[2024-01-24 11:43:25,081] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:25,083] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:25,083] [INFO] DQC Reference Directory: /var/lib/cwl/stge186e080-75d3-4efa-92dd-710046ee1065/dqc_reference
[2024-01-24 11:43:30,055] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:30,056] [INFO] Task started: Prodigal
[2024-01-24 11:43:30,057] [INFO] Running command: gunzip -c /var/lib/cwl/stg0352e4f1-3bd8-48a2-99ab-501b220529df/GCF_003336755.1_ASM333675v1_genomic.fna.gz | prodigal -d GCF_003336755.1_ASM333675v1_genomic.fna/cds.fna -a GCF_003336755.1_ASM333675v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:38,762] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:38,762] [INFO] Task started: HMMsearch
[2024-01-24 11:43:38,762] [INFO] Running command: hmmsearch --tblout GCF_003336755.1_ASM333675v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge186e080-75d3-4efa-92dd-710046ee1065/dqc_reference/reference_markers.hmm GCF_003336755.1_ASM333675v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:39,021] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:39,022] [INFO] Found 6/6 markers.
[2024-01-24 11:43:39,049] [INFO] Query marker FASTA was written to GCF_003336755.1_ASM333675v1_genomic.fna/markers.fasta
[2024-01-24 11:43:39,050] [INFO] Task started: Blastn
[2024-01-24 11:43:39,050] [INFO] Running command: blastn -query GCF_003336755.1_ASM333675v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge186e080-75d3-4efa-92dd-710046ee1065/dqc_reference/reference_markers.fasta -out GCF_003336755.1_ASM333675v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:39,924] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:39,927] [INFO] Selected 16 target genomes.
[2024-01-24 11:43:39,928] [INFO] Target genome list was writen to GCF_003336755.1_ASM333675v1_genomic.fna/target_genomes.txt
[2024-01-24 11:43:39,953] [INFO] Task started: fastANI
[2024-01-24 11:43:39,954] [INFO] Running command: fastANI --query /var/lib/cwl/stg0352e4f1-3bd8-48a2-99ab-501b220529df/GCF_003336755.1_ASM333675v1_genomic.fna.gz --refList GCF_003336755.1_ASM333675v1_genomic.fna/target_genomes.txt --output GCF_003336755.1_ASM333675v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:43:53,093] [INFO] Task succeeded: fastANI
[2024-01-24 11:43:53,093] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge186e080-75d3-4efa-92dd-710046ee1065/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:43:53,093] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge186e080-75d3-4efa-92dd-710046ee1065/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:43:53,107] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:43:53,107] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:43:53,108] [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
Elioraea thermophila	strain=YIM 72297	GCA_003336755.1	2185104	2185104	type	True	100.0	999	1003	95	conclusive
Elioraea tepida	strain=MS-P2	GCA_019203965.1	2843330	2843330	type	True	79.4927	558	1003	95	below_threshold
Elioraea rosea	strain=PF-30	GCA_007644105.1	2492390	2492390	type	True	79.1673	527	1003	95	below_threshold
Roseomonas alkaliterrae	strain=DSM 25895	GCA_014199195.1	1452450	1452450	type	True	78.1274	446	1003	95	below_threshold
Roseomonas rhizosphaerae	strain=YW11	GCA_002631185.1	1335062	1335062	type	True	77.5831	361	1003	95	below_threshold
Acidisphaera rubrifaciens	strain=HS-AP3	GCA_000964365.1	50715	50715	type	True	77.5792	205	1003	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	77.5443	343	1003	95	below_threshold
Roseomonas cervicalis	strain=ATCC 49957	GCA_000164635.1	204525	204525	type	True	77.543	326	1003	95	below_threshold
Roseomonas oryzicola	strain=KCTC 22478	GCA_012163135.1	535904	535904	type	True	77.3829	405	1003	95	below_threshold
Roseomonas gilardii subsp. rosea	strain=NCTC13290	GCA_900455865.1	243956	257708	type	True	77.3447	286	1003	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	77.1253	296	1003	95	below_threshold
Belnapia moabensis	strain=DSM 16746	GCA_000745835.1	365533	365533	type	True	77.0711	357	1003	95	below_threshold
Roseococcus thiosulfatophilus	strain=RB-3	GCA_017311575.1	35813	35813	type	True	76.9507	311	1003	95	below_threshold
Belnapia mucosa	strain=T6	GCA_016775475.1	2804532	2804532	type	True	76.8779	359	1003	95	below_threshold
Roseomonas rosea	strain=DSM 14916	GCA_900141905.1	198092	198092	type	True	76.8569	299	1003	95	below_threshold
