[2024-01-24 11:22:49,055] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:22:49,057] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:22:49,057] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb96ad4c-6cc6-4057-93a3-e57b06c40f62/dqc_reference
[2024-01-24 11:22:50,318] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:22:50,319] [INFO] Task started: Prodigal
[2024-01-24 11:22:50,319] [INFO] Running command: gunzip -c /var/lib/cwl/stga755d549-711d-472a-99cd-cfbdd5f3216e/GCF_004796535.1_ASM479653v1_genomic.fna.gz | prodigal -d GCF_004796535.1_ASM479653v1_genomic.fna/cds.fna -a GCF_004796535.1_ASM479653v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:22:58,520] [INFO] Task succeeded: Prodigal
[2024-01-24 11:22:58,521] [INFO] Task started: HMMsearch
[2024-01-24 11:22:58,521] [INFO] Running command: hmmsearch --tblout GCF_004796535.1_ASM479653v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb96ad4c-6cc6-4057-93a3-e57b06c40f62/dqc_reference/reference_markers.hmm GCF_004796535.1_ASM479653v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:22:58,742] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:22:58,743] [INFO] Found 6/6 markers.
[2024-01-24 11:22:58,775] [INFO] Query marker FASTA was written to GCF_004796535.1_ASM479653v1_genomic.fna/markers.fasta
[2024-01-24 11:22:58,775] [INFO] Task started: Blastn
[2024-01-24 11:22:58,775] [INFO] Running command: blastn -query GCF_004796535.1_ASM479653v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb96ad4c-6cc6-4057-93a3-e57b06c40f62/dqc_reference/reference_markers.fasta -out GCF_004796535.1_ASM479653v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:22:59,822] [INFO] Task succeeded: Blastn
[2024-01-24 11:22:59,826] [INFO] Selected 23 target genomes.
[2024-01-24 11:22:59,827] [INFO] Target genome list was writen to GCF_004796535.1_ASM479653v1_genomic.fna/target_genomes.txt
[2024-01-24 11:22:59,869] [INFO] Task started: fastANI
[2024-01-24 11:22:59,869] [INFO] Running command: fastANI --query /var/lib/cwl/stga755d549-711d-472a-99cd-cfbdd5f3216e/GCF_004796535.1_ASM479653v1_genomic.fna.gz --refList GCF_004796535.1_ASM479653v1_genomic.fna/target_genomes.txt --output GCF_004796535.1_ASM479653v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:23:22,452] [INFO] Task succeeded: fastANI
[2024-01-24 11:23:22,453] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb96ad4c-6cc6-4057-93a3-e57b06c40f62/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:23:22,454] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb96ad4c-6cc6-4057-93a3-e57b06c40f62/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:23:22,472] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:23:22,473] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:23:22,473] [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 flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	100.0	1003	1006	95	conclusive
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	79.9279	451	1006	95	below_threshold
Sphingomonas horti	strain=MAH-20	GCA_009753715.1	2682842	2682842	type	True	79.602	481	1006	95	below_threshold
Sphingomonas gilva	strain=ZDH117	GCA_003515075.1	2305907	2305907	type	True	79.5944	465	1006	95	below_threshold
Sphingomonas fennica	strain=K101	GCA_003034225.1	114404	114404	type	True	79.359	450	1006	95	below_threshold
Sphingomonas changbaiensis	strain=NBRC 104936	GCA_000974765.1	529705	529705	type	True	79.2464	439	1006	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	79.1085	459	1006	95	below_threshold
Sphingomonas desiccabilis	strain=CP1D	GCA_004135605.1	429134	429134	type	True	78.9774	391	1006	95	below_threshold
Sphingomonas desiccabilis	strain=DSM 16792	GCA_014196135.1	429134	429134	type	True	78.9424	396	1006	95	below_threshold
Sphingosinicella ginsenosidimutans	strain=BS-11	GCA_007995055.1	1176539	1176539	type	True	78.8597	377	1006	95	below_threshold
Sphingomonas colocasiae	strain=JCM 31229	GCA_019880585.1	1848973	1848973	type	True	78.7182	515	1006	95	below_threshold
Sphingomonas jejuensis	strain=DSM 27651	GCA_011927695.1	904715	904715	type	True	78.7004	392	1006	95	below_threshold
Sphingomonas hengshuiensis	strain=WHSC-8	GCA_000935025.1	1609977	1609977	type	True	78.6582	445	1006	95	below_threshold
Sphingomonas oligoaromativorans	strain=DSM 102246	GCA_011762195.1	575322	575322	type	True	78.6462	418	1006	95	below_threshold
Sphingobium jiangsuense	strain=DSM 26189	GCA_014196495.1	870476	870476	type	True	78.5956	432	1006	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	78.5941	399	1006	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	78.5552	375	1006	95	below_threshold
Sphingomonas hankookensis	strain=KCTC 22579	GCA_022664465.1	563996	563996	type	True	78.5495	399	1006	95	below_threshold
Sphingomonas koreensis	strain=JSS26	GCA_002797435.1	93064	93064	type	True	78.543	411	1006	95	below_threshold
Sphingomonas koreensis	strain=NBRC 16723	GCA_001598395.1	93064	93064	type	True	78.4697	411	1006	95	below_threshold
Sphingomonas koreensis	strain=KCTC 2882	GCA_003953035.1	93064	93064	type	True	78.4056	413	1006	95	below_threshold
Sphingomonas glacialis	strain=CGMCC 1.8957	GCA_014653575.1	658225	658225	type	True	78.2415	386	1006	95	below_threshold
Novosphingobium lentum	strain=NBRC 107847	GCA_001590965.1	145287	145287	type	True	78.0316	323	1006	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:23:22,475] [INFO] DFAST Taxonomy check result was written to GCF_004796535.1_ASM479653v1_genomic.fna/tc_result.tsv
