	strain=WHSC-8	GCA_000935025.1	1609977	1609977	type	True	77.637	422	2019	95	below_threshold
Sphingosinithalassobacter tenebrarum	strain=zrk23	GCA_011057975.1	2711215	2711215	type	True	77.6087	332	2019	95	below_threshold
Sphingomonas dokdonensis	strain=DSM 21029	GCA_002197685.1	344880	344880	type	True	77.3669	331	2019	95	below_threshold
Sphingomicrobium aestuariivivum	strain=KCTC 42286	GCA_024721585.1	1582356	1582356	type	True	77.3446	265	2019	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:04:09,505] [INFO] DFAST Taxonomy check result was written to GCF_003012735.1_ASM301273v1_genomic.fna/tc_result.tsv
[2024-01-25 19:04:09,506] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:04:09,506] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:04:09,506] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5db21171-6d47-48b9-8b57-feee35834e07/dqc_reference/checkm_data
[2024-01-25 19:04:09,507] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:04:09,602] [INFO] Task started: CheckM
[2024-01-25 19:04:09,603] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003012735.1_ASM301273v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003012735.1_ASM301273v1_genomic.fna/checkm_input GCF_003012735.1_ASM301273v1_genomic.fna/checkm_result
[2024-01-25 19:04:55,719] [INFO] Task succeeded: CheckM
[2024-01-25 19:04:55,720] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:04:55,740] [INFO] ===== Completeness check finished =====
[2024-01-25 19:04:55,740] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:04:55,741] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003012735.1_ASM301273v1_genomic.fna/markers.fasta)
[2024-01-25 19:04:55,741] [INFO] Task started: Blastn
[2024-01-25 19:04:55,741] [INFO] Running command: blastn -query GCF_003012735.1_ASM301273v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5db21171-6d47-48b9-8b57-feee35834e07/dqc_reference/reference_markers_gtdb.fasta -out GCF_003012735.1_ASM301273v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:04:57,492] [INFO] Task succeeded: Blastn
[2024-01-25 19:04:57,612] [INFO] Selected 16 target genomes.
[2024-01-25 19:04:57,612] [INFO] Target genome list was writen to GCF_003012735.1_ASM301273v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:04:57,625] [INFO] Task started: fastANI
[2024-01-25 19:04:57,625] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0db50c2-96b0-46ad-8b16-22b3fd7616a1/GCF_003012735.1_ASM301273v1_genomic.fna.gz --refList GCF_003012735.1_ASM301273v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003012735.1_ASM301273v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:05:12,791] [INFO] Task succeeded: fastANI
[2024-01-25 19:05:12,801] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:05:12,802] [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_003012735.1	s__Allosphingosinicella deserti	100.0	2016	2019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004135585.1	s__Allosphingosinicella sp004135585	84.2689	1388	2019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004564275.1	s__Allosphingosinicella parva	82.2183	834	2019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005882415.1	s__Allosphingosinicella sp005882415	79.7351	499	2019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019232625.1	s__Allosphingosinicella sp019232625	79.668	575	2019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	99.90	99.89	0.98	0.97	3	-
GCA_019239415.1	s__Allosphingosinicella sp019239415	79.4567	566	2019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177405.1	s__Allosphingosinicella indica	79.3274	460	2019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003129465.1	s__Allosphingosinicella humi	79.1981	483	2019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806315.1	s__Allosphingosinicella sp902806315	79.1299	428	2019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003347635.1	s__Allosphingosinicella sp003347635	78.9782	638	2019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014489075.1	s__Sphingomonas sp014489075	78.1865	469	2019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188165.1	s__Sphingomonas_E laterariae	78.0875	394	2019	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	78.0619	379	2019	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_900113315.1	s__Sphingomonas_G jatrophae	78.0481	412	2019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_G	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903871605.1	s__Sphingomonas_N sp903871605	77.9342	437	2019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_N	95.0	99.98	99.98	0.98	0.98	2	-
GCF_011057975.1	s__Sphingomonas sp011057975	77.6283	330	2019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:05:12,803] [INFO] GTDB search result was written to GCF_003012735.1_ASM301273v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:05:12,804] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:05:12,809] [INFO] DFAST_QC result json was written to GCF_003012735.1_ASM301273v1_genomic.fna/dqc_result.json
[2024-01-25 19:05:12,810] [INFO] DFAST_QC completed!
[2024-01-25 19:05:12,810] [INFO] Total running time: 0h1m37s