[2023-06-17 06:12:36,765] [INFO] DFAST_QC pipeline started.
[2023-06-17 06:12:36,768] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 06:12:36,769] [INFO] DQC Reference Directory: /var/lib/cwl/stg074d5d40-2a85-478b-9c18-4f6ebf20c25b/dqc_reference
[2023-06-17 06:12:38,021] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 06:12:38,022] [INFO] Task started: Prodigal
[2023-06-17 06:12:38,022] [INFO] Running command: gunzip -c /var/lib/cwl/stg91b9e864-9afd-4436-90f6-b3b3c1b422fd/GCA_003220855.1_ASM322085v1_genomic.fna.gz | prodigal -d GCA_003220855.1_ASM322085v1_genomic.fna/cds.fna -a GCA_003220855.1_ASM322085v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 06:12:45,407] [INFO] Task succeeded: Prodigal
[2023-06-17 06:12:45,408] [INFO] Task started: HMMsearch
[2023-06-17 06:12:45,408] [INFO] Running command: hmmsearch --tblout GCA_003220855.1_ASM322085v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg074d5d40-2a85-478b-9c18-4f6ebf20c25b/dqc_reference/reference_markers.hmm GCA_003220855.1_ASM322085v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 06:12:45,647] [INFO] Task succeeded: HMMsearch
[2023-06-17 06:12:45,649] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg91b9e864-9afd-4436-90f6-b3b3c1b422fd/GCA_003220855.1_ASM322085v1_genomic.fna.gz]
[2023-06-17 06:12:45,687] [INFO] Query marker FASTA was written to GCA_003220855.1_ASM322085v1_genomic.fna/markers.fasta
[2023-06-17 06:12:45,687] [INFO] Task started: Blastn
[2023-06-17 06:12:45,687] [INFO] Running command: blastn -query GCA_003220855.1_ASM322085v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg074d5d40-2a85-478b-9c18-4f6ebf20c25b/dqc_reference/reference_markers.fasta -out GCA_003220855.1_ASM322085v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 06:12:46,355] [INFO] Task succeeded: Blastn
[2023-06-17 06:12:46,361] [INFO] Selected 28 target genomes.
[2023-06-17 06:12:46,361] [INFO] Target genome list was writen to GCA_003220855.1_ASM322085v1_genomic.fna/target_genomes.txt
[2023-06-17 06:12:46,372] [INFO] Task started: fastANI
[2023-06-17 06:12:46,372] [INFO] Running command: fastANI --query /var/lib/cwl/stg91b9e864-9afd-4436-90f6-b3b3c1b422fd/GCA_003220855.1_ASM322085v1_genomic.fna.gz --refList GCA_003220855.1_ASM322085v1_genomic.fna/target_genomes.txt --output GCA_003220855.1_ASM322085v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 06:13:12,622] [INFO] Task succeeded: fastANI
[2023-06-17 06:13:12,623] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg074d5d40-2a85-478b-9c18-4f6ebf20c25b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 06:13:12,623] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg074d5d40-2a85-478b-9c18-4f6ebf20c25b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 06:13:12,644] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 06:13:12,644] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 06:13:12,644] [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
Gemmatirosa kalamazoonensis	strain=KBS708	GCA_000522985.1	861299	861299	type	True	75.6668	229	812	95	below_threshold
Longimicrobium terrae	strain=DSM 29007	GCA_014202995.1	1639882	1639882	type	True	75.2177	102	812	95	below_threshold
Longimicrobium terrae	strain=CECT 8660	GCA_014198875.1	1639882	1639882	type	True	75.2093	103	812	95	below_threshold
Longimicrobium terrae	strain=CB-286315	GCA_013000925.1	1639882	1639882	type	True	75.2014	104	812	95	below_threshold
Sphaerisporangium krabiense	strain=NBRC 107571	GCA_016863355.1	763782	763782	type	True	74.8032	87	812	95	below_threshold
Sphaerisporangium krabiense	strain=DSM 45790	GCA_014200435.1	763782	763782	type	True	74.7963	88	812	95	below_threshold
Sphaerisporangium rufum	strain=NBRC 109079	GCA_016863395.1	1381558	1381558	type	True	74.7934	122	812	95	below_threshold
Catenulispora rubra	strain=DSM 44948	GCA_015356825.1	280293	280293	type	True	74.7901	117	812	95	below_threshold
Catenulispora pinisilvae	strain=NH11	GCA_015356865.1	2705253	2705253	type	True	74.7876	95	812	95	below_threshold
Actinospica durhamensis	strain=CSCA 57	GCA_018139695.1	1508375	1508375	type	True	74.7799	104	812	95	below_threshold
Kitasatospora griseola	strain=JCM 3339	GCA_014648555.1	2064	2064	type	True	74.7799	100	812	95	below_threshold
Catenulispora pinistramenti	strain=NL8	GCA_018274385.1	2705254	2705254	type	True	74.7597	95	812	95	below_threshold
Gaiella occulta	strain=F2-233	GCA_003351045.1	1002870	1002870	type	True	74.7468	74	812	95	below_threshold
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	74.6805	103	812	95	below_threshold
Actinomadura oligospora	strain=ATCC 43269	GCA_000518265.1	111804	111804	type	True	74.6785	111	812	95	below_threshold
Kitasatospora cheerisanensis	strain=KCTC 2395	GCA_000696185.1	81942	81942	type	True	74.652	121	812	95	below_threshold
Kitasatospora herbaricolor	strain=JCM 4138	GCA_014648975.1	68217	68217	type	True	74.6516	96	812	95	below_threshold
