[2024-01-24 14:22:32,175] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:32,177] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:32,177] [INFO] DQC Reference Directory: /var/lib/cwl/stg608b1d00-ec9c-4b68-9aa2-cf548a951ea8/dqc_reference
[2024-01-24 14:22:33,454] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:33,455] [INFO] Task started: Prodigal
[2024-01-24 14:22:33,455] [INFO] Running command: gunzip -c /var/lib/cwl/stg921959ec-870b-45ae-8bbd-83e8e51de0be/GCF_004122115.1_ASM412211v1_genomic.fna.gz | prodigal -d GCF_004122115.1_ASM412211v1_genomic.fna/cds.fna -a GCF_004122115.1_ASM412211v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:42,979] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:42,979] [INFO] Task started: HMMsearch
[2024-01-24 14:22:42,980] [INFO] Running command: hmmsearch --tblout GCF_004122115.1_ASM412211v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg608b1d00-ec9c-4b68-9aa2-cf548a951ea8/dqc_reference/reference_markers.hmm GCF_004122115.1_ASM412211v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:43,245] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:43,247] [INFO] Found 6/6 markers.
[2024-01-24 14:22:43,281] [INFO] Query marker FASTA was written to GCF_004122115.1_ASM412211v1_genomic.fna/markers.fasta
[2024-01-24 14:22:43,281] [INFO] Task started: Blastn
[2024-01-24 14:22:43,281] [INFO] Running command: blastn -query GCF_004122115.1_ASM412211v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg608b1d00-ec9c-4b68-9aa2-cf548a951ea8/dqc_reference/reference_markers.fasta -out GCF_004122115.1_ASM412211v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:44,098] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:44,108] [INFO] Selected 26 target genomes.
[2024-01-24 14:22:44,109] [INFO] Target genome list was writen to GCF_004122115.1_ASM412211v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:44,128] [INFO] Task started: fastANI
[2024-01-24 14:22:44,128] [INFO] Running command: fastANI --query /var/lib/cwl/stg921959ec-870b-45ae-8bbd-83e8e51de0be/GCF_004122115.1_ASM412211v1_genomic.fna.gz --refList GCF_004122115.1_ASM412211v1_genomic.fna/target_genomes.txt --output GCF_004122115.1_ASM412211v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:03,349] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:03,349] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg608b1d00-ec9c-4b68-9aa2-cf548a951ea8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:03,350] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg608b1d00-ec9c-4b68-9aa2-cf548a951ea8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:03,371] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:23:03,371] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:23:03,372] [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
Sphingobium fluviale	strain=CHR27	GCA_004122115.1	2506423	2506423	type	True	100.0	997	1000	95	conclusive
Sphingobium jiangsuense	strain=DSM 26189	GCA_014196495.1	870476	870476	type	True	80.5518	475	1000	95	below_threshold
Sphingobium cloacae	strain=JCM 10874	GCA_002355855.1	120107	120107	type	True	79.5605	378	1000	95	below_threshold
Sphingobium subterraneum	strain=DSM 102255	GCA_014199435.1	627688	627688	type	True	79.4728	392	1000	95	below_threshold
Sphingobium phenoxybenzoativorans	strain=SC_3	GCA_001757355.1	1592790	1592790	type	True	79.3393	349	1000	95	below_threshold
Sphingobium lactosutens	strain=DS20	GCA_000445105.1	522773	522773	type	True	79.1183	332	1000	95	below_threshold
Sphingobium indicum	strain=B90A	GCA_000264945.2	332055	332055	type	True	79.1035	359	1000	95	below_threshold
Sphingobium terrigena	strain=EO9	GCA_003591655.1	2304063	2304063	type	True	79.0944	345	1000	95	below_threshold
Sphingobium baderi	strain=LL03	GCA_000445145.1	1332080	1332080	type	True	79.0078	357	1000	95	below_threshold
Sphingobium baderi	strain=LL03	GCA_001046655.1	1332080	1332080	type	True	78.9861	360	1000	95	below_threshold
Sphingobium wenxiniae	strain=JZ-1	GCA_014205735.1	595605	595605	type	True	78.9538	343	1000	95	below_threshold
Sphingobium ummariense	strain=RL-3	GCA_000447205.1	420994	420994	type	True	78.8118	352	1000	95	below_threshold
Sphingobium fuliginis	strain=CCM 7327	GCA_014636045.1	336203	336203	type	True	78.781	355	1000	95	below_threshold
Sphingobium fuliginis	strain=DSM 18781	GCA_004152845.1	336203	336203	type	True	78.7723	355	1000	95	below_threshold
Sphingobium cupriresistens	strain=CCTCC AB 2011146	GCA_004152865.1	1132417	1132417	type	True	78.7494	359	1000	95	below_threshold
Sphingobium quisquiliarum	strain=P25	GCA_000445065.1	538379	538379	type	True	78.7151	319	1000	95	below_threshold
Sphingobium abikonense	strain=NBRC 16140	GCA_001598335.1	86193	86193	type	True	78.4684	308	1000	95	below_threshold
Sphingobium psychrophilum	strain=AR-3-1	GCA_012927105.1	2728834	2728834	type	True	78.2383	338	1000	95	below_threshold
Sphingomonas pokkalii	strain=L3B27	GCA_003096275.1	2175090	2175090	type	True	78.0711	255	1000	95	below_threshold
Sphingobium limneticum	strain=DSM 25076	GCA_008710155.1	1007511	1007511	type	True	78.0528	349	1000	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	77.8176	234	1000	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	77.7262	288	1000	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	77.6909	268	1000	95	below_threshold
