[2024-01-24 12:52:51,110] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:52:51,112] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:52:51,112] [INFO] DQC Reference Directory: /var/lib/cwl/stg072d16e4-b080-40a3-b131-0bfb0d669c43/dqc_reference
[2024-01-24 12:52:53,753] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:52:53,754] [INFO] Task started: Prodigal
[2024-01-24 12:52:53,754] [INFO] Running command: gunzip -c /var/lib/cwl/stg73c00f6a-149c-4fc4-97b4-65f585bf33c4/GCF_000171235.2_ASM17123v2_genomic.fna.gz | prodigal -d GCF_000171235.2_ASM17123v2_genomic.fna/cds.fna -a GCF_000171235.2_ASM17123v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:53:30,433] [INFO] Task succeeded: Prodigal
[2024-01-24 12:53:30,433] [INFO] Task started: HMMsearch
[2024-01-24 12:53:30,434] [INFO] Running command: hmmsearch --tblout GCF_000171235.2_ASM17123v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg072d16e4-b080-40a3-b131-0bfb0d669c43/dqc_reference/reference_markers.hmm GCF_000171235.2_ASM17123v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:53:30,722] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:53:30,724] [INFO] Found 6/6 markers.
[2024-01-24 12:53:30,772] [INFO] Query marker FASTA was written to GCF_000171235.2_ASM17123v2_genomic.fna/markers.fasta
[2024-01-24 12:53:30,772] [INFO] Task started: Blastn
[2024-01-24 12:53:30,773] [INFO] Running command: blastn -query GCF_000171235.2_ASM17123v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg072d16e4-b080-40a3-b131-0bfb0d669c43/dqc_reference/reference_markers.fasta -out GCF_000171235.2_ASM17123v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:53:31,445] [INFO] Task succeeded: Blastn
[2024-01-24 12:53:31,449] [INFO] Selected 18 target genomes.
[2024-01-24 12:53:31,450] [INFO] Target genome list was writen to GCF_000171235.2_ASM17123v2_genomic.fna/target_genomes.txt
[2024-01-24 12:53:31,475] [INFO] Task started: fastANI
[2024-01-24 12:53:31,475] [INFO] Running command: fastANI --query /var/lib/cwl/stg73c00f6a-149c-4fc4-97b4-65f585bf33c4/GCF_000171235.2_ASM17123v2_genomic.fna.gz --refList GCF_000171235.2_ASM17123v2_genomic.fna/target_genomes.txt --output GCF_000171235.2_ASM17123v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:53:48,277] [INFO] Task succeeded: fastANI
[2024-01-24 12:53:48,278] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg072d16e4-b080-40a3-b131-0bfb0d669c43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:53:48,279] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg072d16e4-b080-40a3-b131-0bfb0d669c43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:53:48,288] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:53:48,288] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:53:48,288] [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
Geminisphaera colitermitum	strain=TAV2	GCA_000171235.2	1148786	1148786	type	True	100.0	1778	1787	95	conclusive
Ereboglobus luteus	strain=Ho45	GCA_003096195.1	1796921	1796921	type	True	78.5288	241	1787	95	below_threshold
Rariglobus hedericola	strain=53C-WASEF	GCA_007559335.1	2597822	2597822	type	True	77.941	256	1787	95	below_threshold
Nibricoccus aquaticus	strain=HZ-65	GCA_002310495.1	2576891	2576891	type	True	77.8761	249	1787	95	below_threshold
Cephaloticoccus capnophilus	strain=CV41	GCA_001580045.1	1548208	1548208	type	True	77.5168	117	1787	95	below_threshold
Opitutus terrae	strain=PB90-1	GCA_000019965.1	107709	107709	type	True	76.7799	148	1787	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	74.9051	81	1787	95	below_threshold
Actinacidiphila acididurans	strain=KK5PA1	GCA_016918855.1	2784346	2784346	type	True	74.8573	80	1787	95	below_threshold
Actinoplanes rishiriensis	strain=NBRC 108556	GCA_016862375.1	1050105	1050105	type	True	74.7415	85	1787	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:53:48,290] [INFO] DFAST Taxonomy check result was written to GCF_000171235.2_ASM17123v2_genomic.fna/tc_result.tsv
[2024-01-24 12:53:48,290] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:53:48,290] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:53:48,291] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg072d16e4-b080-40a3-b131-0bfb0d669c43/dqc_reference/checkm_data
[2024-01-24 12:53:48,291] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:53:48,345] [INFO] Task started: CheckM
