[2024-01-24 12:45:10,394] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:45:10,396] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:45:10,397] [INFO] DQC Reference Directory: /var/lib/cwl/stg9d6ae67f-8c94-4943-9d06-42081c4de6c4/dqc_reference
[2024-01-24 12:45:13,087] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:45:13,088] [INFO] Task started: Prodigal
[2024-01-24 12:45:13,089] [INFO] Running command: gunzip -c /var/lib/cwl/stgb4abb7bd-70af-46aa-9940-79fe9c7a0858/GCF_024211275.1_ASM2421127v1_genomic.fna.gz | prodigal -d GCF_024211275.1_ASM2421127v1_genomic.fna/cds.fna -a GCF_024211275.1_ASM2421127v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:26,770] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:26,770] [INFO] Task started: HMMsearch
[2024-01-24 12:45:26,771] [INFO] Running command: hmmsearch --tblout GCF_024211275.1_ASM2421127v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9d6ae67f-8c94-4943-9d06-42081c4de6c4/dqc_reference/reference_markers.hmm GCF_024211275.1_ASM2421127v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:27,044] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:27,046] [INFO] Found 6/6 markers.
[2024-01-24 12:45:27,096] [INFO] Query marker FASTA was written to GCF_024211275.1_ASM2421127v1_genomic.fna/markers.fasta
[2024-01-24 12:45:27,097] [INFO] Task started: Blastn
[2024-01-24 12:45:27,097] [INFO] Running command: blastn -query GCF_024211275.1_ASM2421127v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d6ae67f-8c94-4943-9d06-42081c4de6c4/dqc_reference/reference_markers.fasta -out GCF_024211275.1_ASM2421127v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:28,186] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:28,191] [INFO] Selected 16 target genomes.
[2024-01-24 12:45:28,191] [INFO] Target genome list was writen to GCF_024211275.1_ASM2421127v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:28,222] [INFO] Task started: fastANI
[2024-01-24 12:45:28,223] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4abb7bd-70af-46aa-9940-79fe9c7a0858/GCF_024211275.1_ASM2421127v1_genomic.fna.gz --refList GCF_024211275.1_ASM2421127v1_genomic.fna/target_genomes.txt --output GCF_024211275.1_ASM2421127v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:42,089] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:42,089] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9d6ae67f-8c94-4943-9d06-42081c4de6c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:42,090] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9d6ae67f-8c94-4943-9d06-42081c4de6c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:42,103] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:45:42,103] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:45:42,103] [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 koreensis	strain=KCTC 2882	GCA_003953035.1	93064	93064	type	True	83.8911	756	1530	95	below_threshold
Sphingomonas koreensis	strain=JSS26	GCA_002797435.1	93064	93064	type	True	83.8719	760	1530	95	below_threshold
Sphingomonas koreensis	strain=NBRC 16723	GCA_001598395.1	93064	93064	type	True	83.8194	769	1530	95	below_threshold
Sphingomonas turrisvirgatae	strain=MCT13	GCA_001721295.1	1888892	1888892	type	True	83.7279	766	1530	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	82.5839	751	1530	95	below_threshold
Sphingomonas naasensis	strain=DSM 100060	GCA_011762145.1	1344951	1344951	type	True	81.1875	660	1530	95	below_threshold
Sphingomonas naasensis	strain=KIS18-15	GCA_004792695.1	1344951	1344951	type	True	81.1052	666	1530	95	below_threshold
Sphingomonas leidyi	strain=DSM 4733	GCA_011761945.1	68569	68569	type	True	80.5901	633	1530	95	below_threshold
Sphingomonas kyeonggiensis	strain=DSM 101806	GCA_014196745.1	1268553	1268553	type	True	80.4653	670	1530	95	below_threshold
Sphingomonas trueperi	strain=DSM 7225	GCA_011927635.1	53317	53317	type	True	80.4635	572	1530	95	below_threshold
Sphingomonas azotifigens	strain=NBRC 15497	GCA_002091475.1	330920	330920	type	True	80.1541	589	1530	95	below_threshold
Sphingomonas soli	strain=NBRC 100801	GCA_001591025.1	266127	266127	type	True	80.0427	550	1530	95	below_threshold
