[2024-01-24 14:54:51,001] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:54:51,003] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:54:51,003] [INFO] DQC Reference Directory: /var/lib/cwl/stg6fdb1e25-3dbc-4bd2-9d57-6e3d1bc77799/dqc_reference
[2024-01-24 14:54:52,287] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:54:52,288] [INFO] Task started: Prodigal
[2024-01-24 14:54:52,288] [INFO] Running command: gunzip -c /var/lib/cwl/stg686f58d8-5155-496c-96ea-f599cfd0cbef/GCF_012396345.1_ASM1239634v1_genomic.fna.gz | prodigal -d GCF_012396345.1_ASM1239634v1_genomic.fna/cds.fna -a GCF_012396345.1_ASM1239634v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:09,961] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:09,962] [INFO] Task started: HMMsearch
[2024-01-24 14:55:09,962] [INFO] Running command: hmmsearch --tblout GCF_012396345.1_ASM1239634v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6fdb1e25-3dbc-4bd2-9d57-6e3d1bc77799/dqc_reference/reference_markers.hmm GCF_012396345.1_ASM1239634v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:10,288] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:10,289] [INFO] Found 6/6 markers.
[2024-01-24 14:55:10,362] [INFO] Query marker FASTA was written to GCF_012396345.1_ASM1239634v1_genomic.fna/markers.fasta
[2024-01-24 14:55:10,362] [INFO] Task started: Blastn
[2024-01-24 14:55:10,362] [INFO] Running command: blastn -query GCF_012396345.1_ASM1239634v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6fdb1e25-3dbc-4bd2-9d57-6e3d1bc77799/dqc_reference/reference_markers.fasta -out GCF_012396345.1_ASM1239634v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:11,673] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:11,677] [INFO] Selected 13 target genomes.
[2024-01-24 14:55:11,677] [INFO] Target genome list was writen to GCF_012396345.1_ASM1239634v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:11,687] [INFO] Task started: fastANI
[2024-01-24 14:55:11,688] [INFO] Running command: fastANI --query /var/lib/cwl/stg686f58d8-5155-496c-96ea-f599cfd0cbef/GCF_012396345.1_ASM1239634v1_genomic.fna.gz --refList GCF_012396345.1_ASM1239634v1_genomic.fna/target_genomes.txt --output GCF_012396345.1_ASM1239634v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:34,108] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:34,108] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6fdb1e25-3dbc-4bd2-9d57-6e3d1bc77799/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:34,108] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6fdb1e25-3dbc-4bd2-9d57-6e3d1bc77799/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:34,121] [INFO] Found 13 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 14:55:34,122] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:55:34,122] [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
Nocardiopsis dassonvillei	strain=ATCC 23218	GCA_012396345.1	2014	2014	type	True	100.0	2040	2051	95	conclusive
Nocardiopsis dassonvillei	strain=NCTC10488	GCA_900638215.1	2014	2014	type	True	99.9886	2051	2051	95	conclusive
Nocardiopsis dassonvillei subsp. dassonvillei	strain=DSM 43111	GCA_000092985.1	568208	2014	type	True	99.9881	2050	2051	95	conclusive
Nocardiopsis dassonvillei subsp. crassaminis	strain=D1	GCA_902825375.1	2580523	2014	type	True	97.7211	1611	2051	95	conclusive
Nocardiopsis alborubida	strain=ATCC 23612	GCA_012396365.1	146802	146802	type	True	94.7037	1798	2051	95	below_threshold
Nocardiopsis alborubida	strain=NBRC 13392	GCA_001552695.1	146802	146802	type	True	94.6403	1743	2051	95	below_threshold
Nocardiopsis deserti	strain=H13	GCA_008638355.1	2605988	2605988	type	True	94.4544	1781	2051	95	below_threshold
Nocardiopsis halotolerans	strain=DSM 44410	GCA_000341065.1	124252	124252	type	True	89.1396	1424	2051	95	below_threshold
Nocardiopsis sinuspersici	strain=UTMC 00102	GCA_001998325.1	501010	501010	type	True	88.4256	1504	2051	95	below_threshold
Nocardiopsis exhalans	strain=JCM11759T	GCA_024134545.1	163604	163604	type	True	83.7563	1305	2051	95	below_threshold
Nocardiopsis kunsanensis	strain=DSM 44524	GCA_000340965.1	141693	141693	type	True	81.6377	1025	2051	95	below_threshold
