[2024-01-24 13:48:59,926] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:59,929] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:59,929] [INFO] DQC Reference Directory: /var/lib/cwl/stgf1583e66-5b22-410d-ad96-676b4558e7e1/dqc_reference
[2024-01-24 13:49:01,201] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:01,202] [INFO] Task started: Prodigal
[2024-01-24 13:49:01,203] [INFO] Running command: gunzip -c /var/lib/cwl/stge66ea9cc-eec8-47a6-9e84-0b7dddb32563/GCF_007995095.1_ASM799509v1_genomic.fna.gz | prodigal -d GCF_007995095.1_ASM799509v1_genomic.fna/cds.fna -a GCF_007995095.1_ASM799509v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:08,586] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:08,587] [INFO] Task started: HMMsearch
[2024-01-24 13:49:08,587] [INFO] Running command: hmmsearch --tblout GCF_007995095.1_ASM799509v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf1583e66-5b22-410d-ad96-676b4558e7e1/dqc_reference/reference_markers.hmm GCF_007995095.1_ASM799509v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:08,832] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:08,833] [INFO] Found 6/6 markers.
[2024-01-24 13:49:08,856] [INFO] Query marker FASTA was written to GCF_007995095.1_ASM799509v1_genomic.fna/markers.fasta
[2024-01-24 13:49:08,856] [INFO] Task started: Blastn
[2024-01-24 13:49:08,856] [INFO] Running command: blastn -query GCF_007995095.1_ASM799509v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1583e66-5b22-410d-ad96-676b4558e7e1/dqc_reference/reference_markers.fasta -out GCF_007995095.1_ASM799509v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:09,814] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:09,819] [INFO] Selected 25 target genomes.
[2024-01-24 13:49:09,820] [INFO] Target genome list was writen to GCF_007995095.1_ASM799509v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:09,827] [INFO] Task started: fastANI
[2024-01-24 13:49:09,827] [INFO] Running command: fastANI --query /var/lib/cwl/stge66ea9cc-eec8-47a6-9e84-0b7dddb32563/GCF_007995095.1_ASM799509v1_genomic.fna.gz --refList GCF_007995095.1_ASM799509v1_genomic.fna/target_genomes.txt --output GCF_007995095.1_ASM799509v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:27,358] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:27,358] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf1583e66-5b22-410d-ad96-676b4558e7e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:27,359] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf1583e66-5b22-410d-ad96-676b4558e7e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:27,379] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:27,380] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:27,380] [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
Sphingorhabdus soli	strain=D-2Q-5-6	GCA_007995095.1	2601267	2601267	type	True	100.0	861	861	95	conclusive
Sphingopyxis indica	strain=DS15	GCA_900188185.1	436663	436663	type	True	79.0457	392	861	95	below_threshold
Sphingopyxis panaciterrulae	strain=DSM 27163	GCA_014199295.1	462372	462372	type	True	78.9001	405	861	95	below_threshold
Sphingopyxis lindanitolerans	strain=WS5A3p	GCA_002993885.1	2054227	2054227	type	True	78.8785	405	861	95	below_threshold
Sphingopyxis italica	strain=DSM 25229	GCA_011926545.1	1129133	1129133	type	True	78.8257	403	861	95	below_threshold
Sphingopyxis macrogoltabida	strain=203	GCA_001314325.1	33050	33050	type	True	78.7613	402	861	95	below_threshold
Sphingopyxis terrae subsp. terrae	strain=NBRC 15098	GCA_001598815.1	2448440	33052	type	True	78.7118	367	861	95	below_threshold
Sphingopyxis microcysteis	strain=Z10-6	GCA_012274265.1	2484145	2484145	type	True	78.6696	375	861	95	below_threshold
Sphingomonas glacialis	strain=CGMCC 1.8957	GCA_014653575.1	658225	658225	type	True	78.6372	343	861	95	below_threshold
Sphingopyxis granuli	strain=NBRC 100800	GCA_001591045.1	267128	267128	type	True	78.6246	410	861	95	below_threshold
Sphingopyxis terrae subsp. ummariensis	strain=DSM 24316	GCA_002374275.1	429001	33052	type	True	78.6057	373	861	95	below_threshold
Sphingomonas leidyi	strain=DSM 4733	GCA_011761945.1	68569	68569	type	True	78.3094	335	861	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	78.2558	321	861	95	below_threshold
Sphingomonas colocasiae	strain=JCM 31229	GCA_019880585.1	1848973	1848973	type	True	78.1958	352	861	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	78.1467	259	861	95	below_threshold
Rhizorhabdus histidinilytica	strain=UM2	GCA_900167915.1	439228	439228	type	True	78.1447	322	861	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	78.14	363	861	95	below_threshold
Sphingomonas horti	strain=MAH-20	GCA_009753715.1	2682842	2682842	type	True	78.097	317	861	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	78.0814	308	861	95	below_threshold
Sphingomonas panacisoli	strain=HKS19	GCA_007859635.1	1813879	1813879	type	True	78.0338	323	861	95	below_threshold
Novosphingobium kunmingense	strain=CGMCC 1.12274	GCA_002813245.1	1211806	1211806	type	True	78.0274	260	861	95	below_threshold
Sphingosinicella ginsenosidimutans	strain=BS-11	GCA_007995055.1	1176539	1176539	type	True	78.0228	300	861	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	78.0015	326	861	95	below_threshold
Sphingomonas laterariae	strain=LNB2	GCA_900188165.1	861865	861865	type	True	77.8018	301	861	95	below_threshold
