[2024-01-24 14:05:33,077] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:33,079] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:33,079] [INFO] DQC Reference Directory: /var/lib/cwl/stgbade764a-86ef-4020-826b-2011067d76ba/dqc_reference
[2024-01-24 14:05:34,346] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:34,347] [INFO] Task started: Prodigal
[2024-01-24 14:05:34,347] [INFO] Running command: gunzip -c /var/lib/cwl/stg368e33e3-2701-49c1-8a68-d72fea892a7d/GCF_018863195.1_ASM1886319v1_genomic.fna.gz | prodigal -d GCF_018863195.1_ASM1886319v1_genomic.fna/cds.fna -a GCF_018863195.1_ASM1886319v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:44,735] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:44,735] [INFO] Task started: HMMsearch
[2024-01-24 14:05:44,735] [INFO] Running command: hmmsearch --tblout GCF_018863195.1_ASM1886319v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbade764a-86ef-4020-826b-2011067d76ba/dqc_reference/reference_markers.hmm GCF_018863195.1_ASM1886319v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:44,975] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:44,976] [INFO] Found 6/6 markers.
[2024-01-24 14:05:45,008] [INFO] Query marker FASTA was written to GCF_018863195.1_ASM1886319v1_genomic.fna/markers.fasta
[2024-01-24 14:05:45,009] [INFO] Task started: Blastn
[2024-01-24 14:05:45,009] [INFO] Running command: blastn -query GCF_018863195.1_ASM1886319v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbade764a-86ef-4020-826b-2011067d76ba/dqc_reference/reference_markers.fasta -out GCF_018863195.1_ASM1886319v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:46,009] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:46,012] [INFO] Selected 27 target genomes.
[2024-01-24 14:05:46,013] [INFO] Target genome list was writen to GCF_018863195.1_ASM1886319v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:46,045] [INFO] Task started: fastANI
[2024-01-24 14:05:46,046] [INFO] Running command: fastANI --query /var/lib/cwl/stg368e33e3-2701-49c1-8a68-d72fea892a7d/GCF_018863195.1_ASM1886319v1_genomic.fna.gz --refList GCF_018863195.1_ASM1886319v1_genomic.fna/target_genomes.txt --output GCF_018863195.1_ASM1886319v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:07,674] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:07,675] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbade764a-86ef-4020-826b-2011067d76ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:07,675] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbade764a-86ef-4020-826b-2011067d76ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:07,696] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:06:07,696] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:06:07,697] [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 oligoaromativorans	strain=DSM 102246	GCA_011762195.1	575322	575322	type	True	79.8362	534	1206	95	below_threshold
Sphingomonas fennica	strain=K101	GCA_003034225.1	114404	114404	type	True	79.7991	525	1206	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	79.7497	540	1206	95	below_threshold
Sphingomonas oleivorans	strain=FW-11	GCA_003050615.1	1735121	1735121	type	True	79.7398	458	1206	95	below_threshold
Rhizorhabdus dicambivorans	strain=Ndbn-20	GCA_002355275.1	1850238	1850238	type	True	79.6738	487	1206	95	below_threshold
Sphingomonas chungangi	strain=CGMCC 1.13654	GCA_013778325.1	2683589	2683589	type	True	79.6146	503	1206	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	79.4945	528	1206	95	below_threshold
Sphingomonas jatrophae	strain=S5-249	GCA_900113315.1	1166337	1166337	type	True	79.4371	482	1206	95	below_threshold
Sphingomonas formosensis	strain=CC-Nfb-2	GCA_009755815.1	861534	861534	type	True	79.3791	501	1206	95	below_threshold
Sphingomonas sanxanigenens	strain=NX02	GCA_000512205.2	397260	397260	type	True	79.2169	506	1206	95	below_threshold
Sphingomonas gilva	strain=ZDH117	GCA_003515075.1	2305907	2305907	type	True	79.144	453	1206	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	79.1132	409	1206	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	79.1092	416	1206	95	below_threshold
Sphingomonas naasensis	strain=KIS18-15	GCA_004792695.1	1344951	1344951	type	True	79.0656	486	1206	95	below_threshold
Sphingomonas naasensis	strain=DSM 100060	GCA_011762145.1	1344951	1344951	type	True	79.0535	489	1206	95	below_threshold
Sphingomonas pituitosa	strain=NBRC 102491	GCA_001598435.1	99597	99597	type	True	79.0051	465	1206	95	below_threshold
Rhizorhabdus phycosphaerae	strain=MK52	GCA_011044255.1	2711156	2711156	type	True	78.9348	412	1206	95	below_threshold
Sphingomonas vulcanisoli	strain=CECT 8804	GCA_011761305.1	1658060	1658060	type	True	78.8948	371	1206	95	below_threshold
Sphingosinicella humi	strain=QZX222	GCA_003129465.1	2068657	2068657	type	True	78.8403	363	1206	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	78.8162	485	1206	95	below_threshold
Sphingosinicella ginsenosidimutans	strain=BS-11	GCA_007995055.1	1176539	1176539	type	True	78.7391	380	1206	95	below_threshold
Sphingomonas parva	strain=17J27-24	GCA_004564275.1	2555898	2555898	type	True	78.7117	439	1206	95	below_threshold
Sphingomonas crusticola	strain=MIMD3	GCA_003391115.1	1697973	1697973	type	True	78.6506	371	1206	95	below_threshold
Sphingomonas japonica	strain=DSM 22753	GCA_011762085.1	511662	511662	type	True	78.3583	357	1206	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	78.3411	393	1206	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	78.3098	422	1206	95	below_threshold
Sphingomonas pruni	strain=NBRC 15498	GCA_001598455.1	40683	40683	type	True	78.2745	372	1206	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:07,698] [INFO] DFAST Taxonomy check result was written to GCF_018863195.1_ASM1886319v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:07,699] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:07,700] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:07,700] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbade764a-86ef-4020-826b-2011067d76ba/dqc_reference/checkm_data
