[2024-01-24 15:26:55,223] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:55,225] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:55,225] [INFO] DQC Reference Directory: /var/lib/cwl/stg44127b48-9ca0-45b7-95af-c27335b6ae9f/dqc_reference
[2024-01-24 15:26:56,627] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:56,628] [INFO] Task started: Prodigal
[2024-01-24 15:26:56,628] [INFO] Running command: gunzip -c /var/lib/cwl/stg123abeba-5939-4b7e-af74-2cca2f7bd6b5/GCF_026013415.1_ASM2601341v1_genomic.fna.gz | prodigal -d GCF_026013415.1_ASM2601341v1_genomic.fna/cds.fna -a GCF_026013415.1_ASM2601341v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:08,902] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:08,902] [INFO] Task started: HMMsearch
[2024-01-24 15:27:08,902] [INFO] Running command: hmmsearch --tblout GCF_026013415.1_ASM2601341v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg44127b48-9ca0-45b7-95af-c27335b6ae9f/dqc_reference/reference_markers.hmm GCF_026013415.1_ASM2601341v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:09,171] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:09,172] [INFO] Found 6/6 markers.
[2024-01-24 15:27:09,209] [INFO] Query marker FASTA was written to GCF_026013415.1_ASM2601341v1_genomic.fna/markers.fasta
[2024-01-24 15:27:09,210] [INFO] Task started: Blastn
[2024-01-24 15:27:09,210] [INFO] Running command: blastn -query GCF_026013415.1_ASM2601341v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44127b48-9ca0-45b7-95af-c27335b6ae9f/dqc_reference/reference_markers.fasta -out GCF_026013415.1_ASM2601341v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:10,229] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:10,235] [INFO] Selected 22 target genomes.
[2024-01-24 15:27:10,236] [INFO] Target genome list was writen to GCF_026013415.1_ASM2601341v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:10,241] [INFO] Task started: fastANI
[2024-01-24 15:27:10,241] [INFO] Running command: fastANI --query /var/lib/cwl/stg123abeba-5939-4b7e-af74-2cca2f7bd6b5/GCF_026013415.1_ASM2601341v1_genomic.fna.gz --refList GCF_026013415.1_ASM2601341v1_genomic.fna/target_genomes.txt --output GCF_026013415.1_ASM2601341v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:33,024] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:33,025] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg44127b48-9ca0-45b7-95af-c27335b6ae9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:33,025] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg44127b48-9ca0-45b7-95af-c27335b6ae9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:33,042] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:27:33,042] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:27:33,043] [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 naasensis	strain=KIS18-15	GCA_004792695.1	1344951	1344951	type	True	81.8327	809	1356	95	below_threshold
Sphingomonas naasensis	strain=DSM 100060	GCA_011762145.1	1344951	1344951	type	True	81.7489	828	1356	95	below_threshold
Sphingomonas kyeonggiensis	strain=DSM 101806	GCA_014196745.1	1268553	1268553	type	True	81.3359	783	1356	95	below_threshold
Sphingomonas gei	strain=ZFGT-11	GCA_004792685.1	1395960	1395960	type	True	81.134	727	1356	95	below_threshold
Sphingomonas hengshuiensis	strain=WHSC-8	GCA_000935025.1	1609977	1609977	type	True	81.0508	747	1356	95	below_threshold
Sphingomonas psychrotolerans	strain=Cra20	GCA_002796605.1	1327635	1327635	type	True	80.9025	759	1356	95	below_threshold
Sphingomonas soli	strain=NBRC 100801	GCA_001591025.1	266127	266127	type	True	80.7393	678	1356	95	below_threshold
Sphingomonas pituitosa	strain=NBRC 102491	GCA_001598435.1	99597	99597	type	True	80.3671	656	1356	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	79.9171	622	1356	95	below_threshold
Sphingomonas baiyangensis	strain=L-1-4 w-11	GCA_005144715.1	2572576	2572576	type	True	79.6707	547	1356	95	below_threshold
Sphingomonas xinjiangensis	strain=DSM 26736	GCA_014199255.1	643568	643568	type	True	79.5644	518	1356	95	below_threshold
Sphingomonas taxi	strain=ATCC 55669	GCA_000764535.1	1549858	1549858	type	True	79.5174	584	1356	95	below_threshold
Sphingomonas mali	strain=NBRC 15500	GCA_001598415.1	40682	40682	type	True	79.4082	585	1356	95	below_threshold
Sphingomonas pruni	strain=NBRC 15498	GCA_001598455.1	40683	40683	type	True	79.3757	552	1356	95	below_threshold
Sphingomonas panacis	strain=DCY99	GCA_001717955.1	1560345	1560345	type	True	79.3216	554	1356	95	below_threshold
Sphingomonas asaccharolytica	strain=NBRC 15499	GCA_001598355.1	40681	40681	type	True	79.2976	571	1356	95	below_threshold
Sphingomonas populi	strain=3-7	GCA_004208535.1	2484750	2484750	type	True	79.2586	559	1356	95	below_threshold
Sphingomonas panacisoli	strain=HKS19	GCA_007859635.1	1813879	1813879	type	True	79.2413	539	1356	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	79.1165	559	1356	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	79.0483	548	1356	95	below_threshold
