[2024-01-25 18:25:20,569] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:25:20,570] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:25:20,570] [INFO] DQC Reference Directory: /var/lib/cwl/stga04f9e61-37e6-4e8c-b0f0-f1fa84bf224b/dqc_reference
[2024-01-25 18:25:21,724] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:25:21,725] [INFO] Task started: Prodigal
[2024-01-25 18:25:21,725] [INFO] Running command: gunzip -c /var/lib/cwl/stg0a821db3-6266-48d2-b84f-28ee03ca0a4c/GCF_000445065.1_ASM44506v1_genomic.fna.gz | prodigal -d GCF_000445065.1_ASM44506v1_genomic.fna/cds.fna -a GCF_000445065.1_ASM44506v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:25:32,003] [INFO] Task succeeded: Prodigal
[2024-01-25 18:25:32,003] [INFO] Task started: HMMsearch
[2024-01-25 18:25:32,004] [INFO] Running command: hmmsearch --tblout GCF_000445065.1_ASM44506v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga04f9e61-37e6-4e8c-b0f0-f1fa84bf224b/dqc_reference/reference_markers.hmm GCF_000445065.1_ASM44506v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:25:32,205] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:25:32,206] [INFO] Found 6/6 markers.
[2024-01-25 18:25:32,241] [INFO] Query marker FASTA was written to GCF_000445065.1_ASM44506v1_genomic.fna/markers.fasta
[2024-01-25 18:25:32,241] [INFO] Task started: Blastn
[2024-01-25 18:25:32,241] [INFO] Running command: blastn -query GCF_000445065.1_ASM44506v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga04f9e61-37e6-4e8c-b0f0-f1fa84bf224b/dqc_reference/reference_markers.fasta -out GCF_000445065.1_ASM44506v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:25:33,108] [INFO] Task succeeded: Blastn
[2024-01-25 18:25:33,110] [INFO] Selected 21 target genomes.
[2024-01-25 18:25:33,111] [INFO] Target genome list was writen to GCF_000445065.1_ASM44506v1_genomic.fna/target_genomes.txt
[2024-01-25 18:25:33,120] [INFO] Task started: fastANI
[2024-01-25 18:25:33,121] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a821db3-6266-48d2-b84f-28ee03ca0a4c/GCF_000445065.1_ASM44506v1_genomic.fna.gz --refList GCF_000445065.1_ASM44506v1_genomic.fna/target_genomes.txt --output GCF_000445065.1_ASM44506v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:25:51,654] [INFO] Task succeeded: fastANI
[2024-01-25 18:25:51,654] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga04f9e61-37e6-4e8c-b0f0-f1fa84bf224b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:25:51,655] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga04f9e61-37e6-4e8c-b0f0-f1fa84bf224b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:25:51,667] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:25:51,667] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:25:51,668] [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
Sphingobium quisquiliarum	strain=P25	GCA_000445065.1	538379	538379	type	True	100.0	1287	1300	95	conclusive
Sphingobium vermicomposti	strain=DSM 21299	GCA_011762025.1	529005	529005	type	True	84.4925	734	1300	95	below_threshold
Sphingobium indicum	strain=B90A	GCA_000264945.2	332055	332055	type	True	84.3682	706	1300	95	below_threshold
Sphingobium fuliginis	strain=DSM 18781	GCA_004152845.1	336203	336203	type	True	83.9539	714	1300	95	below_threshold
Sphingobium chlorophenolicum	strain=NBRC 16172	GCA_000722875.1	46429	46429	type	True	83.9353	669	1300	95	below_threshold
Sphingobium fuliginis	strain=CCM 7327	GCA_014636045.1	336203	336203	type	True	83.8984	724	1300	95	below_threshold
Sphingobium chungbukense	strain=DJ77	GCA_001005725.1	56193	56193	type	True	83.6981	708	1300	95	below_threshold
Sphingobium chlorophenolicum	strain=NBRC 16172	GCA_001598515.1	46429	46429	type	True	83.6928	634	1300	95	below_threshold
Sphingobium cloacae	strain=JCM 10874	GCA_002355855.1	120107	120107	type	True	83.6279	644	1300	95	below_threshold
Sphingobium cloacae	strain=NBRC 102517	GCA_001591285.1	120107	120107	type	True	83.5519	621	1300	95	below_threshold
Sphingobium estronivorans	strain=AXB	GCA_008692605.1	1577690	1577690	type	True	83.511	674	1300	95	below_threshold
Sphingobium wenxiniae	strain=JZ-1	GCA_014205735.1	595605	595605	type	True	83.3881	615	1300	95	below_threshold
Sphingobium herbicidovorans	strain=NBRC 16415	GCA_000632125.2	76947	76947	type	True	83.2595	696	1300	95	below_threshold
Sphingobium bisphenolivorans	strain=YL23	GCA_000412635.1	1335760	1335760	type	True	82.9485	672	1300	95	below_threshold
Sphingobium yanoikuyae	strain=ATCC 51230	GCA_000315525.1	13690	13690	suspected-type	True	82.7302	680	1300	95	below_threshold
Sphingobium scionense	strain=DSM 19371	GCA_014197035.1	1404341	1404341	type	True	82.3491	673	1300	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	78.3104	327	1300	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	78.2595	312	1300	95	below_threshold
Rhizorhabdus phycosphaerae	strain=MK52	GCA_011044255.1	2711156	2711156	type	True	78.0225	294	1300	95	below_threshold