Sphingosinicella ginsenosidimutans	strain=BS-11	GCA_007995055.1	1176539	1176539	type	True	77.6523	202	1000	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	77.6291	237	1000	95	below_threshold
Rhizorhabdus phycosphaerae	strain=MK52	GCA_011044255.1	2711156	2711156	type	True	77.5807	212	1000	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:03,373] [INFO] DFAST Taxonomy check result was written to GCF_004122115.1_ASM412211v1_genomic.fna/tc_result.tsv
[2024-01-24 14:23:03,374] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:03,374] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:03,375] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg608b1d00-ec9c-4b68-9aa2-cf548a951ea8/dqc_reference/checkm_data
[2024-01-24 14:23:03,376] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:03,409] [INFO] Task started: CheckM
[2024-01-24 14:23:03,409] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004122115.1_ASM412211v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004122115.1_ASM412211v1_genomic.fna/checkm_input GCF_004122115.1_ASM412211v1_genomic.fna/checkm_result
[2024-01-24 14:23:35,682] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:35,684] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:35,716] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:35,716] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:35,717] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004122115.1_ASM412211v1_genomic.fna/markers.fasta)
[2024-01-24 14:23:35,717] [INFO] Task started: Blastn
[2024-01-24 14:23:35,717] [INFO] Running command: blastn -query GCF_004122115.1_ASM412211v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg608b1d00-ec9c-4b68-9aa2-cf548a951ea8/dqc_reference/reference_markers_gtdb.fasta -out GCF_004122115.1_ASM412211v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:36,944] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:36,948] [INFO] Selected 19 target genomes.
[2024-01-24 14:23:36,948] [INFO] Target genome list was writen to GCF_004122115.1_ASM412211v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:36,967] [INFO] Task started: fastANI
[2024-01-24 14:23:36,967] [INFO] Running command: fastANI --query /var/lib/cwl/stg921959ec-870b-45ae-8bbd-83e8e51de0be/GCF_004122115.1_ASM412211v1_genomic.fna.gz --refList GCF_004122115.1_ASM412211v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004122115.1_ASM412211v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:52,259] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:52,279] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:52,279] [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_004122115.1	s__Sphingobium fluviale	100.0	997	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017984895.1	s__Sphingobium sp017984895	83.7235	521	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	99.97	99.94	0.94	0.89	4	-
GCF_014196495.1	s__Sphingobium jiangsuense	80.5519	475	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002355855.1	s__Sphingobium cloacae	79.5743	377	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014199435.1	s__Sphingobium subterraneum	79.4849	390	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001757355.1	s__Sphingobium phenoxybenzoativorans	79.3625	346	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	96.17	96.17	0.74	0.74	2	-
GCF_007830065.1	s__Sphingobium wenxiniae	79.179	340	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	99.17	98.76	0.86	0.79	4	-
GCA_000264945.2	s__Sphingobium indicum	79.1165	358	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	98.64	97.75	0.82	0.64	8	-
GCF_000445105.1	s__Sphingobium lactosutens	79.0891	332	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.3976	N/A	N/A	N/A	N/A	1	-
GCF_000447205.1	s__Sphingobium ummariense	78.8427	349	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003248935.1	s__Sphingobium sp003248935	78.8353	292	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201265.1	s__Sphingobium sp014201265	78.5928	292	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	100.00	100.00	1.00	1.00	3	-
GCF_001713415.1	s__Sphingobium sp001713415	78.5766	340	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	95.59	95.59	0.75	0.75	2	-
GCF_004361945.1	s__Sphingobium barthaii_A	78.5408	329	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001421665.1	s__Sphingobium sp001421665	78.4423	336	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000508185.1	s__Sphingobium sp000508185	78.3387	324	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900013425.1	s__Sphingobium sp900013425	78.3223	353	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	99.99	99.97	0.99	0.99	6	-
GCF_013344685.1	s__Sphingomonas sp013344685	78.3099	285	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003345355.1	s__Sphingomonas sp003345355	77.8321	233	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:23:52,281] [INFO] GTDB search result was written to GCF_004122115.1_ASM412211v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:52,282] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:52,287] [INFO] DFAST_QC result json was written to GCF_004122115.1_ASM412211v1_genomic.fna/dqc_result.json
[2024-01-24 14:23:52,287] [INFO] DFAST_QC completed!
[2024-01-24 14:23:52,287] [INFO] Total running time: 0h1m20s