[2024-01-24 10:48:09,162] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:48:09,167] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:48:09,168] [INFO] DQC Reference Directory: /var/lib/cwl/stg6dbe1b83-6f9f-49ae-b653-96ea82ae7f62/dqc_reference
[2024-01-24 10:48:23,956] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:48:23,958] [INFO] Task started: Prodigal
[2024-01-24 10:48:23,958] [INFO] Running command: gunzip -c /var/lib/cwl/stg92c53282-4ea4-4c31-af4d-970295832d5c/GCF_016820445.1_ASM1682044v1_genomic.fna.gz | prodigal -d GCF_016820445.1_ASM1682044v1_genomic.fna/cds.fna -a GCF_016820445.1_ASM1682044v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:48:34,119] [INFO] Task succeeded: Prodigal
[2024-01-24 10:48:34,120] [INFO] Task started: HMMsearch
[2024-01-24 10:48:34,120] [INFO] Running command: hmmsearch --tblout GCF_016820445.1_ASM1682044v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6dbe1b83-6f9f-49ae-b653-96ea82ae7f62/dqc_reference/reference_markers.hmm GCF_016820445.1_ASM1682044v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:48:34,384] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:48:34,386] [INFO] Found 6/6 markers.
[2024-01-24 10:48:34,432] [INFO] Query marker FASTA was written to GCF_016820445.1_ASM1682044v1_genomic.fna/markers.fasta
[2024-01-24 10:48:34,432] [INFO] Task started: Blastn
[2024-01-24 10:48:34,432] [INFO] Running command: blastn -query GCF_016820445.1_ASM1682044v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6dbe1b83-6f9f-49ae-b653-96ea82ae7f62/dqc_reference/reference_markers.fasta -out GCF_016820445.1_ASM1682044v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:35,395] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:35,401] [INFO] Selected 23 target genomes.
[2024-01-24 10:48:35,401] [INFO] Target genome list was writen to GCF_016820445.1_ASM1682044v1_genomic.fna/target_genomes.txt
[2024-01-24 10:48:35,411] [INFO] Task started: fastANI
[2024-01-24 10:48:35,411] [INFO] Running command: fastANI --query /var/lib/cwl/stg92c53282-4ea4-4c31-af4d-970295832d5c/GCF_016820445.1_ASM1682044v1_genomic.fna.gz --refList GCF_016820445.1_ASM1682044v1_genomic.fna/target_genomes.txt --output GCF_016820445.1_ASM1682044v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:54,097] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:54,098] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6dbe1b83-6f9f-49ae-b653-96ea82ae7f62/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:54,098] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6dbe1b83-6f9f-49ae-b653-96ea82ae7f62/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:54,125] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:48:54,126] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:48:54,126] [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 taxi	strain=ATCC 55669	GCA_000764535.1	1549858	1549858	type	True	82.7265	768	1195	95	below_threshold
Sphingomonas aquatilis	strain=NBRC 16722	GCA_007990915.1	93063	93063	type	True	82.3139	698	1195	95	below_threshold
Sphingomonas melonis	strain=DAPP-PG 224	GCA_000379045.1	152682	152682	type	True	82.3011	759	1195	95	below_threshold
Sphingomonas aquatilis	strain=DSM 15581	GCA_014196115.1	93063	93063	type	True	82.2606	759	1195	95	below_threshold
Sphingomonas insulae	strain=DSM 21792	GCA_011762035.1	424800	424800	type	True	81.9166	687	1195	95	below_threshold
Sphingomonas insulae	strain=KCTC 12872	GCA_010450875.1	424800	424800	type	True	81.9135	703	1195	95	below_threshold
Sphingomonas jinjuensis	strain=YC6723	GCA_014197105.1	535907	535907	type	True	81.0896	680	1195	95	below_threshold
Sphingomonas metalli	strain=CGMCC 1.15330	GCA_014641735.1	1779358	1779358	type	True	81.0688	619	1195	95	below_threshold
Sphingomonas endophytica	strain=DSM 101535	GCA_014199415.1	869719	869719	type	True	80.7299	576	1195	95	below_threshold
Sphingomonas abaci	strain=DSM 15867	GCA_014199625.1	237611	237611	type	True	80.7236	644	1195	95	below_threshold
Sphingomonas rubra	strain=CGMCC 1.9113	GCA_900115745.1	634430	634430	type	True	80.5697	607	1195	95	below_threshold
Sphingomonas ginsenosidivorax	strain=KHI67	GCA_007995065.1	862135	862135	type	True	80.4992	618	1195	95	below_threshold
Sphingomonas ginsenosidimutans	strain=KACC 14949	GCA_002374835.1	862134	862134	type	True	80.4256	617	1195	95	below_threshold
Sphingomonas pseudosanguinis	strain=DSM 19512	GCA_014196255.1	413712	413712	type	True	80.3735	637	1195	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	80.3117	656	1195	95	below_threshold