Novosphingobium fuchskuhlense	strain=FNE08-7	GCA_001519075.1	1117702	1117702	type	True	77.5777	225	861	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:27,382] [INFO] DFAST Taxonomy check result was written to GCF_007995095.1_ASM799509v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:27,387] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:27,387] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:27,387] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf1583e66-5b22-410d-ad96-676b4558e7e1/dqc_reference/checkm_data
[2024-01-24 13:49:27,389] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:27,421] [INFO] Task started: CheckM
[2024-01-24 13:49:27,422] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007995095.1_ASM799509v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007995095.1_ASM799509v1_genomic.fna/checkm_input GCF_007995095.1_ASM799509v1_genomic.fna/checkm_result
[2024-01-24 13:49:55,243] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:55,244] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:55,264] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:55,264] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:55,265] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007995095.1_ASM799509v1_genomic.fna/markers.fasta)
[2024-01-24 13:49:55,265] [INFO] Task started: Blastn
[2024-01-24 13:49:55,265] [INFO] Running command: blastn -query GCF_007995095.1_ASM799509v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1583e66-5b22-410d-ad96-676b4558e7e1/dqc_reference/reference_markers_gtdb.fasta -out GCF_007995095.1_ASM799509v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:57,246] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:57,249] [INFO] Selected 21 target genomes.
[2024-01-24 13:49:57,249] [INFO] Target genome list was writen to GCF_007995095.1_ASM799509v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:57,261] [INFO] Task started: fastANI
[2024-01-24 13:49:57,262] [INFO] Running command: fastANI --query /var/lib/cwl/stge66ea9cc-eec8-47a6-9e84-0b7dddb32563/GCF_007995095.1_ASM799509v1_genomic.fna.gz --refList GCF_007995095.1_ASM799509v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007995095.1_ASM799509v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:12,292] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:12,314] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:12,314] [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_007995095.1	s__Sphingorhabdus_C soli	100.0	861	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_C	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_009993585.1	s__Sphingorhabdus_C sp009993585	85.3263	496	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001468285.1	s__Sphingopyxis sp001468285	79.05	411	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.98	99.98	0.98	0.98	2	-
GCF_000756375.1	s__Sphingopyxis sp000756375	78.9663	402	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001984035.1	s__Sphingopyxis sp001984035	78.908	418	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199295.1	s__Sphingopyxis panaciterrulae	78.8735	409	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011926545.1	s__Sphingopyxis italica	78.808	404	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016734905.1	s__Sphingopyxis sp016734905	78.7673	364	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001598815.1	s__Sphingopyxis terrae	78.6887	369	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	96.70	95.58	0.84	0.76	19	-
GCF_012274265.1	s__Sphingopyxis microcysteis	78.6583	376	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	96.26	96.26	0.86	0.86	2	-
GCF_005503695.1	s__Sphingopyxis sp003609815	78.6478	385	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	97.15	97.15	0.90	0.90	2	-
GCF_005502465.1	s__Sphingopyxis sp005502465	78.6426	367	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018122655.1	s__Sphingomonas sp018122655	78.5932	319	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011320075.1	s__Allosphingosinicella sp011320075	78.2403	299	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003240855.1	s__Sphingomonas_L sanxanigenens_A	78.1811	276	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_L	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859635.1	s__Sphingomonas panacisoli	78.0561	321	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813245.1	s__Novosphingobium kunmingense	78.0274	260	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903644055.1	s__Sphingomonas_I sp903644055	77.9725	213	861	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_014201265.1	s__Sphingobium sp014201265	77.7288	207	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	100.00	100.00	1.00	1.00	3	-
GCA_018006725.1	s__Rhizorhabdus sp018006725	77.6358	237	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018599195.1	s__Croceibacterium sp018599195	77.6092	169	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:12,316] [INFO] GTDB search result was written to GCF_007995095.1_ASM799509v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:12,316] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:12,321] [INFO] DFAST_QC result json was written to GCF_007995095.1_ASM799509v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:12,322] [INFO] DFAST_QC completed!
[2024-01-24 13:50:12,322] [INFO] Total running time: 0h1m12s