[2024-01-24 11:35:23,676] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:23,682] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:23,682] [INFO] DQC Reference Directory: /var/lib/cwl/stg9917876c-fb51-45d7-985b-da18d78b843a/dqc_reference
[2024-01-24 11:35:26,244] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:26,245] [INFO] Task started: Prodigal
[2024-01-24 11:35:26,246] [INFO] Running command: gunzip -c /var/lib/cwl/stgd302e258-24f4-4113-8a07-7b73b7adc339/GCF_005160265.1_ASM516026v1_genomic.fna.gz | prodigal -d GCF_005160265.1_ASM516026v1_genomic.fna/cds.fna -a GCF_005160265.1_ASM516026v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:41,506] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:41,507] [INFO] Task started: HMMsearch
[2024-01-24 11:35:41,507] [INFO] Running command: hmmsearch --tblout GCF_005160265.1_ASM516026v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9917876c-fb51-45d7-985b-da18d78b843a/dqc_reference/reference_markers.hmm GCF_005160265.1_ASM516026v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:41,871] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:41,873] [INFO] Found 6/6 markers.
[2024-01-24 11:35:41,919] [INFO] Query marker FASTA was written to GCF_005160265.1_ASM516026v1_genomic.fna/markers.fasta
[2024-01-24 11:35:41,920] [INFO] Task started: Blastn
[2024-01-24 11:35:41,920] [INFO] Running command: blastn -query GCF_005160265.1_ASM516026v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9917876c-fb51-45d7-985b-da18d78b843a/dqc_reference/reference_markers.fasta -out GCF_005160265.1_ASM516026v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:42,965] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:42,968] [INFO] Selected 21 target genomes.
[2024-01-24 11:35:42,968] [INFO] Target genome list was writen to GCF_005160265.1_ASM516026v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:42,978] [INFO] Task started: fastANI
[2024-01-24 11:35:42,978] [INFO] Running command: fastANI --query /var/lib/cwl/stgd302e258-24f4-4113-8a07-7b73b7adc339/GCF_005160265.1_ASM516026v1_genomic.fna.gz --refList GCF_005160265.1_ASM516026v1_genomic.fna/target_genomes.txt --output GCF_005160265.1_ASM516026v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:36:04,576] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:04,577] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9917876c-fb51-45d7-985b-da18d78b843a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:36:04,577] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9917876c-fb51-45d7-985b-da18d78b843a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:36:04,600] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:36:04,600] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:36:04,601] [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
Phreatobacter oligotrophus	strain=DSM 25521	GCA_003046185.1	1122261	1122261	type	True	81.9369	980	1658	95	below_threshold
Phreatobacter cathodiphilus	strain=S-12	GCA_003008515.1	1868589	1868589	type	True	81.7766	977	1658	95	below_threshold
Phreatobacter stygius	strain=KCTC 52518	GCA_005144885.1	1940610	1940610	type	True	81.669	1049	1658	95	below_threshold
Blastochloris sulfoviridis	strain=DSM 729	GCA_008630065.1	50712	50712	type	True	78.1075	369	1658	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	77.9582	390	1658	95	below_threshold
Microvirga splendida	strain=BT325	GCA_016427565.1	2795727	2795727	type	True	77.85	313	1658	95	below_threshold
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	77.8178	432	1658	95	below_threshold
Ancylobacter dichloromethanicus	strain=VKM B-2484	GCA_018390645.1	518825	518825	type	True	77.6976	359	1658	95	below_threshold
Microvirga thermotolerans	strain=HR1	GCA_009363855.1	2651334	2651334	type	True	77.6962	282	1658	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	77.6845	454	1658	95	below_threshold
Bradyrhizobium guangxiense	strain=CCBAU 53363	GCA_004114915.1	1325115	1325115	type	True	77.6644	443	1658	95	below_threshold
Bradyrhizobium niftali	strain=CNPSo 3448	GCA_004571025.1	2560055	2560055	type	True	77.6349	477	1658	95	below_threshold
Azorhizobium caulinodans	strain=ORS 571	GCA_000010525.1	7	7	type	True	77.6168	372	1658	95	below_threshold
Xanthobacter dioxanivorans	strain=YN2	GCA_016807805.1	2528964	2528964	type	True	77.3372	385	1658	95	below_threshold
