[2024-01-24 13:22:31,254] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:31,256] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:31,257] [INFO] DQC Reference Directory: /var/lib/cwl/stgc21f4075-aac0-4aca-a6ef-dcfea4159443/dqc_reference
[2024-01-24 13:22:32,578] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:32,580] [INFO] Task started: Prodigal
[2024-01-24 13:22:32,581] [INFO] Running command: gunzip -c /var/lib/cwl/stg9eece077-6afd-4614-a606-85fe1b17bed7/GCF_002564065.1_ASM256406v1_genomic.fna.gz | prodigal -d GCF_002564065.1_ASM256406v1_genomic.fna/cds.fna -a GCF_002564065.1_ASM256406v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:23:27,591] [INFO] Task succeeded: Prodigal
[2024-01-24 13:23:27,592] [INFO] Task started: HMMsearch
[2024-01-24 13:23:27,592] [INFO] Running command: hmmsearch --tblout GCF_002564065.1_ASM256406v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc21f4075-aac0-4aca-a6ef-dcfea4159443/dqc_reference/reference_markers.hmm GCF_002564065.1_ASM256406v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:23:27,929] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:23:27,930] [INFO] Found 6/6 markers.
[2024-01-24 13:23:27,989] [INFO] Query marker FASTA was written to GCF_002564065.1_ASM256406v1_genomic.fna/markers.fasta
[2024-01-24 13:23:27,989] [INFO] Task started: Blastn
[2024-01-24 13:23:27,989] [INFO] Running command: blastn -query GCF_002564065.1_ASM256406v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc21f4075-aac0-4aca-a6ef-dcfea4159443/dqc_reference/reference_markers.fasta -out GCF_002564065.1_ASM256406v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:29,333] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:29,337] [INFO] Selected 12 target genomes.
[2024-01-24 13:23:29,338] [INFO] Target genome list was writen to GCF_002564065.1_ASM256406v1_genomic.fna/target_genomes.txt
[2024-01-24 13:23:29,651] [INFO] Task started: fastANI
[2024-01-24 13:23:29,651] [INFO] Running command: fastANI --query /var/lib/cwl/stg9eece077-6afd-4614-a606-85fe1b17bed7/GCF_002564065.1_ASM256406v1_genomic.fna.gz --refList GCF_002564065.1_ASM256406v1_genomic.fna/target_genomes.txt --output GCF_002564065.1_ASM256406v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:23:53,379] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:53,380] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc21f4075-aac0-4aca-a6ef-dcfea4159443/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:23:53,380] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc21f4075-aac0-4aca-a6ef-dcfea4159443/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:23:53,394] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:23:53,394] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:23:53,394] [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
Saccharopolyspora erythraea	strain=DSM 40517	GCA_002564065.1	1836	1836	type	True	100.0	2741	2743	95	conclusive
Saccharopolyspora erythraea	strain=NRRL 2338	GCA_000062885.1	1836	1836	type	True	99.9991	2737	2743	95	conclusive
Saccharopolyspora erythraea	strain=NRRL 2338	GCA_000171635.1	1836	1836	type	True	99.9251	2573	2743	95	conclusive
Saccharopolyspora hordei	strain=DSM 44065	GCA_013410345.1	1838	1838	type	True	82.5816	1272	2743	95	below_threshold
Saccharopolyspora hirsuta	strain=VKM Ac-666	GCA_008630535.1	1837	1837	type	True	82.5384	1462	2743	95	below_threshold
Saccharopolyspora subtropica	strain=CGMCC 4.7206	GCA_014646075.1	1530170	1530170	type	True	82.1952	1202	2743	95	below_threshold
Saccharopolyspora antimicrobica	strain=DSM 45119	GCA_003635025.1	455193	455193	type	True	82.1206	1426	2743	95	below_threshold
Saccharopolyspora kobensis	strain=ATCC 20501	GCA_900108315.1	146035	146035	type	True	82.112	1409	2743	95	below_threshold
Saccharopolyspora elongata	strain=7K502	GCA_004348985.1	2530387	2530387	type	True	82.0528	1498	2743	95	below_threshold
Saccharopolyspora shandongensis	strain=CGMCC 4.3530	GCA_900106995.1	418495	418495	type	True	81.9423	1485	2743	95	below_threshold
Saccharopolyspora flava	strain=DSM 44771	GCA_900116135.1	95161	95161	type	True	81.7115	1234	2743	95	below_threshold
Streptoalloteichus hindustanus	strain=DSM 44523	GCA_900129375.1	2017	2017	type	True	78.7957	909	2743	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:23:53,396] [INFO] DFAST Taxonomy check result was written to GCF_002564065.1_ASM256406v1_genomic.fna/tc_result.tsv