Sphingomonas baiyangensis	strain=L-1-4 w-11	GCA_005144715.1	2572576	2572576	type	True	80.0316	545	1530	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	79.808	567	1530	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	79.4105	524	1530	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	78.6831	427	1530	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:42,105] [INFO] DFAST Taxonomy check result was written to GCF_024211275.1_ASM2421127v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:42,106] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:42,106] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:42,107] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9d6ae67f-8c94-4943-9d06-42081c4de6c4/dqc_reference/checkm_data
[2024-01-24 12:45:42,108] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:42,156] [INFO] Task started: CheckM
[2024-01-24 12:45:42,156] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024211275.1_ASM2421127v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024211275.1_ASM2421127v1_genomic.fna/checkm_input GCF_024211275.1_ASM2421127v1_genomic.fna/checkm_result
[2024-01-24 12:46:24,154] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:24,155] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:24,178] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:24,179] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:24,179] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024211275.1_ASM2421127v1_genomic.fna/markers.fasta)
[2024-01-24 12:46:24,180] [INFO] Task started: Blastn
[2024-01-24 12:46:24,180] [INFO] Running command: blastn -query GCF_024211275.1_ASM2421127v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d6ae67f-8c94-4943-9d06-42081c4de6c4/dqc_reference/reference_markers_gtdb.fasta -out GCF_024211275.1_ASM2421127v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:26,149] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:26,154] [INFO] Selected 15 target genomes.
[2024-01-24 12:46:26,155] [INFO] Target genome list was writen to GCF_024211275.1_ASM2421127v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:26,189] [INFO] Task started: fastANI
[2024-01-24 12:46:26,189] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4abb7bd-70af-46aa-9940-79fe9c7a0858/GCF_024211275.1_ASM2421127v1_genomic.fna.gz --refList GCF_024211275.1_ASM2421127v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024211275.1_ASM2421127v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:38,690] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:38,707] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:46:38,707] [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_002797435.1	s__Sphingomonas koreensis	83.8751	760	1530	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.13	98.00	0.88	0.86	72	-
GCF_001721295.1	s__Sphingomonas turrisvirgatae	83.7279	766	1530	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001557215.1	s__Sphingomonas sp001557215	83.1931	620	1530	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.89	99.89	0.91	0.91	2	-
GCA_902826325.1	s__Sphingomonas sp902826325	82.9561	519	1530	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.74	97.74	0.84	0.84	2	-
GCA_002280565.1	s__Sphingomonas sp002280565	82.9055	581	1530	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.98	96.98	0.90	0.90	2	-
GCF_007833215.1	s__Sphingomonas sp007833215	82.5913	751	1530	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004792695.1	s__Sphingomonas naasensis	81.0993	667	1530	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_017744835.1	s__Sphingomonas sp017744835	80.8168	603	1530	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018449795.1	s__Sphingomonas sp018449795	80.7779	610	1530	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	80.6539	655	1530	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428865.1	s__Sphingomonas sp001428865	80.6305	635	1530	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	80.599	632	1530	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.87	98.83	0.90	0.87	3	-
GCF_002127225.1	s__Sphingomonas sp002127225	80.5624	630	1530	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001591025.1	s__Sphingomonas soli	80.0427	550	1530	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014171475.1	s__Sphingomonas alpina_A	79.0705	535	1530	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:38,710] [INFO] GTDB search result was written to GCF_024211275.1_ASM2421127v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:38,710] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:38,714] [INFO] DFAST_QC result json was written to GCF_024211275.1_ASM2421127v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:38,715] [INFO] DFAST_QC completed!
[2024-01-24 12:46:38,715] [INFO] Total running time: 0h1m28s