[2024-01-25 17:54:35,834] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:54:35,836] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:54:35,836] [INFO] DQC Reference Directory: /var/lib/cwl/stg25445dfa-97d4-4eee-89d9-a4576f8e065c/dqc_reference
[2024-01-25 17:54:36,958] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:54:36,958] [INFO] Task started: Prodigal
[2024-01-25 17:54:36,959] [INFO] Running command: gunzip -c /var/lib/cwl/stge9ec370a-2412-4c20-b1b2-116ff5ee3158/GCF_021026375.1_ASM2102637v1_genomic.fna.gz | prodigal -d GCF_021026375.1_ASM2102637v1_genomic.fna/cds.fna -a GCF_021026375.1_ASM2102637v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:54:53,192] [INFO] Task succeeded: Prodigal
[2024-01-25 17:54:53,193] [INFO] Task started: HMMsearch
[2024-01-25 17:54:53,193] [INFO] Running command: hmmsearch --tblout GCF_021026375.1_ASM2102637v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg25445dfa-97d4-4eee-89d9-a4576f8e065c/dqc_reference/reference_markers.hmm GCF_021026375.1_ASM2102637v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:54:53,518] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:54:53,519] [INFO] Found 6/6 markers.
[2024-01-25 17:54:53,572] [INFO] Query marker FASTA was written to GCF_021026375.1_ASM2102637v1_genomic.fna/markers.fasta
[2024-01-25 17:54:53,573] [INFO] Task started: Blastn
[2024-01-25 17:54:53,573] [INFO] Running command: blastn -query GCF_021026375.1_ASM2102637v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25445dfa-97d4-4eee-89d9-a4576f8e065c/dqc_reference/reference_markers.fasta -out GCF_021026375.1_ASM2102637v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:54:54,882] [INFO] Task succeeded: Blastn
[2024-01-25 17:54:54,884] [INFO] Selected 11 target genomes.
[2024-01-25 17:54:54,885] [INFO] Target genome list was writen to GCF_021026375.1_ASM2102637v1_genomic.fna/target_genomes.txt
[2024-01-25 17:54:54,907] [INFO] Task started: fastANI
[2024-01-25 17:54:54,907] [INFO] Running command: fastANI --query /var/lib/cwl/stge9ec370a-2412-4c20-b1b2-116ff5ee3158/GCF_021026375.1_ASM2102637v1_genomic.fna.gz --refList GCF_021026375.1_ASM2102637v1_genomic.fna/target_genomes.txt --output GCF_021026375.1_ASM2102637v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:55:14,305] [INFO] Task succeeded: fastANI
[2024-01-25 17:55:14,306] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg25445dfa-97d4-4eee-89d9-a4576f8e065c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:55:14,306] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg25445dfa-97d4-4eee-89d9-a4576f8e065c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:55:14,314] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:55:14,314] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:55:14,314] [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 endophytica	strain=TBRC 5722	GCA_021026375.1	2291215	2291215	type	True	100.0	2317	2319	95	conclusive
Actinomycetospora soli	strain=SF1	GCA_021026295.1	2893887	2893887	type	True	83.1364	1392	2319	95	below_threshold
Actinomycetospora chiangmaiensis	strain=DSM 45062	GCA_000379625.1	402650	402650	type	True	83.0966	1408	2319	95	below_threshold
Actinomycetospora corticicola	strain=DSM 45772	GCA_013409505.1	663602	663602	type	True	83.079	1412	2319	95	below_threshold
Actinomycetospora succinea	strain=DSM 45775	GCA_004363095.1	663603	663603	type	True	81.0887	1300	2319	95	below_threshold
Actinomycetospora cinnamomea	strain=DSM 45771	GCA_003096675.1	663609	663609	type	True	80.6416	1182	2319	95	below_threshold
Pseudonocardia broussonetiae	strain=Gen 01	GCA_013155125.1	2736640	2736640	type	True	77.7615	960	2319	95	below_threshold
Pseudonocardia antarctica	strain=DSM 44749	GCA_013408715.1	237656	237656	type	True	77.6414	918	2319	95	below_threshold
Pseudonocardia autotrophica	strain=DSM 535	GCA_002119215.1	2074	2074	suspected-type	True	77.4606	867	2319	95	below_threshold
Pseudonocardia hierapolitana	strain=DSM 45671	GCA_007994075.1	1128676	1128676	type	True	77.1156	878	2319	95	below_threshold
Saccharothrix violaceirubra	strain=DSM 45084	GCA_014203755.1	413306	413306	type	True	76.6176	653	2319	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:55:14,316] [INFO] DFAST Taxonomy check result was written to GCF_021026375.1_ASM2102637v1_genomic.fna/tc_result.tsv
