[2024-01-25 17:48:05,695] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:48:05,697] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:48:05,697] [INFO] DQC Reference Directory: /var/lib/cwl/stgba944022-83e6-46aa-95a0-5bd9294bb6ec/dqc_reference
[2024-01-25 17:48:06,797] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:48:06,798] [INFO] Task started: Prodigal
[2024-01-25 17:48:06,798] [INFO] Running command: gunzip -c /var/lib/cwl/stg53ce6017-b946-45be-90aa-d4c12f134eda/GCF_014117445.1_ASM1411744v1_genomic.fna.gz | prodigal -d GCF_014117445.1_ASM1411744v1_genomic.fna/cds.fna -a GCF_014117445.1_ASM1411744v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:48:17,147] [INFO] Task succeeded: Prodigal
[2024-01-25 17:48:17,147] [INFO] Task started: HMMsearch
[2024-01-25 17:48:17,147] [INFO] Running command: hmmsearch --tblout GCF_014117445.1_ASM1411744v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgba944022-83e6-46aa-95a0-5bd9294bb6ec/dqc_reference/reference_markers.hmm GCF_014117445.1_ASM1411744v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:48:17,345] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:48:17,346] [INFO] Found 6/6 markers.
[2024-01-25 17:48:17,372] [INFO] Query marker FASTA was written to GCF_014117445.1_ASM1411744v1_genomic.fna/markers.fasta
[2024-01-25 17:48:17,372] [INFO] Task started: Blastn
[2024-01-25 17:48:17,372] [INFO] Running command: blastn -query GCF_014117445.1_ASM1411744v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgba944022-83e6-46aa-95a0-5bd9294bb6ec/dqc_reference/reference_markers.fasta -out GCF_014117445.1_ASM1411744v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:48:18,189] [INFO] Task succeeded: Blastn
[2024-01-25 17:48:18,191] [INFO] Selected 35 target genomes.
[2024-01-25 17:48:18,192] [INFO] Target genome list was writen to GCF_014117445.1_ASM1411744v1_genomic.fna/target_genomes.txt
[2024-01-25 17:48:18,224] [INFO] Task started: fastANI
[2024-01-25 17:48:18,224] [INFO] Running command: fastANI --query /var/lib/cwl/stg53ce6017-b946-45be-90aa-d4c12f134eda/GCF_014117445.1_ASM1411744v1_genomic.fna.gz --refList GCF_014117445.1_ASM1411744v1_genomic.fna/target_genomes.txt --output GCF_014117445.1_ASM1411744v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:48:41,825] [INFO] Task succeeded: fastANI
[2024-01-25 17:48:41,826] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgba944022-83e6-46aa-95a0-5bd9294bb6ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:48:41,826] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgba944022-83e6-46aa-95a0-5bd9294bb6ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:48:41,844] [INFO] Found 35 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:48:41,844] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:48:41,844] [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
Sandarakinorhabdus oryzae	strain=NM-18	GCA_009733735.1	2675220	2675220	type	True	77.6951	279	1121	95	below_threshold
Sphingomonas gilva	strain=ZDH117	GCA_003515075.1	2305907	2305907	type	True	77.2808	268	1121	95	below_threshold
Sphingomonas baiyangensis	strain=L-1-4 w-11	GCA_005144715.1	2572576	2572576	type	True	77.2598	234	1121	95	below_threshold
Sphingomonas horti	strain=MAH-20	GCA_009753715.1	2682842	2682842	type	True	77.2514	234	1121	95	below_threshold
Sphingomonas trueperi	strain=DSM 7225	GCA_011927635.1	53317	53317	type	True	77.1853	265	1121	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	77.0818	273	1121	95	below_threshold
Tardibacter chloracetimidivorans	strain=JJ-A5	GCA_001890385.1	1921510	1921510	type	True	77.0574	174	1121	95	below_threshold
Sphingopyxis indica	strain=DS15	GCA_900188185.1	436663	436663	type	True	77.0425	235	1121	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	77.0205	261	1121	95	below_threshold
Sphingobium jiangsuense	strain=DSM 26189	GCA_014196495.1	870476	870476	type	True	77.0114	276	1121	95	below_threshold
Sphingosinicella humi	strain=QZX222	GCA_003129465.1	2068657	2068657	type	True	77.0052	187	1121	95	below_threshold
Sphingomonas ginsenosidivorax	strain=KHI67	GCA_007995065.1	862135	862135	type	True	76.9869	222	1121	95	below_threshold