Sphingomonas pseudosanguinis	strain=DSM 19512	GCA_017052355.1	413712	413712	type	True	80.2983	646	1195	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	80.2963	652	1195	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	80.2207	640	1195	95	below_threshold
Sphingomonas phyllosphaerae	strain=FA2	GCA_000427645.1	257003	257003	type	True	80.1971	583	1195	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	79.8772	554	1195	95	below_threshold
Sphingomonas panni	strain=DSM 15761	GCA_022664435.1	237612	237612	type	True	79.3813	502	1195	95	below_threshold
Sphingomonas lenta	strain=1PNM-20	GCA_002288825.1	1141887	1141887	type	True	79.2348	520	1195	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	78.938	449	1195	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:54,136] [INFO] DFAST Taxonomy check result was written to GCF_016820445.1_ASM1682044v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:54,137] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:54,138] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:54,138] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6dbe1b83-6f9f-49ae-b653-96ea82ae7f62/dqc_reference/checkm_data
[2024-01-24 10:48:54,141] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:54,184] [INFO] Task started: CheckM
[2024-01-24 10:48:54,184] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016820445.1_ASM1682044v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016820445.1_ASM1682044v1_genomic.fna/checkm_input GCF_016820445.1_ASM1682044v1_genomic.fna/checkm_result
[2024-01-24 10:49:34,010] [INFO] Task succeeded: CheckM
[2024-01-24 10:49:34,011] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:49:34,048] [INFO] ===== Completeness check finished =====
[2024-01-24 10:49:34,048] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:49:34,049] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016820445.1_ASM1682044v1_genomic.fna/markers.fasta)
[2024-01-24 10:49:34,049] [INFO] Task started: Blastn
[2024-01-24 10:49:34,049] [INFO] Running command: blastn -query GCF_016820445.1_ASM1682044v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6dbe1b83-6f9f-49ae-b653-96ea82ae7f62/dqc_reference/reference_markers_gtdb.fasta -out GCF_016820445.1_ASM1682044v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:35,954] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:35,957] [INFO] Selected 13 target genomes.
[2024-01-24 10:49:35,957] [INFO] Target genome list was writen to GCF_016820445.1_ASM1682044v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:49:35,968] [INFO] Task started: fastANI
[2024-01-24 10:49:35,969] [INFO] Running command: fastANI --query /var/lib/cwl/stg92c53282-4ea4-4c31-af4d-970295832d5c/GCF_016820445.1_ASM1682044v1_genomic.fna.gz --refList GCF_016820445.1_ASM1682044v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016820445.1_ASM1682044v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:49,328] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:49,339] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:49:49,340] [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_016820445.1	s__Sphingomonas sp016820445	100.0	1192	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.21	97.21	0.90	0.90	2	conclusive
GCF_003355005.1	s__Sphingomonas sp003355005	86.103	873	1195	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	84.5912	856	1195	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	82.8092	721	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409985.1	s__Sphingomonas melonis_A	82.7426	765	1195	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	82.7036	771	1195	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	82.5957	778	1195	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	82.2564	760	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.36	95.86	0.87	0.82	11	-
GCF_010450875.1	s__Sphingomonas insulae	81.932	701	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014197105.1	s__Sphingomonas jinjuensis	81.0699	683	1195	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	81.0685	619	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007995065.1	s__Sphingomonas ginsenosidivorax	80.4765	620	1195	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	80.3619	638	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 10:49:49,342] [INFO] GTDB search result was written to GCF_016820445.1_ASM1682044v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:49,344] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:49,351] [INFO] DFAST_QC result json was written to GCF_016820445.1_ASM1682044v1_genomic.fna/dqc_result.json
[2024-01-24 10:49:49,352] [INFO] DFAST_QC completed!
[2024-01-24 10:49:49,352] [INFO] Total running time: 0h1m40s