[2024-01-25 18:49:20,767] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:49:20,768] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:49:20,768] [INFO] DQC Reference Directory: /var/lib/cwl/stgccc0649a-c79e-418d-b5de-ebe0e047acb8/dqc_reference
[2024-01-25 18:49:21,878] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:49:21,879] [INFO] Task started: Prodigal
[2024-01-25 18:49:21,879] [INFO] Running command: gunzip -c /var/lib/cwl/stga31c0b43-8b24-4fdc-8427-472adb68c49c/GCF_002351485.1_ASM235148v1_genomic.fna.gz | prodigal -d GCF_002351485.1_ASM235148v1_genomic.fna/cds.fna -a GCF_002351485.1_ASM235148v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:49:31,038] [INFO] Task succeeded: Prodigal
[2024-01-25 18:49:31,039] [INFO] Task started: HMMsearch
[2024-01-25 18:49:31,039] [INFO] Running command: hmmsearch --tblout GCF_002351485.1_ASM235148v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgccc0649a-c79e-418d-b5de-ebe0e047acb8/dqc_reference/reference_markers.hmm GCF_002351485.1_ASM235148v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:49:31,239] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:49:31,240] [INFO] Found 6/6 markers.
[2024-01-25 18:49:31,269] [INFO] Query marker FASTA was written to GCF_002351485.1_ASM235148v1_genomic.fna/markers.fasta
[2024-01-25 18:49:31,270] [INFO] Task started: Blastn
[2024-01-25 18:49:31,270] [INFO] Running command: blastn -query GCF_002351485.1_ASM235148v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgccc0649a-c79e-418d-b5de-ebe0e047acb8/dqc_reference/reference_markers.fasta -out GCF_002351485.1_ASM235148v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:49:32,197] [INFO] Task succeeded: Blastn
[2024-01-25 18:49:32,199] [INFO] Selected 21 target genomes.
[2024-01-25 18:49:32,200] [INFO] Target genome list was writen to GCF_002351485.1_ASM235148v1_genomic.fna/target_genomes.txt
[2024-01-25 18:49:32,209] [INFO] Task started: fastANI
[2024-01-25 18:49:32,210] [INFO] Running command: fastANI --query /var/lib/cwl/stga31c0b43-8b24-4fdc-8427-472adb68c49c/GCF_002351485.1_ASM235148v1_genomic.fna.gz --refList GCF_002351485.1_ASM235148v1_genomic.fna/target_genomes.txt --output GCF_002351485.1_ASM235148v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:49:48,441] [INFO] Task succeeded: fastANI
[2024-01-25 18:49:48,441] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgccc0649a-c79e-418d-b5de-ebe0e047acb8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:49:48,441] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgccc0649a-c79e-418d-b5de-ebe0e047acb8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:49:48,463] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:49:48,463] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:49:48,463] [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 spermidinifaciens	strain=9NM-10	GCA_002351485.1	1141889	1141889	type	True	100.0	1209	1209	95	conclusive
Sphingomonas yantingensis	strain=DSM 27244	GCA_014199325.1	1241761	1241761	type	True	87.2944	887	1209	95	below_threshold
Sphingomonas baiyangensis	strain=L-1-4 w-11	GCA_005144715.1	2572576	2572576	type	True	81.1154	624	1209	95	below_threshold
Sphingomonas naasensis	strain=KIS18-15	GCA_004792695.1	1344951	1344951	type	True	79.89	593	1209	95	below_threshold
Sphingomonas naasensis	strain=DSM 100060	GCA_011762145.1	1344951	1344951	type	True	79.8416	598	1209	95	below_threshold
Sphingomonas pseudosanguinis	strain=DSM 19512	GCA_014196255.1	413712	413712	type	True	79.691	534	1209	95	below_threshold
Sphingomonas koreensis	strain=JSS26	GCA_002797435.1	93064	93064	type	True	79.6786	558	1209	95	below_threshold
Sphingomonas koreensis	strain=NBRC 16723	GCA_001598395.1	93064	93064	type	True	79.675	556	1209	95	below_threshold
Sphingomonas rubra	strain=CGMCC 1.9113	GCA_900115745.1	634430	634430	type	True	79.6702	503	1209	95	below_threshold
Sphingomonas abaci	strain=DSM 15867	GCA_014199625.1	237611	237611	type	True	79.6248	535	1209	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	79.5333	562	1209	95	below_threshold
Sphingomonas endophytica	strain=DSM 101535	GCA_014199415.1	869719	869719	type	True	79.4116	528	1209	95	below_threshold
Sphingomonas panni	strain=DSM 15761	GCA_022664435.1	237612	237612	type	True	79.3886	547	1209	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	79.3712	590	1209	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	79.3482	589	1209	95	below_threshold
Sphingomonas turrisvirgatae	strain=MCT13	GCA_001721295.1	1888892	1888892	type	True	79.3442	498	1209	95	below_threshold
Sphingomonas hankookensis	strain=KCTC 22579	GCA_022664465.1	563996	563996	type	True	79.3286	540	1209	95	below_threshold
Sphingomonas dokdonensis	strain=DSM 21029	GCA_002197685.1	344880	344880	type	True	79.1228	435	1209	95	below_threshold
Sphingosinithalassobacter tenebrarum	strain=zrk23	GCA_011057975.1	2711215	2711215	type	True	78.9431	474	1209	95	below_threshold
Sphingomonas gellani	strain=S6-262	GCA_900110035.1	1166340	1166340	type	True	78.6105	421	1209	95	below_threshold
