[2024-01-25 18:02:35,585] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:02:35,586] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:02:35,586] [INFO] DQC Reference Directory: /var/lib/cwl/stg28857585-cd49-4504-a2a7-97fc66322c5e/dqc_reference
[2024-01-25 18:02:36,708] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:02:36,709] [INFO] Task started: Prodigal
[2024-01-25 18:02:36,709] [INFO] Running command: gunzip -c /var/lib/cwl/stgefeb2a9f-202d-4e84-af8c-65457d044c99/GCF_025370105.1_ASM2537010v1_genomic.fna.gz | prodigal -d GCF_025370105.1_ASM2537010v1_genomic.fna/cds.fna -a GCF_025370105.1_ASM2537010v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:02:46,800] [INFO] Task succeeded: Prodigal
[2024-01-25 18:02:46,800] [INFO] Task started: HMMsearch
[2024-01-25 18:02:46,800] [INFO] Running command: hmmsearch --tblout GCF_025370105.1_ASM2537010v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg28857585-cd49-4504-a2a7-97fc66322c5e/dqc_reference/reference_markers.hmm GCF_025370105.1_ASM2537010v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:02:47,021] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:02:47,022] [INFO] Found 6/6 markers.
[2024-01-25 18:02:47,054] [INFO] Query marker FASTA was written to GCF_025370105.1_ASM2537010v1_genomic.fna/markers.fasta
[2024-01-25 18:02:47,054] [INFO] Task started: Blastn
[2024-01-25 18:02:47,054] [INFO] Running command: blastn -query GCF_025370105.1_ASM2537010v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg28857585-cd49-4504-a2a7-97fc66322c5e/dqc_reference/reference_markers.fasta -out GCF_025370105.1_ASM2537010v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:02:47,988] [INFO] Task succeeded: Blastn
[2024-01-25 18:02:47,990] [INFO] Selected 18 target genomes.
[2024-01-25 18:02:47,990] [INFO] Target genome list was writen to GCF_025370105.1_ASM2537010v1_genomic.fna/target_genomes.txt
[2024-01-25 18:02:48,001] [INFO] Task started: fastANI
[2024-01-25 18:02:48,001] [INFO] Running command: fastANI --query /var/lib/cwl/stgefeb2a9f-202d-4e84-af8c-65457d044c99/GCF_025370105.1_ASM2537010v1_genomic.fna.gz --refList GCF_025370105.1_ASM2537010v1_genomic.fna/target_genomes.txt --output GCF_025370105.1_ASM2537010v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:03:03,956] [INFO] Task succeeded: fastANI
[2024-01-25 18:03:03,956] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg28857585-cd49-4504-a2a7-97fc66322c5e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:03:03,957] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg28857585-cd49-4504-a2a7-97fc66322c5e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:03:03,967] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:03:03,967] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:03:03,967] [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 hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	100.0	1284	1285	95	conclusive
Sphingomonas aliaeris	strain=DH-S5	GCA_016743815.1	2759526	2759526	type	True	81.8437	714	1285	95	below_threshold
Sphingomonas glacialis	strain=CGMCC 1.8957	GCA_014653575.1	658225	658225	type	True	81.4286	719	1285	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_014490665.1	653931	653931	type	True	81.4177	718	1285	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	81.4151	716	1285	95	below_threshold
Sphingomonas echinoides	strain=ATCC 14820	GCA_000241465.1	59803	59803	type	True	80.8445	641	1285	95	below_threshold
Sphingomonas ginsenosidivorax	strain=KHI67	GCA_007995065.1	862135	862135	type	True	80.8432	659	1285	95	below_threshold
Sphingomonas psychrolutea	strain=CGMCC 1.10106	GCA_014636175.1	1259676	1259676	type	True	80.5944	615	1285	95	below_threshold
Sphingomonas populi	strain=3-7	GCA_004208535.1	2484750	2484750	type	True	80.5501	631	1285	95	below_threshold
Sphingomonas panacis	strain=DCY99	GCA_001717955.1	1560345	1560345	type	True	80.3323	653	1285	95	below_threshold
Sphingomonas adhaesiva	strain=NBRC 15099	GCA_001592345.1	28212	28212	type	True	79.9064	480	1285	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	79.6734	572	1285	95	below_threshold
Sphingomonas adhaesiva	strain=DSM 7418	GCA_002374855.1	28212	28212	type	True	79.6496	581	1285	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	79.3732	614	1285	95	below_threshold
Sphingomonas pseudosanguinis	strain=DSM 19512	GCA_014196255.1	413712	413712	type	True	79.3636	554	1285	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	79.3174	622	1285	95	below_threshold
Sphingomonas paucimobilis	strain=NBRC 13935	GCA_000739895.2	13689	13689	type	True	79.2846	506	1285	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	79.2511	599	1285	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:03:03,969] [INFO] DFAST Taxonomy check result was written to GCF_025370105.1_ASM2537010v1_genomic.fna/tc_result.tsv
