[2023-07-01 03:10:05,600] [INFO] DFAST_QC pipeline started.
[2023-07-01 03:10:05,603] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 03:10:05,603] [INFO] DQC Reference Directory: /var/lib/cwl/stgdede9886-7cfe-4cd8-8692-cf57647819d3/dqc_reference
[2023-07-01 03:10:07,829] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 03:10:07,830] [INFO] Task started: Prodigal
[2023-07-01 03:10:07,831] [INFO] Running command: gunzip -c /var/lib/cwl/stg1ef7e87c-9918-4404-b95f-1474af0406ee/GCA_016209665.1_ASM1620966v1_genomic.fna.gz | prodigal -d GCA_016209665.1_ASM1620966v1_genomic.fna/cds.fna -a GCA_016209665.1_ASM1620966v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 03:10:19,441] [INFO] Task succeeded: Prodigal
[2023-07-01 03:10:19,442] [INFO] Task started: HMMsearch
[2023-07-01 03:10:19,442] [INFO] Running command: hmmsearch --tblout GCA_016209665.1_ASM1620966v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdede9886-7cfe-4cd8-8692-cf57647819d3/dqc_reference/reference_markers.hmm GCA_016209665.1_ASM1620966v1_genomic.fna/protein.faa > /dev/null
[2023-07-01 03:10:19,685] [INFO] Task succeeded: HMMsearch
[2023-07-01 03:10:19,687] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg1ef7e87c-9918-4404-b95f-1474af0406ee/GCA_016209665.1_ASM1620966v1_genomic.fna.gz]
[2023-07-01 03:10:19,764] [INFO] Query marker FASTA was written to GCA_016209665.1_ASM1620966v1_genomic.fna/markers.fasta
[2023-07-01 03:10:19,764] [INFO] Task started: Blastn
[2023-07-01 03:10:19,764] [INFO] Running command: blastn -query GCA_016209665.1_ASM1620966v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdede9886-7cfe-4cd8-8692-cf57647819d3/dqc_reference/reference_markers.fasta -out GCA_016209665.1_ASM1620966v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 03:10:20,361] [INFO] Task succeeded: Blastn
[2023-07-01 03:10:20,366] [INFO] Selected 15 target genomes.
[2023-07-01 03:10:20,366] [INFO] Target genome list was writen to GCA_016209665.1_ASM1620966v1_genomic.fna/target_genomes.txt
[2023-07-01 03:10:20,374] [INFO] Task started: fastANI
[2023-07-01 03:10:20,374] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ef7e87c-9918-4404-b95f-1474af0406ee/GCA_016209665.1_ASM1620966v1_genomic.fna.gz --refList GCA_016209665.1_ASM1620966v1_genomic.fna/target_genomes.txt --output GCA_016209665.1_ASM1620966v1_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 03:10:34,830] [INFO] Task succeeded: fastANI
[2023-07-01 03:10:34,831] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdede9886-7cfe-4cd8-8692-cf57647819d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 03:10:34,831] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdede9886-7cfe-4cd8-8692-cf57647819d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 03:10:34,845] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 03:10:34,845] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-07-01 03:10:34,845] [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
Paludisphaera rhizosphaereae	strain=JC665	GCA_011065895.1	2711216	2711216	type	True	75.1392	75	1111	95	below_threshold
Gemmata obscuriglobus	strain=DSM 5831	GCA_003149495.1	114	114	type	True	74.9108	58	1111	95	below_threshold
Gemmata obscuriglobus		GCA_901538385.1	114	114	type	True	74.9108	58	1111	95	below_threshold
Gemmata obscuriglobus	strain=DSM 5831	GCA_008065095.1	114	114	type	True	74.9045	59	1111	95	below_threshold
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	74.883	96	1111	95	below_threshold
Gemmata obscuriglobus	strain=UQM 2246	GCA_000171775.1	114	114	type	True	74.851	54	1111	95	below_threshold
Aquisphaera giovannonii	strain=OJF2	GCA_008087625.1	406548	406548	type	True	74.7982	119	1111	95	below_threshold
Tautonia plasticadhaerens	strain=ElP	GCA_007752535.1	2527974	2527974	type	True	74.7135	107	1111	95	below_threshold
Acrocarpospora pleiomorpha	strain=NBRC 16267	GCA_009687885.1	90975	90975	type	True	74.6645	90	1111	95	below_threshold
Streptomyces fructofermentans	strain=JCM 4956	GCA_014651055.1	152141	152141	type	True	74.6382	58	1111	95	below_threshold
--------------------------------------------------------------------------------
[2023-07-01 03:10:34,856] [INFO] DFAST Taxonomy check result was written to GCA_016209665.1_ASM1620966v1_genomic.fna/tc_result.tsv
[2023-07-01 03:10:34,856] [INFO] ===== Taxonomy check completed =====
