[2024-01-24 11:43:36,697] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:36,701] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:36,702] [INFO] DQC Reference Directory: /var/lib/cwl/stg3086e906-d345-453c-b454-29d2085bf590/dqc_reference
[2024-01-24 11:43:38,002] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:38,002] [INFO] Task started: Prodigal
[2024-01-24 11:43:38,003] [INFO] Running command: gunzip -c /var/lib/cwl/stgedad8c57-0563-442f-8c98-0ce67c2b7a20/GCF_008638365.1_ASM863836v1_genomic.fna.gz | prodigal -d GCF_008638365.1_ASM863836v1_genomic.fna/cds.fna -a GCF_008638365.1_ASM863836v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:54,985] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:54,986] [INFO] Task started: HMMsearch
[2024-01-24 11:43:54,986] [INFO] Running command: hmmsearch --tblout GCF_008638365.1_ASM863836v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3086e906-d345-453c-b454-29d2085bf590/dqc_reference/reference_markers.hmm GCF_008638365.1_ASM863836v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:55,456] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:55,457] [INFO] Found 6/6 markers.
[2024-01-24 11:43:55,504] [INFO] Query marker FASTA was written to GCF_008638365.1_ASM863836v1_genomic.fna/markers.fasta
[2024-01-24 11:43:55,504] [INFO] Task started: Blastn
[2024-01-24 11:43:55,504] [INFO] Running command: blastn -query GCF_008638365.1_ASM863836v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3086e906-d345-453c-b454-29d2085bf590/dqc_reference/reference_markers.fasta -out GCF_008638365.1_ASM863836v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:56,811] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:56,815] [INFO] Selected 11 target genomes.
[2024-01-24 11:43:56,815] [INFO] Target genome list was writen to GCF_008638365.1_ASM863836v1_genomic.fna/target_genomes.txt
[2024-01-24 11:43:56,820] [INFO] Task started: fastANI
[2024-01-24 11:43:56,820] [INFO] Running command: fastANI --query /var/lib/cwl/stgedad8c57-0563-442f-8c98-0ce67c2b7a20/GCF_008638365.1_ASM863836v1_genomic.fna.gz --refList GCF_008638365.1_ASM863836v1_genomic.fna/target_genomes.txt --output GCF_008638365.1_ASM863836v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:13,097] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:13,098] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3086e906-d345-453c-b454-29d2085bf590/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:13,098] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3086e906-d345-453c-b454-29d2085bf590/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:13,108] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:13,108] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:13,108] [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 quinghaiensis	strain=YIM 28A4	GCA_008638365.1	464995	464995	type	True	100.0	1936	1948	95	conclusive
Nocardiopsis sinuspersici	strain=UTMC 00102	GCA_001998325.1	501010	501010	type	True	93.2594	1574	1948	95	below_threshold
Nocardiopsis halotolerans	strain=DSM 44410	GCA_000341065.1	124252	124252	type	True	88.5399	1348	1948	95	below_threshold
Nocardiopsis alborubida	strain=NBRC 13392	GCA_001552695.1	146802	146802	type	True	88.4345	1453	1948	95	below_threshold
Nocardiopsis deserti	strain=H13	GCA_008638355.1	2605988	2605988	type	True	88.4077	1524	1948	95	below_threshold
Nocardiopsis alborubida	strain=ATCC 23612	GCA_012396365.1	146802	146802	type	True	88.378	1487	1948	95	below_threshold
Nocardiopsis dassonvillei subsp. crassaminis	strain=D1	GCA_902825375.1	2580523	2014	type	True	88.1534	1258	1948	95	below_threshold
Nocardiopsis exhalans	strain=JCM11759T	GCA_024134545.1	163604	163604	type	True	83.805	1263	1948	95	below_threshold
Nocardiopsis kunsanensis	strain=DSM 44524	GCA_000340965.1	141693	141693	type	True	81.6873	993	1948	95	below_threshold
Thermobifida alba	strain=DSM 43795	GCA_023208015.1	53522	53522	type	True	79.9905	719	1948	95	below_threshold
Streptomonospora litoralis	strain=M2	GCA_004323735.1	2498135	2498135	type	True	79.4308	813	1948	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:13,110] [INFO] DFAST Taxonomy check result was written to GCF_008638365.1_ASM863836v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:13,110] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:13,111] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:13,111] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3086e906-d345-453c-b454-29d2085bf590/dqc_reference/checkm_data
[2024-01-24 11:44:13,113] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:13,172] [INFO] Task started: CheckM
[2024-01-24 11:44:13,173] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008638365.1_ASM863836v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008638365.1_ASM863836v1_genomic.fna/checkm_input GCF_008638365.1_ASM863836v1_genomic.fna/checkm_result
[2024-01-24 11:45:11,407] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:11,409] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:11,428] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:11,428] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:11,429] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008638365.1_ASM863836v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:11,429] [INFO] Task started: Blastn
[2024-01-24 11:45:11,429] [INFO] Running command: blastn -query GCF_008638365.1_ASM863836v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3086e906-d345-453c-b454-29d2085bf590/dqc_reference/reference_markers_gtdb.fasta -out GCF_008638365.1_ASM863836v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:13,392] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:13,395] [INFO] Selected 8 target genomes.
[2024-01-24 11:45:13,395] [INFO] Target genome list was writen to GCF_008638365.1_ASM863836v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:13,401] [INFO] Task started: fastANI
[2024-01-24 11:45:13,401] [INFO] Running command: fastANI --query /var/lib/cwl/stgedad8c57-0563-442f-8c98-0ce67c2b7a20/GCF_008638365.1_ASM863836v1_genomic.fna.gz --refList GCF_008638365.1_ASM863836v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008638365.1_ASM863836v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:26,804] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:26,812] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:26,812] [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_008638365.1	s__Nocardiopsis quinghaiensis	100.0	1936	1948	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_008638415.1	s__Nocardiopsis sinuspersici	93.263	1570	1948	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	99.63	98.89	0.96	0.91	4	-
GCF_001905145.1	s__Nocardiopsis sp001905145	92.9373	1562	1948	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002529455.1	s__Nocardiopsis fusca	88.8901	1504	1948	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	88.5313	1348	1948	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012396365.1	s__Nocardiopsis alborubida	88.3684	1488	1948	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	96.95	95.06	0.88	0.80	4	-
GCF_009830945.1	s__Nocardiopsis sp009830945	87.9583	1452	1948	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	99.72	99.66	0.93	0.93	3	-
GCF_003634495.1	s__Nocardiopsis sp003634495	83.8427	1351	1948	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 11:45:26,814] [INFO] GTDB search result was written to GCF_008638365.1_ASM863836v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:26,814] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:26,817] [INFO] DFAST_QC result json was written to GCF_008638365.1_ASM863836v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:26,817] [INFO] DFAST_QC completed!
[2024-01-24 11:45:26,817] [INFO] Total running time: 0h1m50s