[2023-06-13 02:32:50,666] [INFO] DFAST_QC pipeline started.
[2023-06-13 02:32:50,669] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 02:32:50,669] [INFO] DQC Reference Directory: /var/lib/cwl/stg2fa9c073-a190-4cce-b991-13ccca43eaf0/dqc_reference
[2023-06-13 02:32:51,994] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 02:32:51,995] [INFO] Task started: Prodigal
[2023-06-13 02:32:51,995] [INFO] Running command: gunzip -c /var/lib/cwl/stgda175d26-9d1b-4e0f-a1bd-7488f8bfa0e8/GCA_022563435.1_ASM2256343v1_genomic.fna.gz | prodigal -d GCA_022563435.1_ASM2256343v1_genomic.fna/cds.fna -a GCA_022563435.1_ASM2256343v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 02:32:59,670] [INFO] Task succeeded: Prodigal
[2023-06-13 02:32:59,671] [INFO] Task started: HMMsearch
[2023-06-13 02:32:59,671] [INFO] Running command: hmmsearch --tblout GCA_022563435.1_ASM2256343v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2fa9c073-a190-4cce-b991-13ccca43eaf0/dqc_reference/reference_markers.hmm GCA_022563435.1_ASM2256343v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 02:32:59,908] [INFO] Task succeeded: HMMsearch
[2023-06-13 02:32:59,910] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgda175d26-9d1b-4e0f-a1bd-7488f8bfa0e8/GCA_022563435.1_ASM2256343v1_genomic.fna.gz]
[2023-06-13 02:32:59,946] [INFO] Query marker FASTA was written to GCA_022563435.1_ASM2256343v1_genomic.fna/markers.fasta
[2023-06-13 02:32:59,947] [INFO] Task started: Blastn
[2023-06-13 02:32:59,947] [INFO] Running command: blastn -query GCA_022563435.1_ASM2256343v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2fa9c073-a190-4cce-b991-13ccca43eaf0/dqc_reference/reference_markers.fasta -out GCA_022563435.1_ASM2256343v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 02:33:00,845] [INFO] Task succeeded: Blastn
[2023-06-13 02:33:00,849] [INFO] Selected 14 target genomes.
[2023-06-13 02:33:00,850] [INFO] Target genome list was writen to GCA_022563435.1_ASM2256343v1_genomic.fna/target_genomes.txt
[2023-06-13 02:33:00,853] [INFO] Task started: fastANI
[2023-06-13 02:33:00,853] [INFO] Running command: fastANI --query /var/lib/cwl/stgda175d26-9d1b-4e0f-a1bd-7488f8bfa0e8/GCA_022563435.1_ASM2256343v1_genomic.fna.gz --refList GCA_022563435.1_ASM2256343v1_genomic.fna/target_genomes.txt --output GCA_022563435.1_ASM2256343v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 02:33:12,081] [INFO] Task succeeded: fastANI
[2023-06-13 02:33:12,081] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2fa9c073-a190-4cce-b991-13ccca43eaf0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 02:33:12,082] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2fa9c073-a190-4cce-b991-13ccca43eaf0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 02:33:12,099] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 02:33:12,099] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 02:33:12,099] [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 leidyi	strain=DSM 4733	GCA_011761945.1	68569	68569	type	True	91.8294	635	729	95	below_threshold
Sphingomonas kyeonggiensis	strain=DSM 101806	GCA_014196745.1	1268553	1268553	type	True	86.97	557	729	95	below_threshold
Sphingomonas naasensis	strain=KIS18-15	GCA_004792695.1	1344951	1344951	type	True	82.1025	441	729	95	below_threshold
Sphingomonas naasensis	strain=DSM 100060	GCA_011762145.1	1344951	1344951	type	True	82.0221	446	729	95	below_threshold
Sphingomonas trueperi	strain=DSM 7225	GCA_011927635.1	53317	53317	type	True	81.4083	399	729	95	below_threshold
Sphingomonas azotifigens	strain=NBRC 15497	GCA_002091475.1	330920	330920	type	True	81.1218	393	729	95	below_threshold
Sphingomonas psychrotolerans	strain=Cra20	GCA_002796605.1	1327635	1327635	type	True	80.8038	422	729	95	below_threshold
Sphingomonas hengshuiensis	strain=WHSC-8	GCA_000935025.1	1609977	1609977	type	True	80.4617	413	729	95	below_threshold
Sphingomonas soli	strain=NBRC 100801	GCA_001591025.1	266127	266127	type	True	80.2564	353	729	95	below_threshold
