[2024-01-24 13:18:27,167] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:27,170] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:27,170] [INFO] DQC Reference Directory: /var/lib/cwl/stgb5b060ea-f2a9-4406-a81d-b3c704017192/dqc_reference
[2024-01-24 13:18:28,503] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:28,504] [INFO] Task started: Prodigal
[2024-01-24 13:18:28,504] [INFO] Running command: gunzip -c /var/lib/cwl/stg7455aff7-d5d4-46a9-817d-f8b14fe3d2ff/GCF_000178975.2_ASM17897v2_genomic.fna.gz | prodigal -d GCF_000178975.2_ASM17897v2_genomic.fna/cds.fna -a GCF_000178975.2_ASM17897v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:44,101] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:44,102] [INFO] Task started: HMMsearch
[2024-01-24 13:18:44,102] [INFO] Running command: hmmsearch --tblout GCF_000178975.2_ASM17897v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb5b060ea-f2a9-4406-a81d-b3c704017192/dqc_reference/reference_markers.hmm GCF_000178975.2_ASM17897v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:44,430] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:44,432] [INFO] Found 6/6 markers.
[2024-01-24 13:18:44,485] [INFO] Query marker FASTA was written to GCF_000178975.2_ASM17897v2_genomic.fna/markers.fasta
[2024-01-24 13:18:44,485] [INFO] Task started: Blastn
[2024-01-24 13:18:44,485] [INFO] Running command: blastn -query GCF_000178975.2_ASM17897v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgb5b060ea-f2a9-4406-a81d-b3c704017192/dqc_reference/reference_markers.fasta -out GCF_000178975.2_ASM17897v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:45,239] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:45,251] [INFO] Selected 10 target genomes.
[2024-01-24 13:18:45,252] [INFO] Target genome list was writen to GCF_000178975.2_ASM17897v2_genomic.fna/target_genomes.txt
[2024-01-24 13:18:45,258] [INFO] Task started: fastANI
[2024-01-24 13:18:45,258] [INFO] Running command: fastANI --query /var/lib/cwl/stg7455aff7-d5d4-46a9-817d-f8b14fe3d2ff/GCF_000178975.2_ASM17897v2_genomic.fna.gz --refList GCF_000178975.2_ASM17897v2_genomic.fna/target_genomes.txt --output GCF_000178975.2_ASM17897v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:56,346] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:56,347] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb5b060ea-f2a9-4406-a81d-b3c704017192/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:56,348] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb5b060ea-f2a9-4406-a81d-b3c704017192/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:56,360] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:18:56,360] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:56,361] [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
Granulicella tundricola	strain=MP5ACTX9	GCA_000178975.2	940615	940615	type	True	100.0	1832	1832	95	conclusive
Edaphobacter lichenicola	strain=DSM 104462	GCA_025264645.1	2051959	2051959	suspected-type	True	78.4906	311	1832	95	below_threshold
Granulicella pectinivorans	strain=DSM 21001	GCA_900114625.1	474950	474950	type	True	78.4415	362	1832	95	below_threshold
Granulicella sibirica	strain=AF10	GCA_004115155.1	2479048	2479048	type	True	78.3952	328	1832	95	below_threshold
Granulicella rosea	strain=DSM 18704	GCA_900188085.1	474952	474952	type	True	78.1693	449	1832	95	below_threshold
Edaphobacter aggregans	strain=DSM 19364	GCA_000745965.1	570835	570835	type	True	78.1679	344	1832	95	below_threshold
Edaphobacter dinghuensis	strain=CGMCC 1.12997	GCA_014640335.1	1560005	1560005	type	True	77.8194	242	1832	95	below_threshold
Granulicella mallensis	strain=MP5ACTX8	GCA_000178955.2	940614	940614	type	True	77.5298	286	1832	95	below_threshold
Bryocella elongata	strain=DSM 22489	GCA_900108185.1	863522	863522	type	True	77.4728	289	1832	95	below_threshold
Acidobacterium capsulatum	strain=ATCC 51196	GCA_000022565.1	33075	33075	type	True	76.8127	121	1832	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:56,365] [INFO] DFAST Taxonomy check result was written to GCF_000178975.2_ASM17897v2_genomic.fna/tc_result.tsv
[2024-01-24 13:18:56,365] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:56,366] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:56,366] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb5b060ea-f2a9-4406-a81d-b3c704017192/dqc_reference/checkm_data
[2024-01-24 13:18:56,367] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:56,423] [INFO] Task started: CheckM
[2024-01-24 13:18:56,423] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000178975.2_ASM17897v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000178975.2_ASM17897v2_genomic.fna/checkm_input GCF_000178975.2_ASM17897v2_genomic.fna/checkm_result
