[2024-01-25 18:59:35,583] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:59:35,589] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:59:35,589] [INFO] DQC Reference Directory: /var/lib/cwl/stg5296a197-9f86-490d-9a35-2876f02fcdfd/dqc_reference
[2024-01-25 18:59:36,762] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:59:36,763] [INFO] Task started: Prodigal
[2024-01-25 18:59:36,763] [INFO] Running command: gunzip -c /var/lib/cwl/stgfaff67a6-cd13-4a17-95fe-12aeb95cada0/GCF_026619435.1_ASM2661943v1_genomic.fna.gz | prodigal -d GCF_026619435.1_ASM2661943v1_genomic.fna/cds.fna -a GCF_026619435.1_ASM2661943v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:59:51,716] [INFO] Task succeeded: Prodigal
[2024-01-25 18:59:51,717] [INFO] Task started: HMMsearch
[2024-01-25 18:59:51,717] [INFO] Running command: hmmsearch --tblout GCF_026619435.1_ASM2661943v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5296a197-9f86-490d-9a35-2876f02fcdfd/dqc_reference/reference_markers.hmm GCF_026619435.1_ASM2661943v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:59:51,962] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:59:51,963] [INFO] Found 6/6 markers.
[2024-01-25 18:59:52,008] [INFO] Query marker FASTA was written to GCF_026619435.1_ASM2661943v1_genomic.fna/markers.fasta
[2024-01-25 18:59:52,008] [INFO] Task started: Blastn
[2024-01-25 18:59:52,009] [INFO] Running command: blastn -query GCF_026619435.1_ASM2661943v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5296a197-9f86-490d-9a35-2876f02fcdfd/dqc_reference/reference_markers.fasta -out GCF_026619435.1_ASM2661943v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:59:53,021] [INFO] Task succeeded: Blastn
[2024-01-25 18:59:53,024] [INFO] Selected 12 target genomes.
[2024-01-25 18:59:53,025] [INFO] Target genome list was writen to GCF_026619435.1_ASM2661943v1_genomic.fna/target_genomes.txt
[2024-01-25 18:59:53,033] [INFO] Task started: fastANI
[2024-01-25 18:59:53,033] [INFO] Running command: fastANI --query /var/lib/cwl/stgfaff67a6-cd13-4a17-95fe-12aeb95cada0/GCF_026619435.1_ASM2661943v1_genomic.fna.gz --refList GCF_026619435.1_ASM2661943v1_genomic.fna/target_genomes.txt --output GCF_026619435.1_ASM2661943v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:00:07,056] [INFO] Task succeeded: fastANI
[2024-01-25 19:00:07,056] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5296a197-9f86-490d-9a35-2876f02fcdfd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:00:07,057] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5296a197-9f86-490d-9a35-2876f02fcdfd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:00:07,065] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:00:07,065] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:00:07,066] [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
Hoeflea alexandrii	strain=DSM 16655	GCA_024105735.1	288436	288436	type	True	82.5763	997	1705	95	below_threshold
Hoeflea olei	strain=JC234	GCA_001703635.1	1480615	1480615	type	True	82.4752	986	1705	95	below_threshold
Hoeflea halophila	strain=KCTC 23107	GCA_900220985.1	714899	714899	type	True	82.215	957	1705	95	below_threshold
Hoeflea phototrophica	strain=DFL-43	GCA_000154705.2	244596	244596	type	True	81.0683	835	1705	95	below_threshold
Hoeflea marina	strain=DSM 16791	GCA_003182275.1	274592	274592	type	True	80.5615	841	1705	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	78.1874	535	1705	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	78.1823	455	1705	95	below_threshold
Ciceribacter thiooxidans	strain=F43B	GCA_014126615.1	1969821	1969821	type	True	78.1085	363	1705	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	78.0682	485	1705	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	78.0118	448	1705	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	77.9788	456	1705	95	below_threshold
Rhizobium freirei	strain=PRF 81	GCA_000359745.1	1353277	1353277	type	True	77.7116	392	1705	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:00:07,067] [INFO] DFAST Taxonomy check result was written to GCF_026619435.1_ASM2661943v1_genomic.fna/tc_result.tsv
[2024-01-25 19:00:07,067] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:00:07,068] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:00:07,068] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5296a197-9f86-490d-9a35-2876f02fcdfd/dqc_reference/checkm_data
[2024-01-25 19:00:07,069] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:00:07,120] [INFO] Task started: CheckM
[2024-01-25 19:00:07,120] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026619435.1_ASM2661943v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026619435.1_ASM2661943v1_genomic.fna/checkm_input GCF_026619435.1_ASM2661943v1_genomic.fna/checkm_result
[2024-01-25 19:01:16,670] [INFO] Task succeeded: CheckM
[2024-01-25 19:01:16,671] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:01:16,692] [INFO] ===== Completeness check finished =====
[2024-01-25 19:01:16,692] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:01:16,693] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026619435.1_ASM2661943v1_genomic.fna/markers.fasta)
[2024-01-25 19:01:16,693] [INFO] Task started: Blastn
[2024-01-25 19:01:16,693] [INFO] Running command: blastn -query GCF_026619435.1_ASM2661943v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5296a197-9f86-490d-9a35-2876f02fcdfd/dqc_reference/reference_markers_gtdb.fasta -out GCF_026619435.1_ASM2661943v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:01:18,792] [INFO] Task succeeded: Blastn
[2024-01-25 19:01:18,795] [INFO] Selected 10 target genomes.
[2024-01-25 19:01:18,795] [INFO] Target genome list was writen to GCF_026619435.1_ASM2661943v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:01:18,811] [INFO] Task started: fastANI
[2024-01-25 19:01:18,811] [INFO] Running command: fastANI --query /var/lib/cwl/stgfaff67a6-cd13-4a17-95fe-12aeb95cada0/GCF_026619435.1_ASM2661943v1_genomic.fna.gz --refList GCF_026619435.1_ASM2661943v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026619435.1_ASM2661943v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:01:30,092] [INFO] Task succeeded: fastANI
[2024-01-25 19:01:30,100] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:01:30,100] [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_001011155.1	s__Hoeflea sp001011155	86.3181	1215	1705	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000961635.1	s__Hoeflea sp000961635	84.5628	719	1705	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000759435.1	s__Hoeflea sp000759435	83.3132	1019	1705	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733955.1	s__Hoeflea sp002733955	83.2517	1078	1705	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019084245.1	s__Hoeflea sp019084245	83.1852	1038	1705	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	100.00	100.00	0.99	0.99	6	-
GCA_014359905.1	s__Hoeflea sp014359905	83.1848	1031	1705	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018829385.1	s__Hoeflea sp018829385	82.8557	623	1705	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001703635.1	s__Hoeflea olei	82.4667	985	1705	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902498795.1	s__Hoeflea sp902498795	82.4491	1015	1705	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	97.67	97.67	0.92	0.92	2	-
GCF_900220985.1	s__Hoeflea halophila	82.2351	954	1705	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:01:30,114] [INFO] GTDB search result was written to GCF_026619435.1_ASM2661943v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:01:30,114] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:01:30,117] [INFO] DFAST_QC result json was written to GCF_026619435.1_ASM2661943v1_genomic.fna/dqc_result.json
[2024-01-25 19:01:30,118] [INFO] DFAST_QC completed!
[2024-01-25 19:01:30,118] [INFO] Total running time: 0h1m55s