[2024-01-24 14:14:14,381] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:14,383] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:14,383] [INFO] DQC Reference Directory: /var/lib/cwl/stg0da5eb7c-19ad-4cc0-9bfe-c9a49d356bd4/dqc_reference
[2024-01-24 14:14:15,570] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:15,571] [INFO] Task started: Prodigal
[2024-01-24 14:14:15,571] [INFO] Running command: gunzip -c /var/lib/cwl/stg1df76c5e-a340-40e2-b577-d110c0a80cc2/GCF_006874465.1_ASM687446v1_genomic.fna.gz | prodigal -d GCF_006874465.1_ASM687446v1_genomic.fna/cds.fna -a GCF_006874465.1_ASM687446v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:37,009] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:37,010] [INFO] Task started: HMMsearch
[2024-01-24 14:14:37,010] [INFO] Running command: hmmsearch --tblout GCF_006874465.1_ASM687446v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0da5eb7c-19ad-4cc0-9bfe-c9a49d356bd4/dqc_reference/reference_markers.hmm GCF_006874465.1_ASM687446v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:37,376] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:37,377] [INFO] Found 6/6 markers.
[2024-01-24 14:14:37,437] [INFO] Query marker FASTA was written to GCF_006874465.1_ASM687446v1_genomic.fna/markers.fasta
[2024-01-24 14:14:37,437] [INFO] Task started: Blastn
[2024-01-24 14:14:37,437] [INFO] Running command: blastn -query GCF_006874465.1_ASM687446v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0da5eb7c-19ad-4cc0-9bfe-c9a49d356bd4/dqc_reference/reference_markers.fasta -out GCF_006874465.1_ASM687446v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:38,831] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:38,834] [INFO] Selected 13 target genomes.
[2024-01-24 14:14:38,834] [INFO] Target genome list was writen to GCF_006874465.1_ASM687446v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:38,840] [INFO] Task started: fastANI
[2024-01-24 14:14:38,840] [INFO] Running command: fastANI --query /var/lib/cwl/stg1df76c5e-a340-40e2-b577-d110c0a80cc2/GCF_006874465.1_ASM687446v1_genomic.fna.gz --refList GCF_006874465.1_ASM687446v1_genomic.fna/target_genomes.txt --output GCF_006874465.1_ASM687446v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:07,305] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:07,306] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0da5eb7c-19ad-4cc0-9bfe-c9a49d356bd4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:07,306] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0da5eb7c-19ad-4cc0-9bfe-c9a49d356bd4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:07,318] [INFO] Found 13 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 14:15:07,318] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:15:07,319] [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
Microbispora bryophytorum	strain=DSM 46710	GCA_006874465.1	1460882	1460882	type	True	100.0	2570	2574	95	inconclusive
Microbispora bryophytorum	strain=CGMCC 4.7138	GCA_014645855.1	1460882	1460882	type	True	99.9975	2563	2574	95	inconclusive
Microbispora bryophytorum	strain=NEAU-TX2-2	GCA_014712735.1	1460882	1460882	type	True	99.9945	2564	2574	95	inconclusive
Microbispora camponoti	strain=2C-HV3	GCA_014712745.1	1677852	1677852	type	True	97.6719	2351	2574	95	inconclusive
Microbispora catharanthi	strain=CR1-09	GCA_006334915.2	1712871	1712871	type	True	93.8544	2165	2574	95	below_threshold
Microbispora rosea subsp. rosea	strain=NBRC 14044	GCA_016863055.1	58118	58117	type	True	93.2141	2226	2574	95	below_threshold
Microbispora siamensis	strain=NBRC 104113	GCA_016863095.1	564413	564413	type	True	92.7121	2073	2574	95	below_threshold
Microbispora oryzae	strain=RL4-1S	GCA_017896165.1	2806554	2806554	type	True	83.2624	1503	2574	95	below_threshold
Sphaerimonospora thailandensis	strain=NBRC 107569	GCA_016863115.1	795644	795644	type	True	82.244	1138	2574	95	below_threshold
Microtetraspora malaysiensis	strain=NBRC 100735	GCA_001528665.1	161358	161358	type	True	81.3905	1342	2574	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	79.917	830	2574	95	below_threshold
Nonomuraea aurantiaca	strain=NEAU-L178	GCA_020215705.1	2878562	2878562	type	True	79.5458	1267	2574	95	below_threshold