Sphingomonas mucosissima	strain=DSM 17494	GCA_002197665.1	370959	370959	type	True	78.4067	364	1209	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:49:48,464] [INFO] DFAST Taxonomy check result was written to GCF_002351485.1_ASM235148v1_genomic.fna/tc_result.tsv
[2024-01-25 18:49:48,465] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:49:48,465] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:49:48,466] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgccc0649a-c79e-418d-b5de-ebe0e047acb8/dqc_reference/checkm_data
[2024-01-25 18:49:48,467] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:49:48,508] [INFO] Task started: CheckM
[2024-01-25 18:49:48,508] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002351485.1_ASM235148v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002351485.1_ASM235148v1_genomic.fna/checkm_input GCF_002351485.1_ASM235148v1_genomic.fna/checkm_result
[2024-01-25 18:50:18,509] [INFO] Task succeeded: CheckM
[2024-01-25 18:50:18,509] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:50:18,574] [INFO] ===== Completeness check finished =====
[2024-01-25 18:50:18,574] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:50:18,575] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002351485.1_ASM235148v1_genomic.fna/markers.fasta)
[2024-01-25 18:50:18,575] [INFO] Task started: Blastn
[2024-01-25 18:50:18,575] [INFO] Running command: blastn -query GCF_002351485.1_ASM235148v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgccc0649a-c79e-418d-b5de-ebe0e047acb8/dqc_reference/reference_markers_gtdb.fasta -out GCF_002351485.1_ASM235148v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:50:20,431] [INFO] Task succeeded: Blastn
[2024-01-25 18:50:20,433] [INFO] Selected 19 target genomes.
[2024-01-25 18:50:20,433] [INFO] Target genome list was writen to GCF_002351485.1_ASM235148v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:50:20,465] [INFO] Task started: fastANI
[2024-01-25 18:50:20,465] [INFO] Running command: fastANI --query /var/lib/cwl/stga31c0b43-8b24-4fdc-8427-472adb68c49c/GCF_002351485.1_ASM235148v1_genomic.fna.gz --refList GCF_002351485.1_ASM235148v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002351485.1_ASM235148v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:50:35,832] [INFO] Task succeeded: fastANI
[2024-01-25 18:50:35,844] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:50:35,844] [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_002351485.1	s__Sphingomonas spermidinifaciens	100.0	1209	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014199325.1	s__Sphingomonas yantingensis	87.2798	888	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.75	96.75	0.89	0.89	2	-
GCF_005144715.1	s__Sphingomonas sp005144715	81.1457	620	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006346325.1	s__Sphingomonas japonica	79.982	552	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004792695.1	s__Sphingomonas naasensis	79.8629	596	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_902498785.1	s__Sphingomonas sp902498785	79.7449	515	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000786205.1	s__Sphingomonas sp000786205	79.6838	541	1209	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	79.652	559	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.13	98.00	0.88	0.86	72	-
GCF_900115745.1	s__Sphingomonas rubra	79.6357	506	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012035195.1	s__Sphingomonas sp012035195	79.5702	558	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000226955.1	s__Sphingomonas elodea_A	79.5294	524	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199415.1	s__Sphingomonas endophytica	79.4006	529	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.00	98.00	0.92	0.92	2	-
GCF_001557215.1	s__Sphingomonas sp001557215	79.3574	516	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.89	99.89	0.91	0.91	2	-
GCF_014194975.1	s__Sphingomonas sp014194975	79.3238	585	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014217605.1	s__Sphingomonas sp014217605	79.1564	495	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002197685.1	s__Sphingomonas dokdonensis	79.1158	436	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002117915.1	s__Sphingomonas sp002117915	79.0758	486	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011057975.1	s__Sphingomonas sp011057975	78.9679	472	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903884945.1	s__Sphingomonas sp903884945	78.7539	519	1209	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 18:50:35,846] [INFO] GTDB search result was written to GCF_002351485.1_ASM235148v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:50:35,846] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:50:35,850] [INFO] DFAST_QC result json was written to GCF_002351485.1_ASM235148v1_genomic.fna/dqc_result.json
[2024-01-25 18:50:35,850] [INFO] DFAST_QC completed!
[2024-01-25 18:50:35,850] [INFO] Total running time: 0h1m15s