Thermobifida alba	strain=DSM 43795	GCA_023208015.1	53522	53522	type	True	79.9353	783	2051	95	below_threshold
Streptomonospora litoralis	strain=M2	GCA_004323735.1	2498135	2498135	type	True	79.6801	872	2051	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:34,125] [INFO] DFAST Taxonomy check result was written to GCF_012396345.1_ASM1239634v1_genomic.fna/tc_result.tsv
[2024-01-24 14:55:34,126] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:34,126] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:34,126] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6fdb1e25-3dbc-4bd2-9d57-6e3d1bc77799/dqc_reference/checkm_data
[2024-01-24 14:55:34,128] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:34,194] [INFO] Task started: CheckM
[2024-01-24 14:55:34,194] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012396345.1_ASM1239634v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012396345.1_ASM1239634v1_genomic.fna/checkm_input GCF_012396345.1_ASM1239634v1_genomic.fna/checkm_result
[2024-01-24 14:56:52,668] [INFO] Task succeeded: CheckM
[2024-01-24 14:56:52,670] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 14:56:52,701] [INFO] ===== Completeness check finished =====
[2024-01-24 14:56:52,702] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:56:52,702] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012396345.1_ASM1239634v1_genomic.fna/markers.fasta)
[2024-01-24 14:56:52,702] [INFO] Task started: Blastn
[2024-01-24 14:56:52,703] [INFO] Running command: blastn -query GCF_012396345.1_ASM1239634v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6fdb1e25-3dbc-4bd2-9d57-6e3d1bc77799/dqc_reference/reference_markers_gtdb.fasta -out GCF_012396345.1_ASM1239634v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:54,860] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:54,864] [INFO] Selected 9 target genomes.
[2024-01-24 14:56:54,864] [INFO] Target genome list was writen to GCF_012396345.1_ASM1239634v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:56:54,879] [INFO] Task started: fastANI
[2024-01-24 14:56:54,880] [INFO] Running command: fastANI --query /var/lib/cwl/stg686f58d8-5155-496c-96ea-f599cfd0cbef/GCF_012396345.1_ASM1239634v1_genomic.fna.gz --refList GCF_012396345.1_ASM1239634v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012396345.1_ASM1239634v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:57:09,996] [INFO] Task succeeded: fastANI
[2024-01-24 14:57:10,010] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:57:10,010] [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_000092985.1	s__Nocardiopsis dassonvillei	99.9881	2050	2051	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	97.80	95.11	0.93	0.87	11	conclusive
GCF_012396365.1	s__Nocardiopsis alborubida	94.6919	1799	2051	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	96.95	95.06	0.88	0.80	4	-
GCA_002529455.1	s__Nocardiopsis fusca	93.2628	1694	2051	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000341065.1	s__Nocardiopsis halotolerans	89.1579	1422	2051	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905145.1	s__Nocardiopsis sp001905145	88.7128	1477	2051	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008638415.1	s__Nocardiopsis sinuspersici	88.4279	1487	2051	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	99.63	98.89	0.96	0.91	4	-
GCF_009830945.1	s__Nocardiopsis sp009830945	87.5509	1416	2051	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	99.72	99.66	0.93	0.93	3	-
GCF_900141985.1	s__Nocardiopsis flavescens	83.9093	1407	2051	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000341125.1	s__Nocardiopsis lucentensis	83.5647	1029	2051	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:57:10,012] [INFO] GTDB search result was written to GCF_012396345.1_ASM1239634v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:57:10,013] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:57:10,016] [INFO] DFAST_QC result json was written to GCF_012396345.1_ASM1239634v1_genomic.fna/dqc_result.json
[2024-01-24 14:57:10,016] [INFO] DFAST_QC completed!
[2024-01-24 14:57:10,016] [INFO] Total running time: 0h2m19s