[2024-01-24 14:14:19,723] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:19,727] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:19,727] [INFO] DQC Reference Directory: /var/lib/cwl/stg7511c46b-6832-4385-932f-fa8da6e10978/dqc_reference
[2024-01-24 14:14:21,022] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:21,023] [INFO] Task started: Prodigal
[2024-01-24 14:14:21,023] [INFO] Running command: gunzip -c /var/lib/cwl/stgcb1ad3d2-ccc7-4b36-bd74-842af65a8f11/GCF_003590775.1_ASM359077v1_genomic.fna.gz | prodigal -d GCF_003590775.1_ASM359077v1_genomic.fna/cds.fna -a GCF_003590775.1_ASM359077v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:34,352] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:34,353] [INFO] Task started: HMMsearch
[2024-01-24 14:14:34,353] [INFO] Running command: hmmsearch --tblout GCF_003590775.1_ASM359077v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7511c46b-6832-4385-932f-fa8da6e10978/dqc_reference/reference_markers.hmm GCF_003590775.1_ASM359077v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:34,633] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:34,634] [INFO] Found 6/6 markers.
[2024-01-24 14:14:34,674] [INFO] Query marker FASTA was written to GCF_003590775.1_ASM359077v1_genomic.fna/markers.fasta
[2024-01-24 14:14:34,674] [INFO] Task started: Blastn
[2024-01-24 14:14:34,674] [INFO] Running command: blastn -query GCF_003590775.1_ASM359077v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7511c46b-6832-4385-932f-fa8da6e10978/dqc_reference/reference_markers.fasta -out GCF_003590775.1_ASM359077v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:35,712] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:35,715] [INFO] Selected 21 target genomes.
[2024-01-24 14:14:35,715] [INFO] Target genome list was writen to GCF_003590775.1_ASM359077v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:35,727] [INFO] Task started: fastANI
[2024-01-24 14:14:35,728] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb1ad3d2-ccc7-4b36-bd74-842af65a8f11/GCF_003590775.1_ASM359077v1_genomic.fna.gz --refList GCF_003590775.1_ASM359077v1_genomic.fna/target_genomes.txt --output GCF_003590775.1_ASM359077v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:14:53,812] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:53,812] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7511c46b-6832-4385-932f-fa8da6e10978/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:14:53,813] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7511c46b-6832-4385-932f-fa8da6e10978/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:14:53,829] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:14:53,830] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:14:53,830] [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 cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	100.0	1409	1412	95	conclusive
Sphingomonas colocasiae	strain=JCM 31229	GCA_019880585.1	1848973	1848973	type	True	80.3733	656	1412	95	below_threshold
Sphingomonas gilva	strain=ZDH117	GCA_003515075.1	2305907	2305907	type	True	79.0618	517	1412	95	below_threshold
Sphingomonas naasensis	strain=KIS18-15	GCA_004792695.1	1344951	1344951	type	True	79.0043	519	1412	95	below_threshold
Sphingomonas naasensis	strain=DSM 100060	GCA_011762145.1	1344951	1344951	type	True	78.9437	520	1412	95	below_threshold
Sphingobium boeckii	strain=DSM 25079	GCA_014199215.1	1082345	1082345	type	True	78.9408	536	1412	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	78.7893	405	1412	95	below_threshold
Sphingomonas changbaiensis	strain=NBRC 104936	GCA_000974765.1	529705	529705	type	True	78.6629	394	1412	95	below_threshold
Sphingomonas metalli	strain=CGMCC 1.15330	GCA_014641735.1	1779358	1779358	type	True	78.5911	396	1412	95	below_threshold
Sphingobium ummariense	strain=RL-3	GCA_000447205.1	420994	420994	type	True	78.5867	374	1412	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	78.5159	380	1412	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	78.4908	441	1412	95	below_threshold
Sphingomonas jatrophae	strain=S5-249	GCA_900113315.1	1166337	1166337	type	True	78.4419	371	1412	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	78.4125	444	1412	95	below_threshold
Sphingopyxis lindanitolerans	strain=WS5A3p	GCA_002993885.1	2054227	2054227	type	True	78.4012	427	1412	95	below_threshold
Sphingobium baderi	strain=LL03	GCA_000445145.1	1332080	1332080	type	True	78.3628	343	1412	95	below_threshold
Sphingomonas solaris	strain=R4DWN	GCA_007785815.1	2529389	2529389	type	True	78.2843	366	1412	95	below_threshold
Sphingobium baderi	strain=LL03	GCA_001046655.1	1332080	1332080	type	True	78.245	344	1412	95	below_threshold
Sphingobium chlorophenolicum	strain=NBRC 16172	GCA_001598515.1	46429	46429	type	True	78.0822	330	1412	95	below_threshold
Sphingobium chlorophenolicum	strain=NBRC 16172	GCA_000722875.1	46429	46429	type	True	77.9944	353	1412	95	below_threshold
Sphingomonas deserti	strain=GL-C-18	GCA_003012735.1	2116704	2116704	type	True	77.6737	368	1412	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:14:53,831] [INFO] DFAST Taxonomy check result was written to GCF_003590775.1_ASM359077v1_genomic.fna/tc_result.tsv
