[2024-01-25 19:54:50,547] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:54:50,550] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:54:50,550] [INFO] DQC Reference Directory: /var/lib/cwl/stg5d7d4b22-6a61-41b8-a8f2-10247d6f7234/dqc_reference
[2024-01-25 19:54:51,794] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:54:51,795] [INFO] Task started: Prodigal
[2024-01-25 19:54:51,795] [INFO] Running command: gunzip -c /var/lib/cwl/stg0cbda5b6-f4bd-4ced-b351-5148bac98d4b/GCF_000620785.1_ASM62078v1_genomic.fna.gz | prodigal -d GCF_000620785.1_ASM62078v1_genomic.fna/cds.fna -a GCF_000620785.1_ASM62078v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:55:20,199] [INFO] Task succeeded: Prodigal
[2024-01-25 19:55:20,199] [INFO] Task started: HMMsearch
[2024-01-25 19:55:20,199] [INFO] Running command: hmmsearch --tblout GCF_000620785.1_ASM62078v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5d7d4b22-6a61-41b8-a8f2-10247d6f7234/dqc_reference/reference_markers.hmm GCF_000620785.1_ASM62078v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:55:20,576] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:55:20,577] [INFO] Found 6/6 markers.
[2024-01-25 19:55:20,653] [INFO] Query marker FASTA was written to GCF_000620785.1_ASM62078v1_genomic.fna/markers.fasta
[2024-01-25 19:55:20,653] [INFO] Task started: Blastn
[2024-01-25 19:55:20,653] [INFO] Running command: blastn -query GCF_000620785.1_ASM62078v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d7d4b22-6a61-41b8-a8f2-10247d6f7234/dqc_reference/reference_markers.fasta -out GCF_000620785.1_ASM62078v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:55:22,133] [INFO] Task succeeded: Blastn
[2024-01-25 19:55:22,135] [INFO] Selected 17 target genomes.
[2024-01-25 19:55:22,136] [INFO] Target genome list was writen to GCF_000620785.1_ASM62078v1_genomic.fna/target_genomes.txt
[2024-01-25 19:55:22,156] [INFO] Task started: fastANI
[2024-01-25 19:55:22,156] [INFO] Running command: fastANI --query /var/lib/cwl/stg0cbda5b6-f4bd-4ced-b351-5148bac98d4b/GCF_000620785.1_ASM62078v1_genomic.fna.gz --refList GCF_000620785.1_ASM62078v1_genomic.fna/target_genomes.txt --output GCF_000620785.1_ASM62078v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:55:53,123] [INFO] Task succeeded: fastANI
[2024-01-25 19:55:53,123] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5d7d4b22-6a61-41b8-a8f2-10247d6f7234/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:55:53,124] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5d7d4b22-6a61-41b8-a8f2-10247d6f7234/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:55:53,135] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:55:53,135] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:55:53,135] [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
Pseudonocardia acaciae	strain=DSM 45401	GCA_000620785.1	551276	551276	type	True	100.0	3260	3262	95	conclusive
Pseudonocardia spinosispora	strain=DSM 44797	GCA_000429025.1	103441	103441	type	True	79.6636	1361	3262	95	below_threshold
Pseudonocardia bannensis	strain=DSM 45300	GCA_012911875.1	630973	630973	type	True	78.7711	879	3262	95	below_threshold
Pseudonocardia acidicola	strain=K10HN5	GCA_012911935.1	2724939	2724939	type	True	78.5461	1043	3262	95	below_threshold
Pseudonocardia hydrocarbonoxydans	strain=NBRC 14498	GCA_006539565.1	76726	76726	type	True	78.1643	931	3262	95	below_threshold
Pseudonocardia kunmingensis	strain=DSM 45301	GCA_006716445.1	630975	630975	type	True	77.9008	1245	3262	95	below_threshold
Pseudonocardia oroxyli	strain=CGMCC 4.3143	GCA_900102195.1	366584	366584	type	True	77.9001	869	3262	95	below_threshold
Pseudonocardia petroleophila	strain=CGMCC 4.1532	GCA_014235185.1	37331	37331	type	True	77.8334	1038	3262	95	below_threshold
Pseudonocardia terrae	strain=RS11V-5	GCA_021343995.1	2905831	2905831	type	True	77.7677	1043	3262	95	below_threshold
Pseudonocardia pini	strain=CAP47R	GCA_013870575.1	2758030	2758030	type	True	77.7065	607	3262	95	below_threshold
Saccharopolyspora subtropica	strain=CGMCC 4.7206	GCA_014646075.1	1530170	1530170	type	True	77.5864	752	3262	95	below_threshold
Pseudonocardia autotrophica	strain=NBRC 12743	GCA_003945385.1	2074	2074	suspected-type	True	77.3776	1032	3262	95	below_threshold
Saccharothrix tamanrassetensis	strain=CECT 8640	GCA_014203665.1	1051531	1051531	type	True	77.293	986	3262	95	below_threshold
Actinokineospora enzanensis	strain=DSM 44649	GCA_000374445.1	155975	155975	type	True	77.1719	879	3262	95	below_threshold
Actinokineospora cianjurensis	strain=DSM 45657	GCA_003663795.1	585224	585224	type	True	77.126	830	3262	95	below_threshold
Actinokineospora terrae	strain=DSM 44260	GCA_900111175.1	155974	155974	type	True	77.0802	843	3262	95	below_threshold