Sphingobium indicum	strain=B90A	GCA_000264945.2	332055	332055	type	True	76.9675	247	1121	95	below_threshold
Sphingomonas aquatilis	strain=NBRC 16722	GCA_007990915.1	93063	93063	type	True	76.9639	206	1121	95	below_threshold
Sphingomonas endophytica	strain=DSM 101535	GCA_014199415.1	869719	869719	type	True	76.9619	234	1121	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	76.9609	241	1121	95	below_threshold
Sphingomonas melonis	strain=DAPP-PG 224	GCA_000379045.1	152682	152682	type	True	76.9565	234	1121	95	below_threshold
Sphingomonas sanxanigenens	strain=NX02	GCA_000512205.2	397260	397260	type	True	76.9549	295	1121	95	below_threshold
Sphingosinicella microcystinivorans	strain=DSM 19791	GCA_003634215.1	335406	335406	type	True	76.9468	191	1121	95	below_threshold
Sphingomonas taxi	strain=ATCC 55669	GCA_000764535.1	1549858	1549858	type	True	76.9105	276	1121	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	76.908	343	1121	95	below_threshold
Sphingomonas chungangi	strain=CGMCC 1.13654	GCA_013778325.1	2683589	2683589	type	True	76.8729	235	1121	95	below_threshold
Sphingomonas dokdonensis	strain=DSM 21029	GCA_002197685.1	344880	344880	type	True	76.8152	211	1121	95	below_threshold
Sphingomonas aquatilis	strain=DSM 15581	GCA_014196115.1	93063	93063	type	True	76.8052	224	1121	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	76.778	310	1121	95	below_threshold
Sphingomonas rubra	strain=CGMCC 1.9113	GCA_900115745.1	634430	634430	type	True	76.7773	242	1121	95	below_threshold
Sphingobium lactosutens	strain=DS20	GCA_000445105.1	522773	522773	type	True	76.7589	200	1121	95	below_threshold
Pacificimonas flava	strain=DSM 107612	GCA_014202205.1	1234595	1234595	type	True	76.6949	164	1121	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	76.6684	303	1121	95	below_threshold
Pacificimonas flava	strain=JLT2015	GCA_000342165.1	1234595	1234595	type	True	76.6619	164	1121	95	below_threshold
Sphingomicrobium astaxanthinifaciens	strain=JCM 18551	GCA_022865105.1	1227949	1227949	type	True	76.6299	184	1121	95	below_threshold
Sphingomonas gei	strain=ZFGT-11	GCA_004792685.1	1395960	1395960	type	True	76.5352	212	1121	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	76.5293	254	1121	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	76.5248	279	1121	95	below_threshold
Novosphingobium rosa	strain=NBRC 15208	GCA_001598555.1	76978	76978	type	True	76.4769	200	1121	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:48:41,851] [INFO] DFAST Taxonomy check result was written to GCF_014117445.1_ASM1411744v1_genomic.fna/tc_result.tsv
[2024-01-25 17:48:41,852] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:48:41,852] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:48:41,852] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgba944022-83e6-46aa-95a0-5bd9294bb6ec/dqc_reference/checkm_data
[2024-01-25 17:48:41,853] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:48:41,887] [INFO] Task started: CheckM
[2024-01-25 17:48:41,887] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014117445.1_ASM1411744v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014117445.1_ASM1411744v1_genomic.fna/checkm_input GCF_014117445.1_ASM1411744v1_genomic.fna/checkm_result
[2024-01-25 17:49:29,924] [INFO] Task succeeded: CheckM
[2024-01-25 17:49:29,927] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:49:29,943] [INFO] ===== Completeness check finished =====
[2024-01-25 17:49:29,943] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:49:29,943] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014117445.1_ASM1411744v1_genomic.fna/markers.fasta)
[2024-01-25 17:49:29,944] [INFO] Task started: Blastn
[2024-01-25 17:49:29,944] [INFO] Running command: blastn -query GCF_014117445.1_ASM1411744v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgba944022-83e6-46aa-95a0-5bd9294bb6ec/dqc_reference/reference_markers_gtdb.fasta -out GCF_014117445.1_ASM1411744v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:49:31,628] [INFO] Task succeeded: Blastn
[2024-01-25 17:49:31,630] [INFO] Selected 20 target genomes.