[2024-01-24 12:53:48,345] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000171235.2_ASM17123v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000171235.2_ASM17123v2_genomic.fna/checkm_input GCF_000171235.2_ASM17123v2_genomic.fna/checkm_result
[2024-01-24 12:55:21,431] [INFO] Task succeeded: CheckM
[2024-01-24 12:55:21,432] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:55:21,458] [INFO] ===== Completeness check finished =====
[2024-01-24 12:55:21,458] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:55:21,459] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000171235.2_ASM17123v2_genomic.fna/markers.fasta)
[2024-01-24 12:55:21,459] [INFO] Task started: Blastn
[2024-01-24 12:55:21,459] [INFO] Running command: blastn -query GCF_000171235.2_ASM17123v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg072d16e4-b080-40a3-b131-0bfb0d669c43/dqc_reference/reference_markers_gtdb.fasta -out GCF_000171235.2_ASM17123v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:55:22,613] [INFO] Task succeeded: Blastn
[2024-01-24 12:55:22,620] [INFO] Selected 16 target genomes.
[2024-01-24 12:55:22,621] [INFO] Target genome list was writen to GCF_000171235.2_ASM17123v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:55:22,638] [INFO] Task started: fastANI
[2024-01-24 12:55:22,638] [INFO] Running command: fastANI --query /var/lib/cwl/stg73c00f6a-149c-4fc4-97b4-65f585bf33c4/GCF_000171235.2_ASM17123v2_genomic.fna.gz --refList GCF_000171235.2_ASM17123v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000171235.2_ASM17123v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:55:38,016] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:38,030] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:55:38,031] [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_000171235.2	s__Geminisphaera colitermitum	100.0	1778	1787	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Geminisphaera	95.0	97.34	97.31	0.79	0.79	3	conclusive
GCA_000242935.3	s__Geminisphaera sp000242935	81.6369	867	1787	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Geminisphaera	95.0	96.61	96.61	0.73	0.73	2	-
GCA_001650175.1	s__Ereboglobus sp001650175	78.9877	416	1787	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Ereboglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903876795.1	s__Rariglobus sp903876795	78.1191	272	1787	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Rariglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017991595.1	s__Didemnitutus sp017991595	77.7135	195	1787	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Didemnitutus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000972765.1	s__IMCC26134_A sp000972765	77.699	216	1787	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__IMCC26134_A	95.0	99.41	99.35	0.95	0.94	9	-
GCF_001746835.1	s__Lacunisphaera limnophila	77.4563	198	1787	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Lacunisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004118375.1	s__Lacunisphaera lenta	77.3976	208	1787	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Lacunisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019136515.1	s__CAJCBL01 sp019136515	77.3341	184	1787	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__CAJCBL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010027235.1	s__IMCC26134_A sp010027235	77.1375	135	1787	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__IMCC26134_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002288455.1	s__ER46 sp002288455	77.1366	193	1787	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903948415.1	s__CAITWF01 sp903948415	76.9098	226	1787	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__CAITWF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054705.1	s__ER46 sp003054705	76.8309	176	1787	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903862955.1	s__Opi-474 sp903862955	76.7851	177	1787	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.96	99.95	0.97	0.97	5	-
GCA_003569245.1	s__UBA953 sp003569245	76.4931	82	1787	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:55:38,032] [INFO] GTDB search result was written to GCF_000171235.2_ASM17123v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:55:38,033] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:55:38,037] [INFO] DFAST_QC result json was written to GCF_000171235.2_ASM17123v2_genomic.fna/dqc_result.json
[2024-01-24 12:55:38,037] [INFO] DFAST_QC completed!
[2024-01-24 12:55:38,037] [INFO] Total running time: 0h2m47s