[2024-01-24 11:23:22,475] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:23:22,475] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:23:22,476] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb96ad4c-6cc6-4057-93a3-e57b06c40f62/dqc_reference/checkm_data
[2024-01-24 11:23:22,476] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:23:22,507] [INFO] Task started: CheckM
[2024-01-24 11:23:22,507] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004796535.1_ASM479653v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004796535.1_ASM479653v1_genomic.fna/checkm_input GCF_004796535.1_ASM479653v1_genomic.fna/checkm_result
[2024-01-24 11:23:50,360] [INFO] Task succeeded: CheckM
[2024-01-24 11:23:50,361] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:23:50,383] [INFO] ===== Completeness check finished =====
[2024-01-24 11:23:50,383] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:23:50,384] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004796535.1_ASM479653v1_genomic.fna/markers.fasta)
[2024-01-24 11:23:50,384] [INFO] Task started: Blastn
[2024-01-24 11:23:50,384] [INFO] Running command: blastn -query GCF_004796535.1_ASM479653v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb96ad4c-6cc6-4057-93a3-e57b06c40f62/dqc_reference/reference_markers_gtdb.fasta -out GCF_004796535.1_ASM479653v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:23:52,502] [INFO] Task succeeded: Blastn
[2024-01-24 11:23:52,507] [INFO] Selected 22 target genomes.
[2024-01-24 11:23:52,508] [INFO] Target genome list was writen to GCF_004796535.1_ASM479653v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:23:52,533] [INFO] Task started: fastANI
[2024-01-24 11:23:52,533] [INFO] Running command: fastANI --query /var/lib/cwl/stga755d549-711d-472a-99cd-cfbdd5f3216e/GCF_004796535.1_ASM479653v1_genomic.fna.gz --refList GCF_004796535.1_ASM479653v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004796535.1_ASM479653v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:24:08,415] [INFO] Task succeeded: fastANI
[2024-01-24 11:24:08,444] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:24:08,444] [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_004796535.1	s__Sphingomonas_L sp004796535	100.0	1003	1006	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_L	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001724715.1	s__SCN-67-18 sp001724715	80.5956	522	1006	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	-
GCA_003240855.1	s__Sphingomonas_L sanxanigenens_A	80.4417	505	1006	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_009913435.1	s__Sphingomonas_B sp009913435	79.8871	455	1006	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_009753715.1	s__Sphingomonas_B horti	79.6098	481	1006	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_B	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003515075.1	s__Sphingomonas gilva	79.6054	464	1006	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013344685.1	s__Sphingomonas sp013344685	79.4225	475	1006	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003034225.1	s__Sphingomonas_E fennica	79.3044	455	1006	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_000974765.1	s__Sphingomonas_B changbaiensis	79.2679	437	1006	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002291855.1	s__Sphingomonas_B sp002291855	79.2631	352	1006	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_013044515.1	s__Sphingomonas_B sp013044515	79.1799	404	1006	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_004135605.1	s__Sphingomonas desiccabilis	79.006	388	1006	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007995055.1	s__Allosphingosinicella ginsenosidimutans	78.843	378	1006	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011927695.1	s__Sphingomonas_K jejuensis	78.6807	394	1006	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011762195.1	s__Sphingomonas_N oligoaromativorans	78.6352	419	1006	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_N	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196495.1	s__Sphingobium jiangsuense	78.5952	432	1006	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014334115.1	s__Sphingomonas sp014334115	78.5373	386	1006	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797435.1	s__Sphingomonas koreensis	78.533	412	1006	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.13	98.00	0.88	0.86	72	-
GCA_001899715.1	s__Sphingobium sp001899715	78.4391	368	1006	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003967075.1	s__Sphingobium amiense	78.4325	355	1006	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_006439055.1	s__Sphingomonas glacialis_A	78.4016	401	1006	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014653575.1	s__Sphingomonas glacialis	78.2229	388	1006	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.17	97.17	0.81	0.81	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:24:08,446] [INFO] GTDB search result was written to GCF_004796535.1_ASM479653v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:24:08,447] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:24:08,451] [INFO] DFAST_QC result json was written to GCF_004796535.1_ASM479653v1_genomic.fna/dqc_result.json
[2024-01-24 11:24:08,451] [INFO] DFAST_QC completed!
[2024-01-24 11:24:08,451] [INFO] Total running time: 0h1m19s