[2024-01-24 13:23:53,397] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:23:53,397] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:23:53,397] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc21f4075-aac0-4aca-a6ef-dcfea4159443/dqc_reference/checkm_data
[2024-01-24 13:23:53,399] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:23:53,473] [INFO] Task started: CheckM
[2024-01-24 13:23:53,473] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002564065.1_ASM256406v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002564065.1_ASM256406v1_genomic.fna/checkm_input GCF_002564065.1_ASM256406v1_genomic.fna/checkm_result
[2024-01-24 13:26:57,877] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:57,879] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:26:57,903] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:57,904] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:57,904] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002564065.1_ASM256406v1_genomic.fna/markers.fasta)
[2024-01-24 13:26:57,905] [INFO] Task started: Blastn
[2024-01-24 13:26:57,905] [INFO] Running command: blastn -query GCF_002564065.1_ASM256406v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc21f4075-aac0-4aca-a6ef-dcfea4159443/dqc_reference/reference_markers_gtdb.fasta -out GCF_002564065.1_ASM256406v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:59,868] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:59,872] [INFO] Selected 14 target genomes.
[2024-01-24 13:26:59,872] [INFO] Target genome list was writen to GCF_002564065.1_ASM256406v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:59,893] [INFO] Task started: fastANI
[2024-01-24 13:26:59,894] [INFO] Running command: fastANI --query /var/lib/cwl/stg9eece077-6afd-4614-a606-85fe1b17bed7/GCF_002564065.1_ASM256406v1_genomic.fna.gz --refList GCF_002564065.1_ASM256406v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002564065.1_ASM256406v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:27:25,673] [INFO] Task succeeded: fastANI
[2024-01-24 13:27:25,697] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:27:25,698] [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_000062885.1	s__Saccharopolyspora_D erythraea	99.9991	2736	2743	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora_D	95.0	99.99	99.99	1.00	1.00	5	conclusive
GCF_018141105.1	s__Saccharopolyspora_D erythraea_A	94.5703	2320	2743	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410345.1	s__Saccharopolyspora hordei	82.5945	1270	2743	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008630535.1	s__Saccharopolyspora hirsuta	82.4931	1469	2743	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646075.1	s__Saccharopolyspora subtropica	82.1836	1205	2743	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003635025.1	s__Saccharopolyspora antimicrobica	82.1117	1429	2743	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	96.3257	100.00	100.00	1.00	1.00	2	-
GCF_900112555.1	s__Saccharopolyspora jiangxiensis	82.0817	1427	2743	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	96.3257	100.00	99.99	1.00	1.00	3	-
GCF_004348985.1	s__Saccharopolyspora sp004348985	82.0188	1504	2743	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106995.1	s__Saccharopolyspora shandongensis	81.9536	1482	2743	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116135.1	s__Saccharopolyspora flava	81.7243	1232	2743	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014697215.1	s__Saccharopolyspora pogona	81.6823	1341	2743	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	95.67	95.67	0.80	0.80	2	-
GCF_014203395.1	s__Saccharopolyspora phatthalungensis	81.5314	1197	2743	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	99.57	99.57	0.93	0.93	2	-
GCF_009664835.1	s__Allosaccharopolyspora coralli	79.9183	831	2743	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Allosaccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129375.1	s__Streptoalloteichus hindustanus	78.8171	903	2743	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Streptoalloteichus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:27:25,699] [INFO] GTDB search result was written to GCF_002564065.1_ASM256406v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:27:25,700] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:27:25,703] [INFO] DFAST_QC result json was written to GCF_002564065.1_ASM256406v1_genomic.fna/dqc_result.json
[2024-01-24 13:27:25,703] [INFO] DFAST_QC completed!
[2024-01-24 13:27:25,704] [INFO] Total running time: 0h4m54s