[2024-01-24 10:57:13,151] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:13,159] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:13,159] [INFO] DQC Reference Directory: /var/lib/cwl/stg8028f4ee-c8db-4278-bbcc-2ced76373934/dqc_reference
[2024-01-24 10:57:14,649] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:14,650] [INFO] Task started: Prodigal
[2024-01-24 10:57:14,650] [INFO] Running command: gunzip -c /var/lib/cwl/stg7344c28c-f381-4bcc-9a7c-eb6a7f6b270f/GCF_004348445.1_ASM434844v1_genomic.fna.gz | prodigal -d GCF_004348445.1_ASM434844v1_genomic.fna/cds.fna -a GCF_004348445.1_ASM434844v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:37,964] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:37,964] [INFO] Task started: HMMsearch
[2024-01-24 10:57:37,965] [INFO] Running command: hmmsearch --tblout GCF_004348445.1_ASM434844v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8028f4ee-c8db-4278-bbcc-2ced76373934/dqc_reference/reference_markers.hmm GCF_004348445.1_ASM434844v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:38,298] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:38,299] [INFO] Found 6/6 markers.
[2024-01-24 10:57:38,381] [INFO] Query marker FASTA was written to GCF_004348445.1_ASM434844v1_genomic.fna/markers.fasta
[2024-01-24 10:57:38,382] [INFO] Task started: Blastn
[2024-01-24 10:57:38,382] [INFO] Running command: blastn -query GCF_004348445.1_ASM434844v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8028f4ee-c8db-4278-bbcc-2ced76373934/dqc_reference/reference_markers.fasta -out GCF_004348445.1_ASM434844v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:39,810] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:39,813] [INFO] Selected 9 target genomes.
[2024-01-24 10:57:39,814] [INFO] Target genome list was writen to GCF_004348445.1_ASM434844v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:39,821] [INFO] Task started: fastANI
[2024-01-24 10:57:39,821] [INFO] Running command: fastANI --query /var/lib/cwl/stg7344c28c-f381-4bcc-9a7c-eb6a7f6b270f/GCF_004348445.1_ASM434844v1_genomic.fna.gz --refList GCF_004348445.1_ASM434844v1_genomic.fna/target_genomes.txt --output GCF_004348445.1_ASM434844v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:56,335] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:56,335] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8028f4ee-c8db-4278-bbcc-2ced76373934/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:56,336] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8028f4ee-c8db-4278-bbcc-2ced76373934/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:56,344] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:57:56,344] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:57:56,344] [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 aridisoli	strain=16K404	GCA_004348445.1	2530385	2530385	type	True	100.0	1964	1966	95	conclusive
Saccharopolyspora terrae	strain=16K309	GCA_004348435.1	2530384	2530384	type	True	94.2398	1674	1966	95	below_threshold
Saccharopolyspora endophytica	strain=KCTC 19397	GCA_018070075.1	543886	543886	type	True	94.2382	1682	1966	95	below_threshold
Saccharopolyspora karakumensis	strain=5K548	GCA_004349225.1	2530386	2530386	type	True	94.15	1676	1966	95	below_threshold
Saccharopolyspora dendranthemae	strain=DSM 46699	GCA_007829955.1	1181886	1181886	type	True	88.8482	1614	1966	95	below_threshold
Saccharopolyspora flava	strain=DSM 44771	GCA_900116135.1	95161	95161	type	True	88.5093	1588	1966	95	below_threshold
Saccharopolyspora rhizosphaerae	strain=H219	GCA_003931915.1	2492662	2492662	type	True	87.9837	1510	1966	95	below_threshold
Saccharopolyspora hirsuta	strain=VKM Ac-666	GCA_008630535.1	1837	1837	type	True	83.1571	1272	1966	95	below_threshold
Saccharopolyspora kobensis	strain=ATCC 20501	GCA_900108315.1	146035	146035	type	True	83.0472	1229	1966	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:56,346] [INFO] DFAST Taxonomy check result was written to GCF_004348445.1_ASM434844v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:56,346] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:56,346] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:56,347] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8028f4ee-c8db-4278-bbcc-2ced76373934/dqc_reference/checkm_data
[2024-01-24 10:57:56,347] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:56,410] [INFO] Task started: CheckM
[2024-01-24 10:57:56,411] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004348445.1_ASM434844v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004348445.1_ASM434844v1_genomic.fna/checkm_input GCF_004348445.1_ASM434844v1_genomic.fna/checkm_result
[2024-01-24 10:59:07,078] [INFO] Task succeeded: CheckM
[2024-01-24 10:59:07,079] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:59:07,102] [INFO] ===== Completeness check finished =====
[2024-01-24 10:59:07,103] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:59:07,103] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004348445.1_ASM434844v1_genomic.fna/markers.fasta)
[2024-01-24 10:59:07,103] [INFO] Task started: Blastn
[2024-01-24 10:59:07,104] [INFO] Running command: blastn -query GCF_004348445.1_ASM434844v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8028f4ee-c8db-4278-bbcc-2ced76373934/dqc_reference/reference_markers_gtdb.fasta -out GCF_004348445.1_ASM434844v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:59:09,094] [INFO] Task succeeded: Blastn
[2024-01-24 10:59:09,098] [INFO] Selected 8 target genomes.
[2024-01-24 10:59:09,098] [INFO] Target genome list was writen to GCF_004348445.1_ASM434844v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:59:09,104] [INFO] Task started: fastANI
[2024-01-24 10:59:09,104] [INFO] Running command: fastANI --query /var/lib/cwl/stg7344c28c-f381-4bcc-9a7c-eb6a7f6b270f/GCF_004348445.1_ASM434844v1_genomic.fna.gz --refList GCF_004348445.1_ASM434844v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004348445.1_ASM434844v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:23,402] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:23,413] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:23,413] [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_004348445.1	s__Saccharopolyspora sp004348445	100.0	1964	1966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018070075.1	s__Saccharopolyspora endophytica	94.2579	1680	1966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	96.33	95.95	0.87	0.87	3	-
GCF_007829955.1	s__Saccharopolyspora dendranthemae	88.8285	1620	1966	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	88.4841	1591	1966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003931915.1	s__Saccharopolyspora rhizosphaerae	87.9753	1511	1966	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	83.2045	1264	1966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112555.1	s__Saccharopolyspora jiangxiensis	82.9977	1237	1966	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	82.7366	1237	1966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:59:23,414] [INFO] GTDB search result was written to GCF_004348445.1_ASM434844v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:23,415] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:23,418] [INFO] DFAST_QC result json was written to GCF_004348445.1_ASM434844v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:23,418] [INFO] DFAST_QC completed!
[2024-01-24 10:59:23,419] [INFO] Total running time: 0h2m10s