[2024-01-25 17:49:31,630] [INFO] Target genome list was writen to GCF_014117445.1_ASM1411744v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:49:31,659] [INFO] Task started: fastANI
[2024-01-25 17:49:31,659] [INFO] Running command: fastANI --query /var/lib/cwl/stg53ce6017-b946-45be-90aa-d4c12f134eda/GCF_014117445.1_ASM1411744v1_genomic.fna.gz --refList GCF_014117445.1_ASM1411744v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014117445.1_ASM1411744v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:49:45,553] [INFO] Task succeeded: fastANI
[2024-01-25 17:49:45,565] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:49:45,565] [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_014117445.1	s__GCA-014117445 sp014117445	100.0	1121	1121	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__GCA-014117445	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003248865.1	s__Sandaracinobacter sp003248865	78.1484	370	1121	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sandaracinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016464365.1	s__Sandaracinobacter sp016464365	77.9332	344	1121	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sandaracinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006385875.1	s__Sandaracinobacter neustonicus	77.7623	365	1121	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sandaracinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010994245.1	s__Sandarakinorhabdus rubra	77.6035	264	1121	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sandarakinorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004681125.1	s__Polymorphobacter_A arshaanensis	77.388	265	1121	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Polymorphobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002422985.1	s__Sandaracinobacter sp002422985	77.3794	238	1121	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sandaracinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005144715.1	s__Sphingomonas sp005144715	77.2708	233	1121	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000331225.1	s__Sandarakinorhabdus sp000331225	77.249	287	1121	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sandarakinorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009753715.1	s__Sphingomonas_B horti	77.2385	235	1121	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_B	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003240855.1	s__Sphingomonas_L sanxanigenens_A	76.981	211	1121	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_003634215.1	s__Sphingosinicella microcystinivorans	76.9467	191	1121	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingosinicella	95.0	99.98	99.98	0.98	0.98	2	-
GCF_014199415.1	s__Sphingomonas endophytica	76.9302	236	1121	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.00	98.00	0.92	0.92	2	-
GCF_014194975.1	s__Sphingomonas sp014194975	76.8867	260	1121	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	76.8843	280	1121	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.55	97.55	0.88	0.88	2	-
GCF_006716975.1	s__Sphingomonas trueperi_A	76.6992	241	1121	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	95.23	95.23	0.88	0.88	2	-
GCF_000342165.1	s__Pacificimonas flava	76.6619	164	1121	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pacificimonas	95.0	99.99	99.99	1.00	1.00	2	-
GCA_016793845.1	s__Sphingosinicella sp016793845	76.6275	170	1121	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806285.1	s__Sphingomicrobium sp902806285	76.4503	152	1121	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019239415.1	s__Allosphingosinicella sp019239415	76.3902	219	1121	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:49:45,566] [INFO] GTDB search result was written to GCF_014117445.1_ASM1411744v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:49:45,567] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:49:45,571] [INFO] DFAST_QC result json was written to GCF_014117445.1_ASM1411744v1_genomic.fna/dqc_result.json
[2024-01-25 17:49:45,571] [INFO] DFAST_QC completed!
[2024-01-25 17:49:45,571] [INFO] Total running time: 0h1m40s