Methylobacterium tardum	strain=DSM 19566	GCA_023546765.1	374432	374432	type	True	77.2939	343	1658	95	below_threshold
Microvirga aerilata	strain=5420S-16	GCA_016743775.1	670292	670292	type	True	77.2473	315	1658	95	below_threshold
Methylorubrum aminovorans	strain=NBRC 15686	GCA_022179725.1	269069	269069	type	True	77.2087	297	1658	95	below_threshold
Methylobacterium mesophilicum	strain=NBRC 15688	GCA_022179445.1	39956	39956	type	True	77.2014	300	1658	95	below_threshold
Methylorubrum rhodesianum	strain=DSM 5687	GCA_014199985.1	29427	29427	type	True	77.1628	305	1658	95	below_threshold
Xanthobacter agilis	strain=LMG 16336	GCA_021730435.1	47492	47492	type	True	77.1324	282	1658	95	below_threshold
Methylobacterium tardum	strain=NBRC 103632	GCA_022179585.1	374432	374432	type	True	77.1284	342	1658	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:36:04,602] [INFO] DFAST Taxonomy check result was written to GCF_005160265.1_ASM516026v1_genomic.fna/tc_result.tsv
[2024-01-24 11:36:04,603] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:36:04,603] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:36:04,603] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9917876c-fb51-45d7-985b-da18d78b843a/dqc_reference/checkm_data
[2024-01-24 11:36:04,604] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:36:04,651] [INFO] Task started: CheckM
[2024-01-24 11:36:04,652] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005160265.1_ASM516026v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005160265.1_ASM516026v1_genomic.fna/checkm_input GCF_005160265.1_ASM516026v1_genomic.fna/checkm_result
[2024-01-24 11:37:08,239] [INFO] Task succeeded: CheckM
[2024-01-24 11:37:08,241] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:37:08,268] [INFO] ===== Completeness check finished =====
[2024-01-24 11:37:08,268] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:37:08,269] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005160265.1_ASM516026v1_genomic.fna/markers.fasta)
[2024-01-24 11:37:08,269] [INFO] Task started: Blastn
[2024-01-24 11:37:08,269] [INFO] Running command: blastn -query GCF_005160265.1_ASM516026v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9917876c-fb51-45d7-985b-da18d78b843a/dqc_reference/reference_markers_gtdb.fasta -out GCF_005160265.1_ASM516026v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:37:10,255] [INFO] Task succeeded: Blastn
[2024-01-24 11:37:10,259] [INFO] Selected 8 target genomes.
[2024-01-24 11:37:10,259] [INFO] Target genome list was writen to GCF_005160265.1_ASM516026v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:37:10,267] [INFO] Task started: fastANI
[2024-01-24 11:37:10,268] [INFO] Running command: fastANI --query /var/lib/cwl/stgd302e258-24f4-4113-8a07-7b73b7adc339/GCF_005160265.1_ASM516026v1_genomic.fna.gz --refList GCF_005160265.1_ASM516026v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005160265.1_ASM516026v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:37:20,948] [INFO] Task succeeded: fastANI
[2024-01-24 11:37:20,964] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:37:20,965] [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_005160265.1	s__Phreatobacter sp005160265	100.0	1658	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003046185.1	s__Phreatobacter oligotrophus	81.9219	984	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017304475.1	s__Phreatobacter sp017304475	81.8052	1078	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003008515.1	s__Phreatobacter cathodiphilus	81.7713	980	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793595.1	s__Phreatobacter sp016793595	81.6736	1001	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005144885.1	s__Phreatobacter stygius	81.6535	1054	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464235.1	s__Phreatobacter sp001464235	81.44	825	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000751295.2	s__Phreatobacter sp000751295	81.2839	1004	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:37:20,967] [INFO] GTDB search result was written to GCF_005160265.1_ASM516026v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:37:20,968] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:37:20,974] [INFO] DFAST_QC result json was written to GCF_005160265.1_ASM516026v1_genomic.fna/dqc_result.json
[2024-01-24 11:37:20,974] [INFO] DFAST_QC completed!
[2024-01-24 11:37:20,974] [INFO] Total running time: 0h1m57s