[2024-01-24 13:49:33,531] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:33,533] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:33,533] [INFO] DQC Reference Directory: /var/lib/cwl/stg33bd26c1-1f9b-42d8-bd74-a7c844ff1a31/dqc_reference
[2024-01-24 13:49:34,856] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:34,857] [INFO] Task started: Prodigal
[2024-01-24 13:49:34,857] [INFO] Running command: gunzip -c /var/lib/cwl/stgf8556d75-574f-479f-a916-f5388a1b87a6/GCF_004363095.1_ASM436309v1_genomic.fna.gz | prodigal -d GCF_004363095.1_ASM436309v1_genomic.fna/cds.fna -a GCF_004363095.1_ASM436309v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:52,507] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:52,507] [INFO] Task started: HMMsearch
[2024-01-24 13:49:52,507] [INFO] Running command: hmmsearch --tblout GCF_004363095.1_ASM436309v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg33bd26c1-1f9b-42d8-bd74-a7c844ff1a31/dqc_reference/reference_markers.hmm GCF_004363095.1_ASM436309v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:52,944] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:52,946] [INFO] Found 6/6 markers.
[2024-01-24 13:49:53,004] [INFO] Query marker FASTA was written to GCF_004363095.1_ASM436309v1_genomic.fna/markers.fasta
[2024-01-24 13:49:53,005] [INFO] Task started: Blastn
[2024-01-24 13:49:53,005] [INFO] Running command: blastn -query GCF_004363095.1_ASM436309v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg33bd26c1-1f9b-42d8-bd74-a7c844ff1a31/dqc_reference/reference_markers.fasta -out GCF_004363095.1_ASM436309v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:54,368] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:54,371] [INFO] Selected 9 target genomes.
[2024-01-24 13:49:54,372] [INFO] Target genome list was writen to GCF_004363095.1_ASM436309v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:54,376] [INFO] Task started: fastANI
[2024-01-24 13:49:54,376] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8556d75-574f-479f-a916-f5388a1b87a6/GCF_004363095.1_ASM436309v1_genomic.fna.gz --refList GCF_004363095.1_ASM436309v1_genomic.fna/target_genomes.txt --output GCF_004363095.1_ASM436309v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:13,604] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:13,604] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg33bd26c1-1f9b-42d8-bd74-a7c844ff1a31/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:13,605] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg33bd26c1-1f9b-42d8-bd74-a7c844ff1a31/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:13,615] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:13,615] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:13,615] [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
Actinomycetospora succinea	strain=DSM 45775	GCA_004363095.1	663603	663603	type	True	100.0	2141	2143	95	conclusive
Actinomycetospora cinnamomea	strain=DSM 45771	GCA_003096675.1	663609	663609	type	True	85.3078	1459	2143	95	below_threshold
Actinomycetospora soli	strain=SF1	GCA_021026295.1	2893887	2893887	type	True	81.379	1262	2143	95	below_threshold
Actinomycetospora endophytica	strain=TBRC 5722	GCA_021026375.1	2291215	2291215	type	True	81.2747	1276	2143	95	below_threshold
Actinomycetospora corticicola	strain=DSM 45772	GCA_013409505.1	663602	663602	type	True	81.2502	1225	2143	95	below_threshold
Actinomycetospora chiangmaiensis	strain=DSM 45062	GCA_000379625.1	402650	402650	type	True	81.0272	1163	2143	95	below_threshold
Pseudonocardia cypriaca	strain=DSM 45511	GCA_006717045.1	882449	882449	type	True	77.3907	946	2143	95	below_threshold
Pseudonocardia hierapolitana	strain=DSM 45671	GCA_007994075.1	1128676	1128676	type	True	77.3662	919	2143	95	below_threshold
Saccharothrix algeriensis	strain=DSM 44581	GCA_016907655.1	173560	173560	type	True	76.9104	801	2143	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:13,617] [INFO] DFAST Taxonomy check result was written to GCF_004363095.1_ASM436309v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:13,618] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:13,618] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:13,619] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg33bd26c1-1f9b-42d8-bd74-a7c844ff1a31/dqc_reference/checkm_data
[2024-01-24 13:50:13,620] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:13,685] [INFO] Task started: CheckM
[2024-01-24 13:50:13,685] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004363095.1_ASM436309v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004363095.1_ASM436309v1_genomic.fna/checkm_input GCF_004363095.1_ASM436309v1_genomic.fna/checkm_result
[2024-01-24 13:51:40,389] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:40,390] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:40,413] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:40,413] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:40,414] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004363095.1_ASM436309v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:40,414] [INFO] Task started: Blastn
[2024-01-24 13:51:40,414] [INFO] Running command: blastn -query GCF_004363095.1_ASM436309v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg33bd26c1-1f9b-42d8-bd74-a7c844ff1a31/dqc_reference/reference_markers_gtdb.fasta -out GCF_004363095.1_ASM436309v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:42,450] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:42,453] [INFO] Selected 10 target genomes.
[2024-01-24 13:51:42,454] [INFO] Target genome list was writen to GCF_004363095.1_ASM436309v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:42,469] [INFO] Task started: fastANI
[2024-01-24 13:51:42,469] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8556d75-574f-479f-a916-f5388a1b87a6/GCF_004363095.1_ASM436309v1_genomic.fna.gz --refList GCF_004363095.1_ASM436309v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004363095.1_ASM436309v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:52:00,950] [INFO] Task succeeded: fastANI
[2024-01-24 13:52:00,968] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:52:00,969] [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_004363095.1	s__Actinomycetospora succinea	100.0	2141	2143	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinomycetospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902805495.1	s__Actinomycetospora sp902805495	85.9091	952	2143	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinomycetospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003096675.1	s__Actinomycetospora cinnamomea	85.2927	1461	2143	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinomycetospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012933465.1	s__Actinomycetospora sp012933465	81.3559	1273	2143	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinomycetospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409505.1	s__Actinomycetospora corticicola	81.1625	1243	2143	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinomycetospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379625.1	s__Actinomycetospora chiangmaiensis	81.0624	1158	2143	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinomycetospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006717045.1	s__Pseudonocardia cypriaca	77.4281	934	2143	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007994075.1	s__Pseudonocardia hierapolitana	77.282	945	2143	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907655.1	s__Actinosynnema algeriensis	76.8872	805	2143	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348665.1	s__Spirillospora sp004348665	76.0358	633	2143	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:52:00,971] [INFO] GTDB search result was written to GCF_004363095.1_ASM436309v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:52:00,972] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:52:00,976] [INFO] DFAST_QC result json was written to GCF_004363095.1_ASM436309v1_genomic.fna/dqc_result.json
[2024-01-24 13:52:00,976] [INFO] DFAST_QC completed!
[2024-01-24 13:52:00,976] [INFO] Total running time: 0h2m27s