[2024-01-25 18:03:03,969] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:03:03,969] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:03:03,969] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg28857585-cd49-4504-a2a7-97fc66322c5e/dqc_reference/checkm_data
[2024-01-25 18:03:03,970] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:03:04,008] [INFO] Task started: CheckM
[2024-01-25 18:03:04,008] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025370105.1_ASM2537010v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025370105.1_ASM2537010v1_genomic.fna/checkm_input GCF_025370105.1_ASM2537010v1_genomic.fna/checkm_result
[2024-01-25 18:03:35,341] [INFO] Task succeeded: CheckM
[2024-01-25 18:03:35,342] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:03:35,387] [INFO] ===== Completeness check finished =====
[2024-01-25 18:03:35,388] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:03:35,388] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025370105.1_ASM2537010v1_genomic.fna/markers.fasta)
[2024-01-25 18:03:35,388] [INFO] Task started: Blastn
[2024-01-25 18:03:35,388] [INFO] Running command: blastn -query GCF_025370105.1_ASM2537010v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg28857585-cd49-4504-a2a7-97fc66322c5e/dqc_reference/reference_markers_gtdb.fasta -out GCF_025370105.1_ASM2537010v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:03:37,336] [INFO] Task succeeded: Blastn
[2024-01-25 18:03:37,339] [INFO] Selected 18 target genomes.
[2024-01-25 18:03:37,339] [INFO] Target genome list was writen to GCF_025370105.1_ASM2537010v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:03:37,359] [INFO] Task started: fastANI
[2024-01-25 18:03:37,359] [INFO] Running command: fastANI --query /var/lib/cwl/stgefeb2a9f-202d-4e84-af8c-65457d044c99/GCF_025370105.1_ASM2537010v1_genomic.fna.gz --refList GCF_025370105.1_ASM2537010v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025370105.1_ASM2537010v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:03:55,367] [INFO] Task succeeded: fastANI
[2024-01-25 18:03:55,378] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:03:55,379] [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_001423845.1	s__Sphingomonas sp001423845	83.4563	782	1285	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016743815.1	s__Sphingomonas sp016743815	81.8699	711	1285	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006439055.1	s__Sphingomonas glacialis_A	81.6971	718	1285	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000241485.1	s__Sphingomonas sp000241485	81.6649	707	1285	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	81.4352	719	1285	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.17	97.17	0.81	0.81	2	-
GCF_014490665.1	s__Sphingomonas alpina	81.4056	720	1285	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000803065.1	s__Sphingomonas sp000803065	81.2785	715	1285	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014171475.1	s__Sphingomonas alpina_A	81.2748	716	1285	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000251145.1	s__Sphingomonas sp000251145	80.7387	655	1285	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.28	96.28	0.82	0.82	2	-
GCF_004208535.1	s__Sphingomonas populi	80.5241	634	1285	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103265.1	s__Sphingomonas sp900103265	80.5	610	1285	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001421805.1	s__Sphingomonas sp001421805	80.4599	620	1285	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.24	98.24	0.93	0.93	2	-
GCF_001717955.1	s__Sphingomonas panacis	80.3532	651	1285	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204695.1	s__Sphingomonas sp001897045	79.9961	624	1285	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.82	96.97	0.94	0.83	6	-
GCF_002374855.1	s__Sphingomonas adhaesiva	79.667	583	1285	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.76	99.56	0.89	0.87	3	-
GCF_002374835.1	s__Sphingomonas ginsenosidimutans	79.5921	575	1285	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.62	98.43	0.85	0.81	6	-
GCF_014194975.1	s__Sphingomonas sp014194975	79.3278	617	1285	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014193845.1	s__Sphingomonas sp014193845	79.31	605	1285	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.90	98.90	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:03:55,380] [INFO] GTDB search result was written to GCF_025370105.1_ASM2537010v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:03:55,381] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:03:55,384] [INFO] DFAST_QC result json was written to GCF_025370105.1_ASM2537010v1_genomic.fna/dqc_result.json
[2024-01-25 18:03:55,384] [INFO] DFAST_QC completed!
[2024-01-25 18:03:55,384] [INFO] Total running time: 0h1m20s