Nonomuraea basaltis	strain=160415	GCA_005893125.1	2495887	2495887	type	True	79.2037	1288	2574	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:07,320] [INFO] DFAST Taxonomy check result was written to GCF_006874465.1_ASM687446v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:07,321] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:07,321] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:07,321] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0da5eb7c-19ad-4cc0-9bfe-c9a49d356bd4/dqc_reference/checkm_data
[2024-01-24 14:15:07,323] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:07,396] [INFO] Task started: CheckM
[2024-01-24 14:15:07,397] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006874465.1_ASM687446v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006874465.1_ASM687446v1_genomic.fna/checkm_input GCF_006874465.1_ASM687446v1_genomic.fna/checkm_result
[2024-01-24 14:16:11,516] [INFO] Task succeeded: CheckM
[2024-01-24 14:16:11,517] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.07%
Contamintation: 1.39%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2024-01-24 14:16:11,536] [INFO] ===== Completeness check finished =====
[2024-01-24 14:16:11,536] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:16:11,536] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006874465.1_ASM687446v1_genomic.fna/markers.fasta)
[2024-01-24 14:16:11,537] [INFO] Task started: Blastn
[2024-01-24 14:16:11,537] [INFO] Running command: blastn -query GCF_006874465.1_ASM687446v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0da5eb7c-19ad-4cc0-9bfe-c9a49d356bd4/dqc_reference/reference_markers_gtdb.fasta -out GCF_006874465.1_ASM687446v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:16:13,588] [INFO] Task succeeded: Blastn
[2024-01-24 14:16:13,591] [INFO] Selected 11 target genomes.
[2024-01-24 14:16:13,591] [INFO] Target genome list was writen to GCF_006874465.1_ASM687446v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:16:13,609] [INFO] Task started: fastANI
[2024-01-24 14:16:13,610] [INFO] Running command: fastANI --query /var/lib/cwl/stg1df76c5e-a340-40e2-b577-d110c0a80cc2/GCF_006874465.1_ASM687446v1_genomic.fna.gz --refList GCF_006874465.1_ASM687446v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006874465.1_ASM687446v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:16:39,860] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:39,871] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:16:39,871] [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_006874465.1	s__Microbispora bryophytorum	100.0	2570	2574	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	99.22	97.66	0.97	0.91	4	conclusive
GCF_006334915.2	s__Microbispora catharanthi	93.895	2160	2574	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	96.79	95.45	0.89	0.84	4	-
GCF_900156315.1	s__Microbispora rosea	93.1776	2264	2574	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	99.16	98.33	0.97	0.94	3	-
GCF_016863095.1	s__Microbispora siamensis	92.7151	2072	2574	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	96.99	95.83	0.88	0.87	3	-
GCF_006874475.1	s__Microbispora hainanensis	92.1319	2151	2574	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	95.41	95.40	0.85	0.85	4	-
GCF_014161445.1	s__Microbispora sp014161445	91.1434	2039	2574	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	98.71	98.71	0.93	0.93	2	-
GCF_014647835.1	s__Microbispora aerata	89.772	1762	2574	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	100.00	100.00	1.00	1.00	2	-
GCA_001570385.1	s__Microtetraspora glauca	81.3901	1361	2574	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microtetraspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001528665.1	s__Microtetraspora malaysiensis	81.352	1349	2574	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microtetraspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109355.1	s__Nonomuraea pusilla	79.8514	1246	2574	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	99.44	99.44	0.97	0.97	2	-
GCF_900099965.1	s__Nonomuraea jiangxiensis	79.4297	1283	2574	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:16:39,873] [INFO] GTDB search result was written to GCF_006874465.1_ASM687446v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:16:39,874] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:16:39,877] [INFO] DFAST_QC result json was written to GCF_006874465.1_ASM687446v1_genomic.fna/dqc_result.json
[2024-01-24 14:16:39,877] [INFO] DFAST_QC completed!
[2024-01-24 14:16:39,878] [INFO] Total running time: 0h2m25s