[2024-01-24 14:06:07,701] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:07,740] [INFO] Task started: CheckM
[2024-01-24 14:06:07,740] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018863195.1_ASM1886319v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018863195.1_ASM1886319v1_genomic.fna/checkm_input GCF_018863195.1_ASM1886319v1_genomic.fna/checkm_result
[2024-01-24 14:06:42,157] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:42,158] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:42,174] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:42,175] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:42,175] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018863195.1_ASM1886319v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:42,175] [INFO] Task started: Blastn
[2024-01-24 14:06:42,175] [INFO] Running command: blastn -query GCF_018863195.1_ASM1886319v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbade764a-86ef-4020-826b-2011067d76ba/dqc_reference/reference_markers_gtdb.fasta -out GCF_018863195.1_ASM1886319v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:43,910] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:43,914] [INFO] Selected 25 target genomes.
[2024-01-24 14:06:43,914] [INFO] Target genome list was writen to GCF_018863195.1_ASM1886319v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:43,945] [INFO] Task started: fastANI
[2024-01-24 14:06:43,945] [INFO] Running command: fastANI --query /var/lib/cwl/stg368e33e3-2701-49c1-8a68-d72fea892a7d/GCF_018863195.1_ASM1886319v1_genomic.fna.gz --refList GCF_018863195.1_ASM1886319v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018863195.1_ASM1886319v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:01,764] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:01,785] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:01,786] [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_018863195.1	s__XMGL2 sp018863195	100.0	1204	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__XMGL2	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000383095.1	s__Sphingomonas_N sp000383095	79.9924	504	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_N	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000016765.1	s__Rhizorhabdus wittichii	79.9881	554	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	98.56	98.46	0.83	0.82	5	-
GCF_011762195.1	s__Sphingomonas_N oligoaromativorans	79.8711	531	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_N	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009739515.1	s__Sphingomonas_G sp009739515	79.7452	540	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003050615.1	s__Sphingomonas_H oleivorans	79.7406	458	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_H	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002355275.1	s__Rhizorhabdus dicambivorans	79.6427	490	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	99.99	99.99	1.00	0.99	3	-
GCA_019239915.1	s__Sphingomonas_N sp019239915	79.5886	449	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_N	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113315.1	s__Sphingomonas_G jatrophae	79.4482	481	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009755815.1	s__Sphingomonas_M formosensis	79.3724	502	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_M	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000333335.1	s__Sphingomonas_N sp000333335	79.2176	378	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_N	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003515075.1	s__Sphingomonas gilva	79.1333	454	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004796535.1	s__Sphingomonas_L sp004796535	79.1084	416	1206	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_004792695.1	s__Sphingomonas naasensis	79.086	484	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_001724715.1	s__SCN-67-18 sp001724715	79.0511	402	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__SCN-67-18	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003129465.1	s__Allosphingosinicella humi	78.8419	363	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204695.1	s__Sphingomonas sp001897045	78.8084	463	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.82	96.97	0.94	0.83	6	-
GCF_011320075.1	s__Allosphingosinicella sp011320075	78.8011	373	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013044515.1	s__Sphingomonas_B sp013044515	78.788	361	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008274695.1	s__Rhizorhabdus montanisoli	78.685	395	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002291855.1	s__Sphingomonas_B sp002291855	78.6659	332	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019239415.1	s__Allosphingosinicella sp019239415	78.6639	371	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003391115.1	s__Sphingomonas_I crusticola	78.5955	376	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016025255.1	s__Allosphingosinicella sp016025255	78.3789	309	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806285.1	s__Sphingomicrobium sp902806285	77.7358	231	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:01,787] [INFO] GTDB search result was written to GCF_018863195.1_ASM1886319v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:01,792] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:01,797] [INFO] DFAST_QC result json was written to GCF_018863195.1_ASM1886319v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:01,798] [INFO] DFAST_QC completed!
[2024-01-24 14:07:01,798] [INFO] Total running time: 0h1m29s