[2023-07-01 03:10:34,857] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 03:10:34,857] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdede9886-7cfe-4cd8-8692-cf57647819d3/dqc_reference/checkm_data
[2023-07-01 03:10:34,858] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 03:10:34,914] [INFO] Task started: CheckM
[2023-07-01 03:10:34,915] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016209665.1_ASM1620966v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016209665.1_ASM1620966v1_genomic.fna/checkm_input GCA_016209665.1_ASM1620966v1_genomic.fna/checkm_result
[2023-07-01 03:11:11,520] [INFO] Task succeeded: CheckM
[2023-07-01 03:11:11,522] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.94%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 03:11:11,546] [INFO] ===== Completeness check finished =====
[2023-07-01 03:11:11,546] [INFO] ===== Start GTDB Search =====
[2023-07-01 03:11:11,547] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016209665.1_ASM1620966v1_genomic.fna/markers.fasta)
[2023-07-01 03:11:11,547] [INFO] Task started: Blastn
[2023-07-01 03:11:11,547] [INFO] Running command: blastn -query GCA_016209665.1_ASM1620966v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdede9886-7cfe-4cd8-8692-cf57647819d3/dqc_reference/reference_markers_gtdb.fasta -out GCA_016209665.1_ASM1620966v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 03:11:12,360] [INFO] Task succeeded: Blastn
[2023-07-01 03:11:12,364] [INFO] Selected 12 target genomes.
[2023-07-01 03:11:12,364] [INFO] Target genome list was writen to GCA_016209665.1_ASM1620966v1_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 03:11:12,370] [INFO] Task started: fastANI
[2023-07-01 03:11:12,370] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ef7e87c-9918-4404-b95f-1474af0406ee/GCA_016209665.1_ASM1620966v1_genomic.fna.gz --refList GCA_016209665.1_ASM1620966v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016209665.1_ASM1620966v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 03:11:21,235] [INFO] Task succeeded: fastANI
[2023-07-01 03:11:21,246] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-07-01 03:11:21,247] [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_016209665.1	s__JACQVT01 sp016209665	100.0	1088	1111	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__UBA1845;f__PWPN01;g__JACQVT01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_012719955.1	s__JAAXZI01 sp012719955	76.6043	150	1111	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__UBA1845;f__PWPN01;g__JAAXZI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018003015.1	s__JAGNEZ01 sp018003015	75.8061	139	1111	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__UBA1845;f__PWPN01;g__JAGNEZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003597935.1	s__SURF-32 sp003597935	75.4956	69	1111	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__UBA1845;f__UBA1845;g__SURF-32	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011525745.1	s__PLA4 sp011525745	75.378	68	1111	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__UBA1845;f__UTPLA1;g__PLA4	95.0	99.79	99.79	0.95	0.95	2	-
GCA_017999985.1	s__JAGNKU01 sp017999985	75.3538	81	1111	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__UBA1845;f__Fen-1342;g__JAGNKU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900696535.1	s__CAADGM01 sp900696535	75.2957	76	1111	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__UBA1845;f__Fen-1342;g__CAADGM01	95.0	99.20	99.20	0.91	0.91	2	-
GCA_900696525.1	s__CAADGL01 sp900696525	75.2468	63	1111	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__UBA1845;f__Fen-1342;g__CAADGL01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016741785.1	s__Streptomyces sp016741785	74.7001	65	1111	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014323665.1	s__Actinomadura_C sp014323665	74.544	63	1111	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Actinomadura_C	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-07-01 03:11:21,249] [INFO] GTDB search result was written to GCA_016209665.1_ASM1620966v1_genomic.fna/result_gtdb.tsv
[2023-07-01 03:11:21,249] [INFO] ===== GTDB Search completed =====
[2023-07-01 03:11:21,253] [INFO] DFAST_QC result json was written to GCA_016209665.1_ASM1620966v1_genomic.fna/dqc_result.json
[2023-07-01 03:11:21,253] [INFO] DFAST_QC completed!
[2023-07-01 03:11:21,253] [INFO] Total running time: 0h1m16s