Actinokineospora auranticolor	strain=YU 961-1	GCA_002934265.1	155976	155976	type	True	76.9513	967	3262	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:55:53,136] [INFO] DFAST Taxonomy check result was written to GCF_000620785.1_ASM62078v1_genomic.fna/tc_result.tsv
[2024-01-25 19:55:53,137] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:55:53,137] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:55:53,137] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5d7d4b22-6a61-41b8-a8f2-10247d6f7234/dqc_reference/checkm_data
[2024-01-25 19:55:53,138] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:55:53,227] [INFO] Task started: CheckM
[2024-01-25 19:55:53,227] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000620785.1_ASM62078v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000620785.1_ASM62078v1_genomic.fna/checkm_input GCF_000620785.1_ASM62078v1_genomic.fna/checkm_result
[2024-01-25 19:57:35,528] [INFO] Task succeeded: CheckM
[2024-01-25 19:57:35,529] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:57:35,551] [INFO] ===== Completeness check finished =====
[2024-01-25 19:57:35,551] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:57:35,552] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000620785.1_ASM62078v1_genomic.fna/markers.fasta)
[2024-01-25 19:57:35,552] [INFO] Task started: Blastn
[2024-01-25 19:57:35,552] [INFO] Running command: blastn -query GCF_000620785.1_ASM62078v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d7d4b22-6a61-41b8-a8f2-10247d6f7234/dqc_reference/reference_markers_gtdb.fasta -out GCF_000620785.1_ASM62078v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:57:37,596] [INFO] Task succeeded: Blastn
[2024-01-25 19:57:37,603] [INFO] Selected 16 target genomes.
[2024-01-25 19:57:37,603] [INFO] Target genome list was writen to GCF_000620785.1_ASM62078v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:57:37,617] [INFO] Task started: fastANI
[2024-01-25 19:57:37,617] [INFO] Running command: fastANI --query /var/lib/cwl/stg0cbda5b6-f4bd-4ced-b351-5148bac98d4b/GCF_000620785.1_ASM62078v1_genomic.fna.gz --refList GCF_000620785.1_ASM62078v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000620785.1_ASM62078v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:58:08,871] [INFO] Task succeeded: fastANI
[2024-01-25 19:58:08,881] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:58:08,882] [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_000620785.1	s__Pseudonocardia acaciae	100.0	3260	3262	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014208095.1	s__Pseudonocardia eucalypti	81.4737	1629	3262	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429025.1	s__Pseudonocardia spinosispora	79.6837	1357	3262	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013695005.1	s__Pseudonocardia sp013695005	79.1469	393	3262	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012911875.1	s__Pseudonocardia bannensis	78.7394	885	3262	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012911935.1	s__Pseudonocardia sp012911935	78.4778	1062	3262	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539565.1	s__Pseudonocardia hydrocarbonoxydans	78.1804	926	3262	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019263595.1	s__Pseudonocardia sp019263595	78.0465	890	3262	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005405885.1	s__Gandjariella thermophila	77.9949	930	3262	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Gandjariella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716445.1	s__Pseudonocardia kunmingensis	77.9262	1237	3262	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102195.1	s__Pseudonocardia oroxyli	77.8972	871	3262	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014235185.1	s__Pseudonocardia sp014235185	77.8405	1035	3262	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001698125.1	s__Pseudonocardia sp001698125	77.4219	981	3262	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003945385.1	s__Pseudonocardia autotrophica	77.3709	1034	3262	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	100.00	100.00	1.00	1.00	4	-
GCF_000374445.1	s__Actinokineospora enzanensis	77.1411	890	3262	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002934265.1	s__Actinokineospora auranticolor	76.9526	966	3262	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:58:08,883] [INFO] GTDB search result was written to GCF_000620785.1_ASM62078v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:58:08,883] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:58:08,888] [INFO] DFAST_QC result json was written to GCF_000620785.1_ASM62078v1_genomic.fna/dqc_result.json
[2024-01-25 19:58:08,888] [INFO] DFAST_QC completed!
[2024-01-25 19:58:08,888] [INFO] Total running time: 0h3m18s