[2024-01-24 11:52:04,662] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:52:04,664] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:52:04,664] [INFO] DQC Reference Directory: /var/lib/cwl/stg692835f1-b6b5-4e54-8747-d1cf0a2774ac/dqc_reference
[2024-01-24 11:52:05,896] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:52:05,897] [INFO] Task started: Prodigal
[2024-01-24 11:52:05,898] [INFO] Running command: gunzip -c /var/lib/cwl/stgea274bc9-7599-494d-b5ae-9360df5b76aa/GCF_014197105.1_ASM1419710v1_genomic.fna.gz | prodigal -d GCF_014197105.1_ASM1419710v1_genomic.fna/cds.fna -a GCF_014197105.1_ASM1419710v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:52:16,361] [INFO] Task succeeded: Prodigal
[2024-01-24 11:52:16,361] [INFO] Task started: HMMsearch
[2024-01-24 11:52:16,362] [INFO] Running command: hmmsearch --tblout GCF_014197105.1_ASM1419710v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg692835f1-b6b5-4e54-8747-d1cf0a2774ac/dqc_reference/reference_markers.hmm GCF_014197105.1_ASM1419710v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:52:16,617] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:52:16,618] [INFO] Found 6/6 markers.
[2024-01-24 11:52:16,651] [INFO] Query marker FASTA was written to GCF_014197105.1_ASM1419710v1_genomic.fna/markers.fasta
[2024-01-24 11:52:16,651] [INFO] Task started: Blastn
[2024-01-24 11:52:16,651] [INFO] Running command: blastn -query GCF_014197105.1_ASM1419710v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg692835f1-b6b5-4e54-8747-d1cf0a2774ac/dqc_reference/reference_markers.fasta -out GCF_014197105.1_ASM1419710v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:17,696] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:17,700] [INFO] Selected 21 target genomes.
[2024-01-24 11:52:17,700] [INFO] Target genome list was writen to GCF_014197105.1_ASM1419710v1_genomic.fna/target_genomes.txt
[2024-01-24 11:52:17,708] [INFO] Task started: fastANI
[2024-01-24 11:52:17,708] [INFO] Running command: fastANI --query /var/lib/cwl/stgea274bc9-7599-494d-b5ae-9360df5b76aa/GCF_014197105.1_ASM1419710v1_genomic.fna.gz --refList GCF_014197105.1_ASM1419710v1_genomic.fna/target_genomes.txt --output GCF_014197105.1_ASM1419710v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:34,867] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:34,868] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg692835f1-b6b5-4e54-8747-d1cf0a2774ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:34,869] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg692835f1-b6b5-4e54-8747-d1cf0a2774ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:34,888] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:52:34,888] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:52:34,888] [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 jinjuensis	strain=YC6723	GCA_014197105.1	535907	535907	type	True	100.0	1270	1270	95	conclusive
Sphingomonas taxi	strain=ATCC 55669	GCA_000764535.1	1549858	1549858	type	True	81.6423	743	1270	95	below_threshold
Sphingomonas aquatilis	strain=NBRC 16722	GCA_007990915.1	93063	93063	type	True	81.5061	637	1270	95	below_threshold
Sphingomonas metalli	strain=CGMCC 1.15330	GCA_014641735.1	1779358	1779358	type	True	81.5006	655	1270	95	below_threshold
Sphingomonas aquatilis	strain=DSM 15581	GCA_014196115.1	93063	93063	type	True	81.4972	689	1270	95	below_threshold
Sphingomonas melonis	strain=DAPP-PG 224	GCA_000379045.1	152682	152682	type	True	81.434	696	1270	95	below_threshold
Sphingomonas insulae	strain=KCTC 12872	GCA_010450875.1	424800	424800	type	True	81.3648	672	1270	95	below_threshold
Sphingomonas insulae	strain=DSM 21792	GCA_011762035.1	424800	424800	type	True	81.2761	677	1270	95	below_threshold
Sphingomonas adhaesiva	strain=NBRC 15099	GCA_001592345.1	28212	28212	type	True	81.0888	536	1270	95	below_threshold
Sphingomonas adhaesiva	strain=DSM 7418	GCA_002374855.1	28212	28212	type	True	80.9898	641	1270	95	below_threshold
Sphingomonas ginsenosidimutans	strain=KACC 14949	GCA_002374835.1	862134	862134	type	True	80.7556	644	1270	95	below_threshold
Sphingomonas endophytica	strain=DSM 101535	GCA_014199415.1	869719	869719	type	True	80.7541	619	1270	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	80.7484	679	1270	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	80.6842	668	1270	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	80.508	657	1270	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	80.5054	650	1270	95	below_threshold
Sphingomonas phyllosphaerae	strain=FA2	GCA_000427645.1	257003	257003	type	True	80.4812	627	1270	95	below_threshold
Sphingomonas pseudosanguinis	strain=DSM 19512	GCA_014196255.1	413712	413712	type	True	80.4792	649	1270	95	below_threshold
Sphingomonas gellani	strain=S6-262	GCA_900110035.1	1166340	1166340	type	True	80.226	547	1270	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	79.9615	555	1270	95	below_threshold
Sphingomonas radiodurans	strain=S9-5	GCA_020866845.1	2890321	2890321	type	True	79.5479	532	1270	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:34,890] [INFO] DFAST Taxonomy check result was written to GCF_014197105.1_ASM1419710v1_genomic.fna/tc_result.tsv