Sphingomonas koreensis	strain=NBRC 16723	GCA_001598395.1	93064	93064	type	True	79.3691	360	729	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	79.0249	303	729	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	79.006	296	729	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	78.1879	288	729	95	below_threshold
Sphingomonas radiodurans	strain=S9-5	GCA_020866845.1	2890321	2890321	type	True	77.5222	226	729	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 02:33:12,101] [INFO] DFAST Taxonomy check result was written to GCA_022563435.1_ASM2256343v1_genomic.fna/tc_result.tsv
[2023-06-13 02:33:12,102] [INFO] ===== Taxonomy check completed =====
[2023-06-13 02:33:12,102] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 02:33:12,103] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2fa9c073-a190-4cce-b991-13ccca43eaf0/dqc_reference/checkm_data
[2023-06-13 02:33:12,104] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 02:33:12,141] [INFO] Task started: CheckM
[2023-06-13 02:33:12,142] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022563435.1_ASM2256343v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022563435.1_ASM2256343v1_genomic.fna/checkm_input GCA_022563435.1_ASM2256343v1_genomic.fna/checkm_result
[2023-06-13 02:33:39,433] [INFO] Task succeeded: CheckM
[2023-06-13 02:33:39,434] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 48.84%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 02:33:39,456] [INFO] ===== Completeness check finished =====
[2023-06-13 02:33:39,456] [INFO] ===== Start GTDB Search =====
[2023-06-13 02:33:39,457] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022563435.1_ASM2256343v1_genomic.fna/markers.fasta)
[2023-06-13 02:33:39,457] [INFO] Task started: Blastn
[2023-06-13 02:33:39,457] [INFO] Running command: blastn -query GCA_022563435.1_ASM2256343v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2fa9c073-a190-4cce-b991-13ccca43eaf0/dqc_reference/reference_markers_gtdb.fasta -out GCA_022563435.1_ASM2256343v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 02:33:41,169] [INFO] Task succeeded: Blastn
[2023-06-13 02:33:41,173] [INFO] Selected 7 target genomes.
[2023-06-13 02:33:41,173] [INFO] Target genome list was writen to GCA_022563435.1_ASM2256343v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 02:33:41,192] [INFO] Task started: fastANI
[2023-06-13 02:33:41,192] [INFO] Running command: fastANI --query /var/lib/cwl/stgda175d26-9d1b-4e0f-a1bd-7488f8bfa0e8/GCA_022563435.1_ASM2256343v1_genomic.fna.gz --refList GCA_022563435.1_ASM2256343v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022563435.1_ASM2256343v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 02:33:47,665] [INFO] Task succeeded: fastANI
[2023-06-13 02:33:47,679] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 02:33:47,679] [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
GCA_017418975.1	s__Sphingomonas sp017418975	95.9665	657	729	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_002127225.1	s__Sphingomonas sp002127225	92.4767	620	729	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011761945.1	s__Sphingomonas leidyi	91.8294	635	729	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.87	98.83	0.90	0.87	3	-
GCF_005503355.1	s__Sphingomonas sp005503355	90.0231	634	729	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014196745.1	s__Sphingomonas kyeonggiensis	86.9476	558	729	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204495.1	s__Sphingomonas kyeonggiensis_A	86.7692	560	729	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013416555.1	s__Sphingomonas sp013416555	86.1264	533	729	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 02:33:47,681] [INFO] GTDB search result was written to GCA_022563435.1_ASM2256343v1_genomic.fna/result_gtdb.tsv
[2023-06-13 02:33:47,682] [INFO] ===== GTDB Search completed =====
[2023-06-13 02:33:47,686] [INFO] DFAST_QC result json was written to GCA_022563435.1_ASM2256343v1_genomic.fna/dqc_result.json
[2023-06-13 02:33:47,686] [INFO] DFAST_QC completed!
[2023-06-13 02:33:47,686] [INFO] Total running time: 0h0m57s