[2024-01-24 12:06:24,469] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:24,471] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:24,472] [INFO] DQC Reference Directory: /var/lib/cwl/stgab7c4680-8671-446c-9d7c-7ddf356f8d76/dqc_reference
[2024-01-24 12:06:25,789] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:25,790] [INFO] Task started: Prodigal
[2024-01-24 12:06:25,790] [INFO] Running command: gunzip -c /var/lib/cwl/stge308e28f-1f09-445d-aa65-d52ec84948bc/GCF_024648845.1_ASM2464884v1_genomic.fna.gz | prodigal -d GCF_024648845.1_ASM2464884v1_genomic.fna/cds.fna -a GCF_024648845.1_ASM2464884v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:50,527] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:50,528] [INFO] Task started: HMMsearch
[2024-01-24 12:06:50,528] [INFO] Running command: hmmsearch --tblout GCF_024648845.1_ASM2464884v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgab7c4680-8671-446c-9d7c-7ddf356f8d76/dqc_reference/reference_markers.hmm GCF_024648845.1_ASM2464884v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:50,872] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:50,873] [INFO] Found 6/6 markers.
[2024-01-24 12:06:50,948] [INFO] Query marker FASTA was written to GCF_024648845.1_ASM2464884v1_genomic.fna/markers.fasta
[2024-01-24 12:06:50,948] [INFO] Task started: Blastn
[2024-01-24 12:06:50,948] [INFO] Running command: blastn -query GCF_024648845.1_ASM2464884v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgab7c4680-8671-446c-9d7c-7ddf356f8d76/dqc_reference/reference_markers.fasta -out GCF_024648845.1_ASM2464884v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:52,259] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:52,262] [INFO] Selected 11 target genomes.
[2024-01-24 12:06:52,263] [INFO] Target genome list was writen to GCF_024648845.1_ASM2464884v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:52,270] [INFO] Task started: fastANI
[2024-01-24 12:06:52,270] [INFO] Running command: fastANI --query /var/lib/cwl/stge308e28f-1f09-445d-aa65-d52ec84948bc/GCF_024648845.1_ASM2464884v1_genomic.fna.gz --refList GCF_024648845.1_ASM2464884v1_genomic.fna/target_genomes.txt --output GCF_024648845.1_ASM2464884v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:21,092] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:21,092] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgab7c4680-8671-446c-9d7c-7ddf356f8d76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:21,093] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgab7c4680-8671-446c-9d7c-7ddf356f8d76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:21,103] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:07:21,103] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:07:21,103] [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
Actinomadura citrea	strain=DSM 43461	GCA_013409045.1	46158	46158	type	True	93.7502	2548	3070	95	below_threshold
Actinomadura citrea	strain=JCM 3295	GCA_014648455.1	46158	46158	type	True	93.7221	2517	3070	95	below_threshold
Actinomadura mexicana	strain=DSM 44485	GCA_900188105.1	134959	134959	type	True	93.5131	2415	3070	95	below_threshold
Actinomadura coerulea	strain=JCM 3320	GCA_014648535.1	46159	46159	type	True	93.4273	2381	3070	95	below_threshold
Actinomadura coerulea	strain=DSM 43675	GCA_014208105.1	46159	46159	type	True	93.3808	2393	3070	95	below_threshold
Actinomadura syzygii	strain=GKU157	GCA_008085905.1	1427538	1427538	type	True	84.9769	1901	3070	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	84.7029	2068	3070	95	below_threshold
Actinomadura spongiicola	strain=LHW52907	GCA_003432485.1	2303421	2303421	type	True	84.3574	1609	3070	95	below_threshold
Actinomadura graeca	strain=32-07	GCA_019175365.1	2750812	2750812	type	True	83.8599	1721	3070	95	below_threshold
Actinomadura parmotrematis	strain=PM05-2	GCA_019458805.1	2864039	2864039	type	True	81.6054	1531	3070	95	below_threshold
Actinomadura rupiterrae	strain=DSM 45251	GCA_024172125.1	559627	559627	type	True	81.0382	1562	3070	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:21,105] [INFO] DFAST Taxonomy check result was written to GCF_024648845.1_ASM2464884v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:21,106] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:21,106] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:21,106] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgab7c4680-8671-446c-9d7c-7ddf356f8d76/dqc_reference/checkm_data
[2024-01-24 12:07:21,108] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:21,190] [INFO] Task started: CheckM
[2024-01-24 12:07:21,190] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024648845.1_ASM2464884v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024648845.1_ASM2464884v1_genomic.fna/checkm_input GCF_024648845.1_ASM2464884v1_genomic.fna/checkm_result
[2024-01-24 12:09:06,500] [INFO] Task succeeded: CheckM
[2024-01-24 12:09:06,501] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.61%
Contamintation: 9.26%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2024-01-24 12:09:06,525] [INFO] ===== Completeness check finished =====
[2024-01-24 12:09:06,526] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:09:06,526] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024648845.1_ASM2464884v1_genomic.fna/markers.fasta)
[2024-01-24 12:09:06,526] [INFO] Task started: Blastn
[2024-01-24 12:09:06,526] [INFO] Running command: blastn -query GCF_024648845.1_ASM2464884v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgab7c4680-8671-446c-9d7c-7ddf356f8d76/dqc_reference/reference_markers_gtdb.fasta -out GCF_024648845.1_ASM2464884v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:09:08,501] [INFO] Task succeeded: Blastn
[2024-01-24 12:09:08,504] [INFO] Selected 8 target genomes.
[2024-01-24 12:09:08,504] [INFO] Target genome list was writen to GCF_024648845.1_ASM2464884v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:09:08,510] [INFO] Task started: fastANI
[2024-01-24 12:09:08,510] [INFO] Running command: fastANI --query /var/lib/cwl/stge308e28f-1f09-445d-aa65-d52ec84948bc/GCF_024648845.1_ASM2464884v1_genomic.fna.gz --refList GCF_024648845.1_ASM2464884v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024648845.1_ASM2464884v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:09:30,828] [INFO] Task succeeded: fastANI
[2024-01-24 12:09:30,836] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:09:30,836] [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_013409365.1	s__Spirillospora luteofluorescens	98.1476	2835	3070	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013409045.1	s__Spirillospora citrea	93.7564	2548	3070	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900188105.1	s__Spirillospora mexicana	93.5053	2416	3070	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014208105.1	s__Spirillospora coerulea	93.3813	2393	3070	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_008327685.1	s__Spirillospora sp008327685	91.5267	2397	3070	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648675.1	s__Spirillospora livida	85.4068	1835	3070	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	98.54	97.09	0.95	0.91	3	-
GCF_013211575.1	s__Spirillospora verrucosospora	84.7666	2085	3070	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	95.82	95.82	0.89	0.89	2	-
GCF_900659615.1	s__Spirillospora fibrosa	84.2435	1830	3070	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 12:09:30,837] [INFO] GTDB search result was written to GCF_024648845.1_ASM2464884v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:09:30,838] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:09:30,841] [INFO] DFAST_QC result json was written to GCF_024648845.1_ASM2464884v1_genomic.fna/dqc_result.json
[2024-01-24 12:09:30,841] [INFO] DFAST_QC completed!
[2024-01-24 12:09:30,841] [INFO] Total running time: 0h3m6s