Sphingosinicella ginsenosidimutans	strain=BS-11	GCA_007995055.1	1176539	1176539	type	True	77.7806	248	1300	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	77.7164	372	1300	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:25:51,671] [INFO] DFAST Taxonomy check result was written to GCF_000445065.1_ASM44506v1_genomic.fna/tc_result.tsv
[2024-01-25 18:25:51,672] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:25:51,672] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:25:51,672] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga04f9e61-37e6-4e8c-b0f0-f1fa84bf224b/dqc_reference/checkm_data
[2024-01-25 18:25:51,673] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:25:51,713] [INFO] Task started: CheckM
[2024-01-25 18:25:51,713] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000445065.1_ASM44506v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000445065.1_ASM44506v1_genomic.fna/checkm_input GCF_000445065.1_ASM44506v1_genomic.fna/checkm_result
[2024-01-25 18:26:23,347] [INFO] Task succeeded: CheckM
[2024-01-25 18:26:23,348] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:26:23,368] [INFO] ===== Completeness check finished =====
[2024-01-25 18:26:23,368] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:26:23,369] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000445065.1_ASM44506v1_genomic.fna/markers.fasta)
[2024-01-25 18:26:23,369] [INFO] Task started: Blastn
[2024-01-25 18:26:23,369] [INFO] Running command: blastn -query GCF_000445065.1_ASM44506v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga04f9e61-37e6-4e8c-b0f0-f1fa84bf224b/dqc_reference/reference_markers_gtdb.fasta -out GCF_000445065.1_ASM44506v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:26:25,144] [INFO] Task succeeded: Blastn
[2024-01-25 18:26:25,147] [INFO] Selected 17 target genomes.
[2024-01-25 18:26:25,148] [INFO] Target genome list was writen to GCF_000445065.1_ASM44506v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:26:25,174] [INFO] Task started: fastANI
[2024-01-25 18:26:25,174] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a821db3-6266-48d2-b84f-28ee03ca0a4c/GCF_000445065.1_ASM44506v1_genomic.fna.gz --refList GCF_000445065.1_ASM44506v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000445065.1_ASM44506v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:26:42,394] [INFO] Task succeeded: fastANI
[2024-01-25 18:26:42,404] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:26:42,405] [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_000445065.1	s__Sphingobium quisquiliarum	100.0	1287	1300	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	97.94	97.93	0.83	0.83	3	conclusive
GCF_011762025.1	s__Sphingobium vermicomposti	84.4654	736	1300	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000264945.2	s__Sphingobium indicum	84.3806	708	1300	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	98.64	97.75	0.82	0.64	8	-
GCF_000722875.1	s__Sphingobium chlorophenolicum	83.9285	669	1300	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	97.94	95.89	0.87	0.76	3	-
GCF_004152845.1	s__Sphingobium fuliginis	83.92	717	1300	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	98.53	97.80	0.87	0.78	14	-
GCF_001005725.1	s__Sphingobium chungbukense	83.6981	708	1300	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	97.77	97.77	0.72	0.72	2	-
GCF_900218065.1	s__Sphingobium sp900218065	83.6909	690	1300	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	97.42	97.40	0.85	0.85	5	-
GCF_013375535.1	s__Sphingobium sp013375535	83.6269	700	1300	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002355855.1	s__Sphingobium cloacae	83.6186	641	1300	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_008692605.1	s__Sphingobium estronivorans	83.5188	673	1300	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830065.1	s__Sphingobium wenxiniae	83.3505	609	1300	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	99.17	98.76	0.86	0.79	4	-
GCF_013375555.1	s__Sphingobium sp013375555	83.2559	677	1300	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015693305.1	s__Sphingobium sp015693305	83.2048	692	1300	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000412635.1	s__Sphingobium bisphenolivorans	82.9614	671	1300	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873695.1	s__Sphingobium sp014873695	82.7631	719	1300	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100475.1	s__Sphingobium faniae	82.5003	623	1300	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197035.1	s__Sphingobium scionense	82.3573	672	1300	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:26:42,407] [INFO] GTDB search result was written to GCF_000445065.1_ASM44506v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:26:42,407] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:26:42,410] [INFO] DFAST_QC result json was written to GCF_000445065.1_ASM44506v1_genomic.fna/dqc_result.json
[2024-01-25 18:26:42,411] [INFO] DFAST_QC completed!
[2024-01-25 18:26:42,411] [INFO] Total running time: 0h1m22s