[2024-01-25 17:55:14,317] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:55:14,317] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:55:14,317] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg25445dfa-97d4-4eee-89d9-a4576f8e065c/dqc_reference/checkm_data
[2024-01-25 17:55:14,318] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:55:14,383] [INFO] Task started: CheckM
[2024-01-25 17:55:14,384] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021026375.1_ASM2102637v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021026375.1_ASM2102637v1_genomic.fna/checkm_input GCF_021026375.1_ASM2102637v1_genomic.fna/checkm_result
[2024-01-25 17:56:47,685] [INFO] Task succeeded: CheckM
[2024-01-25 17:56:47,686] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:56:47,710] [INFO] ===== Completeness check finished =====
[2024-01-25 17:56:47,710] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:56:47,711] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021026375.1_ASM2102637v1_genomic.fna/markers.fasta)
[2024-01-25 17:56:47,711] [INFO] Task started: Blastn
[2024-01-25 17:56:47,711] [INFO] Running command: blastn -query GCF_021026375.1_ASM2102637v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25445dfa-97d4-4eee-89d9-a4576f8e065c/dqc_reference/reference_markers_gtdb.fasta -out GCF_021026375.1_ASM2102637v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:56:49,775] [INFO] Task succeeded: Blastn
[2024-01-25 17:56:49,777] [INFO] Selected 12 target genomes.
[2024-01-25 17:56:49,777] [INFO] Target genome list was writen to GCF_021026375.1_ASM2102637v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:56:49,796] [INFO] Task started: fastANI
[2024-01-25 17:56:49,796] [INFO] Running command: fastANI --query /var/lib/cwl/stge9ec370a-2412-4c20-b1b2-116ff5ee3158/GCF_021026375.1_ASM2102637v1_genomic.fna.gz --refList GCF_021026375.1_ASM2102637v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021026375.1_ASM2102637v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:57:08,703] [INFO] Task succeeded: fastANI
[2024-01-25 17:57:08,711] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 17:57:08,711] [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_012933465.1	s__Actinomycetospora sp012933465	85.5826	1626	2319	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	83.0906	1409	2319	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	83.0803	1411	2319	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinomycetospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805495.1	s__Actinomycetospora sp902805495	81.3254	775	2319	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinomycetospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363095.1	s__Actinomycetospora succinea	81.1239	1292	2319	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	80.6317	1182	2319	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinomycetospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217185.1	s__Pseudonocardia sediminis	77.9125	935	2319	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013155125.1	s__Pseudonocardia broussonetiae	77.7393	965	2319	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002813375.1	s__Pseudonocardia alni	77.6898	904	2319	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	97.52	96.72	0.89	0.85	6	-
GCA_016794615.1	s__Pseudonocardia sp016794615	77.4259	552	2319	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	77.1661	863	2319	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203755.1	s__Actinosynnema violaceirubrum	76.6153	651	2319	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:57:08,713] [INFO] GTDB search result was written to GCF_021026375.1_ASM2102637v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:57:08,713] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:57:08,716] [INFO] DFAST_QC result json was written to GCF_021026375.1_ASM2102637v1_genomic.fna/dqc_result.json
[2024-01-25 17:57:08,716] [INFO] DFAST_QC completed!
[2024-01-25 17:57:08,716] [INFO] Total running time: 0h2m33s