[2024-01-24 14:14:53,832] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:14:53,832] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:14:53,832] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7511c46b-6832-4385-932f-fa8da6e10978/dqc_reference/checkm_data
[2024-01-24 14:14:53,834] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:14:53,876] [INFO] Task started: CheckM
[2024-01-24 14:14:53,876] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003590775.1_ASM359077v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003590775.1_ASM359077v1_genomic.fna/checkm_input GCF_003590775.1_ASM359077v1_genomic.fna/checkm_result
[2024-01-24 14:15:32,366] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:32,368] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:32,385] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:32,386] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:32,386] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003590775.1_ASM359077v1_genomic.fna/markers.fasta)
[2024-01-24 14:15:32,386] [INFO] Task started: Blastn
[2024-01-24 14:15:32,386] [INFO] Running command: blastn -query GCF_003590775.1_ASM359077v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7511c46b-6832-4385-932f-fa8da6e10978/dqc_reference/reference_markers_gtdb.fasta -out GCF_003590775.1_ASM359077v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:34,217] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:34,220] [INFO] Selected 24 target genomes.
[2024-01-24 14:15:34,221] [INFO] Target genome list was writen to GCF_003590775.1_ASM359077v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:34,252] [INFO] Task started: fastANI
[2024-01-24 14:15:34,252] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb1ad3d2-ccc7-4b36-bd74-842af65a8f11/GCF_003590775.1_ASM359077v1_genomic.fna.gz --refList GCF_003590775.1_ASM359077v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003590775.1_ASM359077v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:15:51,909] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:51,927] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:15:51,927] [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_003590775.1	s__Sphingobium_A sp003590775	100.0	1409	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003240855.1	s__Sphingomonas_L sanxanigenens_A	79.1535	437	1412	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_003515075.1	s__Sphingomonas gilva	79.0581	518	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004792695.1	s__Sphingomonas naasensis	79.0237	516	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014199215.1	s__Sphingobium_A boeckii	78.9546	535	1412	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_003550065.1	s__Sphingomonas caeni	78.8015	454	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009913435.1	s__Sphingomonas_B sp009913435	78.7879	408	1412	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	78.6576	297	1412	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_000974765.1	s__Sphingomonas_B changbaiensis	78.653	395	1412	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_004341505.2	s__Sphingomonas sp004341505	78.6515	384	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	95.45	95.45	0.78	0.78	2	-
GCF_014641735.1	s__Sphingomonas metalli	78.6253	393	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000447205.1	s__Sphingobium ummariense	78.5823	370	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004796535.1	s__Sphingomonas_L sp004796535	78.5277	379	1412	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	78.4569	420	1412	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_016025255.1	s__Allosphingosinicella sp016025255	78.4454	285	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001897375.1	s__Sphingomonas sp001897375	78.4445	420	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.01	98.04	0.97	0.96	3	-
GCF_002993885.1	s__Sphingopyxis lindanitolerans	78.4357	423	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113315.1	s__Sphingomonas_G jatrophae	78.432	372	1412	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_000797515.1	s__Sphingomonas sp000797515	78.3401	350	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.00	97.12	0.86	0.75	5	-
GCA_002281485.1	s__Sphingomonas sp002281485	78.2673	361	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013393185.1	s__Sphingobium lactosutens_A	78.2586	425	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005883305.1	s__Allosphingosinicella sp005883305	78.2081	317	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000722875.1	s__Sphingobium chlorophenolicum	78.0077	351	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	97.94	95.89	0.87	0.76	3	-
GCF_003012735.1	s__Allosphingosinicella deserti	77.6428	372	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:15:51,929] [INFO] GTDB search result was written to GCF_003590775.1_ASM359077v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:15:51,929] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:15:51,934] [INFO] DFAST_QC result json was written to GCF_003590775.1_ASM359077v1_genomic.fna/dqc_result.json
[2024-01-24 14:15:51,934] [INFO] DFAST_QC completed!
[2024-01-24 14:15:51,934] [INFO] Total running time: 0h1m32s