Actinosynnema mirum	strain=DSM 43827	GCA_000023245.1	40567	40567	type	True	74.6451	128	812	95	below_threshold
Kitasatospora acidiphila	strain=MMS16-CNU292	GCA_006636205.1	2567942	2567942	type	True	74.6399	93	812	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 06:13:12,647] [INFO] DFAST Taxonomy check result was written to GCA_003220855.1_ASM322085v1_genomic.fna/tc_result.tsv
[2023-06-17 06:13:12,647] [INFO] ===== Taxonomy check completed =====
[2023-06-17 06:13:12,647] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 06:13:12,648] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg074d5d40-2a85-478b-9c18-4f6ebf20c25b/dqc_reference/checkm_data
[2023-06-17 06:13:12,649] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 06:13:12,680] [INFO] Task started: CheckM
[2023-06-17 06:13:12,680] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003220855.1_ASM322085v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003220855.1_ASM322085v1_genomic.fna/checkm_input GCA_003220855.1_ASM322085v1_genomic.fna/checkm_result
[2023-06-17 06:13:39,631] [INFO] Task succeeded: CheckM
[2023-06-17 06:13:39,632] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 4.55%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 06:13:39,656] [INFO] ===== Completeness check finished =====
[2023-06-17 06:13:39,656] [INFO] ===== Start GTDB Search =====
[2023-06-17 06:13:39,657] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003220855.1_ASM322085v1_genomic.fna/markers.fasta)
[2023-06-17 06:13:39,657] [INFO] Task started: Blastn
[2023-06-17 06:13:39,657] [INFO] Running command: blastn -query GCA_003220855.1_ASM322085v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg074d5d40-2a85-478b-9c18-4f6ebf20c25b/dqc_reference/reference_markers_gtdb.fasta -out GCA_003220855.1_ASM322085v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 06:13:40,649] [INFO] Task succeeded: Blastn
[2023-06-17 06:13:40,654] [INFO] Selected 11 target genomes.
[2023-06-17 06:13:40,654] [INFO] Target genome list was writen to GCA_003220855.1_ASM322085v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 06:13:40,660] [INFO] Task started: fastANI
[2023-06-17 06:13:40,660] [INFO] Running command: fastANI --query /var/lib/cwl/stg91b9e864-9afd-4436-90f6-b3b3c1b422fd/GCA_003220855.1_ASM322085v1_genomic.fna.gz --refList GCA_003220855.1_ASM322085v1_genomic.fna/target_genomes_gtdb.txt --output GCA_003220855.1_ASM322085v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 06:13:47,920] [INFO] Task succeeded: fastANI
[2023-06-17 06:13:47,934] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 06:13:47,934] [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
GCA_003220855.1	s__AG41 sp003220855	100.0	802	812	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__AG41	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003222155.1	s__AG41 sp003222155	88.259	679	812	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__AG41	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003222055.1	s__AG41 sp003222055	88.2275	678	812	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__AG41	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003222085.1	s__AG41 sp003222085	80.8758	568	812	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__AG41	95.0	99.39	98.99	0.94	0.93	4	-
GCA_003220905.1	s__AG41 sp003220905	80.6538	409	812	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__AG41	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016880225.1	s__AG41 sp016880225	80.3497	309	812	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__AG41	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003221085.1	s__AG41 sp003221085	80.319	453	812	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__AG41	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003220975.1	s__AG41 sp003220975	80.1096	432	812	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__AG41	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003220935.1	s__20CM-4-69-16 sp003220935	79.4703	463	812	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__20CM-4-69-16	95.0	99.20	99.20	0.88	0.88	2	-
GCA_003222235.1	s__AG12 sp003222235	78.8223	383	812	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__AG12	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003222115.1	s__AG29 sp003222115	78.7462	411	812	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__AG29	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 06:13:47,936] [INFO] GTDB search result was written to GCA_003220855.1_ASM322085v1_genomic.fna/result_gtdb.tsv
[2023-06-17 06:13:47,937] [INFO] ===== GTDB Search completed =====
[2023-06-17 06:13:47,941] [INFO] DFAST_QC result json was written to GCA_003220855.1_ASM322085v1_genomic.fna/dqc_result.json
[2023-06-17 06:13:47,941] [INFO] DFAST_QC completed!
[2023-06-17 06:13:47,941] [INFO] Total running time: 0h1m11s