[2024-01-25 19:40:20,576] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:40:20,578] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:40:20,578] [INFO] DQC Reference Directory: /var/lib/cwl/stg3489a1d7-0fd9-40b3-b305-38800b8d2340/dqc_reference
[2024-01-25 19:40:21,711] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:40:21,712] [INFO] Task started: Prodigal
[2024-01-25 19:40:21,712] [INFO] Running command: gunzip -c /var/lib/cwl/stg0a59ce8d-63a0-4db7-abcf-f16e8247d0d6/GCF_028994805.1_ASM2899480v1_genomic.fna.gz | prodigal -d GCF_028994805.1_ASM2899480v1_genomic.fna/cds.fna -a GCF_028994805.1_ASM2899480v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:40:36,619] [INFO] Task succeeded: Prodigal
[2024-01-25 19:40:36,620] [INFO] Task started: HMMsearch
[2024-01-25 19:40:36,620] [INFO] Running command: hmmsearch --tblout GCF_028994805.1_ASM2899480v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3489a1d7-0fd9-40b3-b305-38800b8d2340/dqc_reference/reference_markers.hmm GCF_028994805.1_ASM2899480v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:40:36,907] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:40:36,909] [INFO] Found 6/6 markers.
[2024-01-25 19:40:36,954] [INFO] Query marker FASTA was written to GCF_028994805.1_ASM2899480v1_genomic.fna/markers.fasta
[2024-01-25 19:40:36,955] [INFO] Task started: Blastn
[2024-01-25 19:40:36,955] [INFO] Running command: blastn -query GCF_028994805.1_ASM2899480v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3489a1d7-0fd9-40b3-b305-38800b8d2340/dqc_reference/reference_markers.fasta -out GCF_028994805.1_ASM2899480v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:40:38,159] [INFO] Task succeeded: Blastn
[2024-01-25 19:40:38,162] [INFO] Selected 9 target genomes.
[2024-01-25 19:40:38,162] [INFO] Target genome list was writen to GCF_028994805.1_ASM2899480v1_genomic.fna/target_genomes.txt
[2024-01-25 19:40:38,165] [INFO] Task started: fastANI
[2024-01-25 19:40:38,166] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a59ce8d-63a0-4db7-abcf-f16e8247d0d6/GCF_028994805.1_ASM2899480v1_genomic.fna.gz --refList GCF_028994805.1_ASM2899480v1_genomic.fna/target_genomes.txt --output GCF_028994805.1_ASM2899480v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:40:49,349] [INFO] Task succeeded: fastANI
[2024-01-25 19:40:49,349] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3489a1d7-0fd9-40b3-b305-38800b8d2340/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:40:49,350] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3489a1d7-0fd9-40b3-b305-38800b8d2340/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:40:49,358] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:40:49,358] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:40:49,358] [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
Promicromonospora umidemergens	strain=DSM 22081	GCA_024171995.1	629679	629679	type	True	87.8869	1494	1933	95	below_threshold
Promicromonospora soli	strain=CGMCC 4.7398	GCA_014653785.1	2035533	2035533	type	True	87.082	1263	1933	95	below_threshold
Promicromonospora sukumoe	strain=DSM 44121	GCA_014137995.1	88382	88382	type	True	85.7842	1408	1933	95	below_threshold
Promicromonospora kroppenstedtii	strain=DSM 19349	GCA_000515355.1	440482	440482	type	True	85.3245	1227	1933	95	below_threshold
Promicromonospora citrea	strain=ATCC 15908	GCA_013004695.1	43677	43677	type	True	84.3396	1131	1933	95	below_threshold
Oerskovia merdavium	strain=Sa2CUA9	GCA_014836755.1	2762227	2762227	type	True	78.7095	605	1933	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	78.2337	543	1933	95	below_threshold
Actinotalea subterranea	strain=HO-Ch2	GCA_008364845.1	2607497	2607497	type	True	77.794	487	1933	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	77.6882	542	1933	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:40:49,359] [INFO] DFAST Taxonomy check result was written to GCF_028994805.1_ASM2899480v1_genomic.fna/tc_result.tsv
[2024-01-25 19:40:49,360] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:40:49,360] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:40:49,361] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3489a1d7-0fd9-40b3-b305-38800b8d2340/dqc_reference/checkm_data
[2024-01-25 19:40:49,362] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:40:49,422] [INFO] Task started: CheckM
[2024-01-25 19:40:49,422] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028994805.1_ASM2899480v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028994805.1_ASM2899480v1_genomic.fna/checkm_input GCF_028994805.1_ASM2899480v1_genomic.fna/checkm_result
[2024-01-25 19:41:43,439] [INFO] Task succeeded: CheckM
[2024-01-25 19:41:43,440] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:41:43,456] [INFO] ===== Completeness check finished =====
[2024-01-25 19:41:43,456] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:41:43,457] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028994805.1_ASM2899480v1_genomic.fna/markers.fasta)
[2024-01-25 19:41:43,457] [INFO] Task started: Blastn
[2024-01-25 19:41:43,457] [INFO] Running command: blastn -query GCF_028994805.1_ASM2899480v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3489a1d7-0fd9-40b3-b305-38800b8d2340/dqc_reference/reference_markers_gtdb.fasta -out GCF_028994805.1_ASM2899480v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:41:45,368] [INFO] Task succeeded: Blastn
[2024-01-25 19:41:45,371] [INFO] Selected 8 target genomes.
[2024-01-25 19:41:45,371] [INFO] Target genome list was writen to GCF_028994805.1_ASM2899480v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:41:45,377] [INFO] Task started: fastANI
[2024-01-25 19:41:45,377] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a59ce8d-63a0-4db7-abcf-f16e8247d0d6/GCF_028994805.1_ASM2899480v1_genomic.fna.gz --refList GCF_028994805.1_ASM2899480v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028994805.1_ASM2899480v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:41:58,345] [INFO] Task succeeded: fastANI
[2024-01-25 19:41:58,351] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:41:58,351] [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_003096495.1	s__Promicromonospora sukumoe_A	88.7466	1483	1933	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900608595.1	s__Promicromonospora panici	87.6075	1400	1933	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003058225.1	s__Promicromonospora sp003058225	87.0973	1401	1933	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	98.27	98.27	0.94	0.94	2	-
GCF_014653785.1	s__Promicromonospora soli	87.0919	1262	1933	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003550025.1	s__Promicromonospora thailandica	86.0079	1380	1933	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000385135.1	s__Promicromonospora sukumoe_B	85.9393	1376	1933	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	95.99	95.99	0.93	0.93	2	-
GCF_014137995.1	s__Promicromonospora sukumoe	85.7997	1406	1933	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000515355.1	s__Promicromonospora kroppenstedtii	85.3254	1228	1933	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	97.09	97.09	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:41:58,353] [INFO] GTDB search result was written to GCF_028994805.1_ASM2899480v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:41:58,353] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:41:58,356] [INFO] DFAST_QC result json was written to GCF_028994805.1_ASM2899480v1_genomic.fna/dqc_result.json
[2024-01-25 19:41:58,356] [INFO] DFAST_QC completed!
[2024-01-25 19:41:58,356] [INFO] Total running time: 0h1m38s