[2024-01-24 11:52:34,890] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:34,891] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:34,891] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg692835f1-b6b5-4e54-8747-d1cf0a2774ac/dqc_reference/checkm_data
[2024-01-24 11:52:34,892] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:34,934] [INFO] Task started: CheckM
[2024-01-24 11:52:34,934] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014197105.1_ASM1419710v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014197105.1_ASM1419710v1_genomic.fna/checkm_input GCF_014197105.1_ASM1419710v1_genomic.fna/checkm_result
[2024-01-24 11:53:08,102] [INFO] Task succeeded: CheckM
[2024-01-24 11:53:08,103] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:53:08,129] [INFO] ===== Completeness check finished =====
[2024-01-24 11:53:08,129] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:53:08,130] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014197105.1_ASM1419710v1_genomic.fna/markers.fasta)
[2024-01-24 11:53:08,130] [INFO] Task started: Blastn
[2024-01-24 11:53:08,130] [INFO] Running command: blastn -query GCF_014197105.1_ASM1419710v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg692835f1-b6b5-4e54-8747-d1cf0a2774ac/dqc_reference/reference_markers_gtdb.fasta -out GCF_014197105.1_ASM1419710v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:53:10,125] [INFO] Task succeeded: Blastn
[2024-01-24 11:53:10,129] [INFO] Selected 22 target genomes.
[2024-01-24 11:53:10,130] [INFO] Target genome list was writen to GCF_014197105.1_ASM1419710v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:53:10,152] [INFO] Task started: fastANI
[2024-01-24 11:53:10,152] [INFO] Running command: fastANI --query /var/lib/cwl/stgea274bc9-7599-494d-b5ae-9360df5b76aa/GCF_014197105.1_ASM1419710v1_genomic.fna.gz --refList GCF_014197105.1_ASM1419710v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014197105.1_ASM1419710v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:53:28,553] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:28,583] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:53:28,583] [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_014197105.1	s__Sphingomonas jinjuensis	100.0	1270	1270	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_013409985.1	s__Sphingomonas melonis_A	81.8562	711	1270	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002292295.1	s__Sphingomonas sp002292295	81.798	716	1270	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	81.5923	749	1270	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.55	97.55	0.88	0.88	2	-
GCF_000632225.1	s__Sphingomonas sp000632225	81.5506	712	1270	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016107325.1	s__Sphingomonas sp016107325	81.5379	732	1270	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196115.1	s__Sphingomonas aquatilis	81.5153	687	1270	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.36	95.86	0.87	0.82	11	-
GCF_003355005.1	s__Sphingomonas sp003355005	81.5049	692	1270	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014641735.1	s__Sphingomonas metalli	81.4694	658	1270	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010450875.1	s__Sphingomonas insulae	81.3256	676	1270	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.99	99.99	0.99	0.99	2	-
GCA_003075315.1	s__Sphingomonas sp003075315	81.318	693	1270	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.84	96.53	0.96	0.89	4	-
GCF_016820445.1	s__Sphingomonas sp016820445	81.0777	666	1270	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.21	97.21	0.90	0.90	2	-
GCF_012035195.1	s__Sphingomonas sp012035195	80.5736	643	1270	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001476895.1	s__Sphingomonas endophytica_A	80.5047	587	1270	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196255.1	s__Sphingomonas pseudosanguinis	80.476	649	1270	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_013344685.1	s__Sphingomonas sp013344685	80.4656	574	1270	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006438955.1	s__Sphingomonas oligophenolica	80.4589	577	1270	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001897375.1	s__Sphingomonas sp001897375	80.3294	570	1270	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.01	98.04	0.97	0.96	3	-
GCF_902498785.1	s__Sphingomonas sp902498785	80.3112	587	1270	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110035.1	s__Sphingomonas gellani	80.2751	542	1270	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003345355.1	s__Sphingomonas sp003345355	79.9573	556	1270	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000980895.1	s__Sphingomonas olei	79.9149	523	1270	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.98	97.88	0.87	0.83	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:53:28,585] [INFO] GTDB search result was written to GCF_014197105.1_ASM1419710v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:53:28,586] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:53:28,591] [INFO] DFAST_QC result json was written to GCF_014197105.1_ASM1419710v1_genomic.fna/dqc_result.json
[2024-01-24 11:53:28,591] [INFO] DFAST_QC completed!
[2024-01-24 11:53:28,591] [INFO] Total running time: 0h1m24s