Acidiphilium iwatense	strain=KCTC 23505	GCA_021556475.1	768198	768198	type	True	76.6471	179	1003	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:43:53,109] [INFO] DFAST Taxonomy check result was written to GCF_003336755.1_ASM333675v1_genomic.fna/tc_result.tsv
[2024-01-24 11:43:53,110] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:43:53,110] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:43:53,110] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge186e080-75d3-4efa-92dd-710046ee1065/dqc_reference/checkm_data
[2024-01-24 11:43:53,112] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:43:53,148] [INFO] Task started: CheckM
[2024-01-24 11:43:53,148] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003336755.1_ASM333675v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003336755.1_ASM333675v1_genomic.fna/checkm_input GCF_003336755.1_ASM333675v1_genomic.fna/checkm_result
[2024-01-24 11:44:30,381] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:30,383] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:30,403] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:30,403] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:30,404] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003336755.1_ASM333675v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:30,404] [INFO] Task started: Blastn
[2024-01-24 11:44:30,405] [INFO] Running command: blastn -query GCF_003336755.1_ASM333675v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge186e080-75d3-4efa-92dd-710046ee1065/dqc_reference/reference_markers_gtdb.fasta -out GCF_003336755.1_ASM333675v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:32,062] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:32,065] [INFO] Selected 10 target genomes.
[2024-01-24 11:44:32,066] [INFO] Target genome list was writen to GCF_003336755.1_ASM333675v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:32,076] [INFO] Task started: fastANI
[2024-01-24 11:44:32,076] [INFO] Running command: fastANI --query /var/lib/cwl/stg0352e4f1-3bd8-48a2-99ab-501b220529df/GCF_003336755.1_ASM333675v1_genomic.fna.gz --refList GCF_003336755.1_ASM333675v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003336755.1_ASM333675v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:44:41,071] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:41,086] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:44:41,087] [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_003336755.1	s__Elioraea thermophila	100.0	1001	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Elioraea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_006704265.1	s__Elioraea sp006704265	81.0481	621	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Elioraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378465.1	s__Elioraea tepidiphila	80.547	665	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Elioraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019203965.1	s__Elioraea_A sp019203965	79.5018	557	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Elioraea_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007644105.1	s__Elioraea_A rosea	79.1788	525	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Elioraea_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014644455.1	s__Caldovatus sediminis	78.1564	475	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Caldovatus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903843125.1	s__CAIMOR01 sp903843125	77.1748	273	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAIMOR01	95.0	99.35	99.29	0.86	0.84	4	-
GCA_019240395.1	s__JAFAYA01 sp019240395	77.091	266	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__JAFAYA01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016805305.1	s__Roseomonas_A sp016805305	77.0306	379	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019029495.1	s__Roseomonas_A sp019029495	76.8145	307	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:44:41,090] [INFO] GTDB search result was written to GCF_003336755.1_ASM333675v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:44:41,090] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:44:41,094] [INFO] DFAST_QC result json was written to GCF_003336755.1_ASM333675v1_genomic.fna/dqc_result.json
[2024-01-24 11:44:41,094] [INFO] DFAST_QC completed!
[2024-01-24 11:44:41,095] [INFO] Total running time: 0h1m16s