Sphingomonas citricola	strain=RHCKR47	GCA_019429535.1	2862498	2862498	type	True	78.8468	454	1356	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	78.5013	516	1356	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:33,046] [INFO] DFAST Taxonomy check result was written to GCF_026013415.1_ASM2601341v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:33,047] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:33,047] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:33,047] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg44127b48-9ca0-45b7-95af-c27335b6ae9f/dqc_reference/checkm_data
[2024-01-24 15:27:33,049] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:33,091] [INFO] Task started: CheckM
[2024-01-24 15:27:33,091] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026013415.1_ASM2601341v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026013415.1_ASM2601341v1_genomic.fna/checkm_input GCF_026013415.1_ASM2601341v1_genomic.fna/checkm_result
[2024-01-24 15:28:10,131] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:10,133] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:10,150] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:10,150] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:10,151] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026013415.1_ASM2601341v1_genomic.fna/markers.fasta)
[2024-01-24 15:28:10,151] [INFO] Task started: Blastn
[2024-01-24 15:28:10,151] [INFO] Running command: blastn -query GCF_026013415.1_ASM2601341v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44127b48-9ca0-45b7-95af-c27335b6ae9f/dqc_reference/reference_markers_gtdb.fasta -out GCF_026013415.1_ASM2601341v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:12,016] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:12,019] [INFO] Selected 18 target genomes.
[2024-01-24 15:28:12,020] [INFO] Target genome list was writen to GCF_026013415.1_ASM2601341v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:12,028] [INFO] Task started: fastANI
[2024-01-24 15:28:12,028] [INFO] Running command: fastANI --query /var/lib/cwl/stg123abeba-5939-4b7e-af74-2cca2f7bd6b5/GCF_026013415.1_ASM2601341v1_genomic.fna.gz --refList GCF_026013415.1_ASM2601341v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026013415.1_ASM2601341v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:29,809] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:29,823] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 15:28:29,824] [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_018449795.1	s__Sphingomonas sp018449795	82.1393	716	1356	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927115.1	s__Sphingomonas sp012927115	82.0188	872	1356	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017745215.1	s__Sphingomonas sp017745215	81.8495	816	1356	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	81.8151	811	1356	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001428865.1	s__Sphingomonas sp001428865	81.7345	740	1356	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014489075.1	s__Sphingomonas sp014489075	81.5928	802	1356	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744835.1	s__Sphingomonas sp017744835	81.5733	717	1356	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017418975.1	s__Sphingomonas sp017418975	81.5477	777	1356	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000712135.1	s__Sphingomonas sp000712135	81.4167	782	1356	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196745.1	s__Sphingomonas kyeonggiensis	81.3391	784	1356	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002002925.1	s__Sphingomonas sp002002925	81.2089	745	1356	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004792685.1	s__Sphingomonas gei	81.1323	728	1356	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012650175.1	s__Sphingomonas sp012650175	80.4531	635	1356	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004173185.1	s__Sphingomonas sp004173185	80.2147	685	1356	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000764535.1	s__Sphingomonas taxi	79.4581	591	1356	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.55	97.55	0.88	0.88	2	-
GCF_900103265.1	s__Sphingomonas sp900103265	79.3791	549	1356	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001717955.1	s__Sphingomonas panacis	79.2744	557	1356	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004208535.1	s__Sphingomonas populi	79.2655	558	1356	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 15:28:29,825] [INFO] GTDB search result was written to GCF_026013415.1_ASM2601341v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:29,826] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:29,829] [INFO] DFAST_QC result json was written to GCF_026013415.1_ASM2601341v1_genomic.fna/dqc_result.json
[2024-01-24 15:28:29,830] [INFO] DFAST_QC completed!
[2024-01-24 15:28:29,830] [INFO] Total running time: 0h1m35s