[2024-01-24 13:19:46,198] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:46,200] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:46,224] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:46,225] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:46,225] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000178975.2_ASM17897v2_genomic.fna/markers.fasta)
[2024-01-24 13:19:46,226] [INFO] Task started: Blastn
[2024-01-24 13:19:46,226] [INFO] Running command: blastn -query GCF_000178975.2_ASM17897v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgb5b060ea-f2a9-4406-a81d-b3c704017192/dqc_reference/reference_markers_gtdb.fasta -out GCF_000178975.2_ASM17897v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:47,175] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:47,179] [INFO] Selected 22 target genomes.
[2024-01-24 13:19:47,179] [INFO] Target genome list was writen to GCF_000178975.2_ASM17897v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:47,203] [INFO] Task started: fastANI
[2024-01-24 13:19:47,203] [INFO] Running command: fastANI --query /var/lib/cwl/stg7455aff7-d5d4-46a9-817d-f8b14fe3d2ff/GCF_000178975.2_ASM17897v2_genomic.fna.gz --refList GCF_000178975.2_ASM17897v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000178975.2_ASM17897v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:07,160] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:07,184] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:07,184] [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_000178975.2	s__Granulicella_C tundricola	100.0	1832	1832	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Granulicella_C	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013410065.1	s__Granulicella_B arctica	78.718	342	1832	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Granulicella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018449545.1	s__Edaphobacter sp018449545	78.5973	358	1832	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765825.1	s__Edaphobacter sp009765825	78.5645	358	1832	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003751275.1	s__Edaphobacter sp003751275	78.5442	343	1832	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201375.1	s__Edaphobacter lichenicola_D	78.5348	337	1832	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009914315.1	s__Granulicella_C sp009914315	78.446	390	1832	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Granulicella_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114625.1	s__Granulicella_C pectinivorans	78.4254	364	1832	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Granulicella_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009766095.1	s__Edaphobacter sp009766095	78.2964	292	1832	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203275.1	s__Granulicella_D aggregans	78.2396	355	1832	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Granulicella_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188085.1	s__Granulicella_C rosea	78.1809	447	1832	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Granulicella_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745965.1	s__Edaphobacter aggregans	78.1683	344	1832	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903970285.1	s__Granulicella_C sp903970285	78.0203	344	1832	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Granulicella_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765785.1	s__UBA5172 sp009765785	77.7049	254	1832	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__UBA5172	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015655585.1	s__Edaphobacter sp015655585	77.6906	246	1832	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003138795.1	s__UBA5172 sp003138795	77.6601	214	1832	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__UBA5172	95.0	99.74	99.67	0.90	0.89	6	-
GCA_018268895.1	s__Edaphobacter sp018268895	77.6233	250	1832	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268775.1	s__Edaphobacter sp018268775	77.6063	212	1832	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000421065.1	s__Edaphobacter sp000421065	77.6037	299	1832	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903904755.1	s__CAIVDV01 sp903904755	77.0227	140	1832	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__CAIVDV01	95.0	99.92	99.89	0.96	0.95	6	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:07,186] [INFO] GTDB search result was written to GCF_000178975.2_ASM17897v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:07,186] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:07,190] [INFO] DFAST_QC result json was written to GCF_000178975.2_ASM17897v2_genomic.fna/dqc_result.json
[2024-01-24 13:20:07,190] [INFO] DFAST_QC completed!
[2024-01-24 13:20:07,190] [INFO] Total running time: 0h1m40s