[2024-01-24 10:57:26,475] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:26,478] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:26,479] [INFO] DQC Reference Directory: /var/lib/cwl/stg728db5d0-b68d-4998-93af-8f178a3fafd3/dqc_reference
[2024-01-24 10:57:27,881] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:27,883] [INFO] Task started: Prodigal
[2024-01-24 10:57:27,883] [INFO] Running command: gunzip -c /var/lib/cwl/stg72223426-8fad-4fd5-abd0-555eb17861be/GCF_013409935.1_ASM1340993v1_genomic.fna.gz | prodigal -d GCF_013409935.1_ASM1340993v1_genomic.fna/cds.fna -a GCF_013409935.1_ASM1340993v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:47,814] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:47,815] [INFO] Task started: HMMsearch
[2024-01-24 10:57:47,815] [INFO] Running command: hmmsearch --tblout GCF_013409935.1_ASM1340993v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg728db5d0-b68d-4998-93af-8f178a3fafd3/dqc_reference/reference_markers.hmm GCF_013409935.1_ASM1340993v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:48,224] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:48,225] [INFO] Found 6/6 markers.
[2024-01-24 10:57:48,278] [INFO] Query marker FASTA was written to GCF_013409935.1_ASM1340993v1_genomic.fna/markers.fasta
[2024-01-24 10:57:48,278] [INFO] Task started: Blastn
[2024-01-24 10:57:48,279] [INFO] Running command: blastn -query GCF_013409935.1_ASM1340993v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg728db5d0-b68d-4998-93af-8f178a3fafd3/dqc_reference/reference_markers.fasta -out GCF_013409935.1_ASM1340993v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:49,667] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:49,671] [INFO] Selected 16 target genomes.
[2024-01-24 10:57:49,671] [INFO] Target genome list was writen to GCF_013409935.1_ASM1340993v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:49,678] [INFO] Task started: fastANI
[2024-01-24 10:57:49,678] [INFO] Running command: fastANI --query /var/lib/cwl/stg72223426-8fad-4fd5-abd0-555eb17861be/GCF_013409935.1_ASM1340993v1_genomic.fna.gz --refList GCF_013409935.1_ASM1340993v1_genomic.fna/target_genomes.txt --output GCF_013409935.1_ASM1340993v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:31,894] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:31,895] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg728db5d0-b68d-4998-93af-8f178a3fafd3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:31,895] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg728db5d0-b68d-4998-93af-8f178a3fafd3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:31,908] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:58:31,908] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 10:58:31,908] [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
Streptosporangium sandarakinum	strain=DSM 45763	GCA_013409935.1	1260955	1260955	type	True	100.0	2546	2547	95	inconclusive
Streptosporangium pseudovulgare	strain=JCM 3115	GCA_014648055.1	35765	35765	type	True	96.6036	2300	2547	95	inconclusive
Streptosporangium canum	strain=CGMCC 4.2126	GCA_900113865.1	324952	324952	type	True	85.2454	1757	2547	95	below_threshold
Streptosporangium roseum	strain=DSM 43021	GCA_000024865.1	2001	2001	type	True	85.1557	1799	2547	95	below_threshold
Streptosporangium minutum	strain=M26	GCA_002149035.1	569862	569862	type	True	85.0226	1672	2547	95	below_threshold
Streptosporangium album	strain=DSM 43023	GCA_014203795.1	47479	47479	type	True	84.5362	1599	2547	95	below_threshold
Planomonospora parontospora subsp. antibiotica	strain=NBRC 15869	GCA_016863235.1	97193	58119	type	True	83.7961	1439	2547	95	below_threshold
Planomonospora parontospora subsp. antibiotica	strain=JCM 3094	GCA_014647955.1	97193	58119	type	True	83.7082	1462	2547	95	below_threshold
Planobispora rosea	strain=NBRC 15558	GCA_016863155.1	35762	35762	type	True	83.5132	1472	2547	95	below_threshold
Planobispora rosea	strain=JCM 3166	GCA_014648175.1	35762	35762	type	True	83.4715	1499	2547	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	80.8015	1466	2547	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	80.5534	931	2547	95	below_threshold
Nonomuraea aridisoli	strain=KC333	GCA_003236395.1	2070368	2070368	type	True	80.4401	1244	2547	95	below_threshold
Nonomuraea phyllanthi	strain=PA1-10	GCA_006334985.2	2219224	2219224	type	True	80.2952	1397	2547	95	below_threshold
Nonomuraea aurantiaca	strain=NEAU-L178	GCA_020215705.1	2878562	2878562	type	True	80.0203	1374	2547	95	below_threshold
Nonomuraea basaltis	strain=160415	GCA_005893125.1	2495887	2495887	type	True	79.938	1354	2547	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:31,910] [INFO] DFAST Taxonomy check result was written to GCF_013409935.1_ASM1340993v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:31,911] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:31,911] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:31,911] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg728db5d0-b68d-4998-93af-8f178a3fafd3/dqc_reference/checkm_data
[2024-01-24 10:58:31,912] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:31,983] [INFO] Task started: CheckM
[2024-01-24 10:58:31,983] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013409935.1_ASM1340993v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013409935.1_ASM1340993v1_genomic.fna/checkm_input GCF_013409935.1_ASM1340993v1_genomic.fna/checkm_result
[2024-01-24 11:00:00,849] [INFO] Task succeeded: CheckM
[2024-01-24 11:00:00,850] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 7.52%
Strain heterogeneity: 71.43%
--------------------------------------------------------------------------------
[2024-01-24 11:00:00,874] [INFO] ===== Completeness check finished =====
[2024-01-24 11:00:00,874] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:00:00,875] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013409935.1_ASM1340993v1_genomic.fna/markers.fasta)
[2024-01-24 11:00:00,875] [INFO] Task started: Blastn
[2024-01-24 11:00:00,875] [INFO] Running command: blastn -query GCF_013409935.1_ASM1340993v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg728db5d0-b68d-4998-93af-8f178a3fafd3/dqc_reference/reference_markers_gtdb.fasta -out GCF_013409935.1_ASM1340993v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:00:02,904] [INFO] Task succeeded: Blastn
[2024-01-24 11:00:02,907] [INFO] Selected 13 target genomes.
[2024-01-24 11:00:02,907] [INFO] Target genome list was writen to GCF_013409935.1_ASM1340993v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:00:02,914] [INFO] Task started: fastANI
[2024-01-24 11:00:02,914] [INFO] Running command: fastANI --query /var/lib/cwl/stg72223426-8fad-4fd5-abd0-555eb17861be/GCF_013409935.1_ASM1340993v1_genomic.fna.gz --refList GCF_013409935.1_ASM1340993v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013409935.1_ASM1340993v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:00:30,630] [INFO] Task succeeded: fastANI
[2024-01-24 11:00:30,640] [INFO] Found 13 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 11:00:30,641] [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_013409935.1	s__Streptosporangium sandarakinum	100.0	2546	2547	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	96.6013	N/A	N/A	N/A	N/A	1	inconclusive
GCF_014648055.1	s__Streptosporangium pseudovulgare	96.6204	2298	2547	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	96.6013	N/A	N/A	N/A	N/A	1	inconclusive
GCF_000024865.1	s__Streptosporangium roseum	85.232	1787	2547	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113865.1	s__Streptosporangium canum	85.2233	1761	2547	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.8736	96.48	96.48	0.86	0.86	2	-
GCF_002149035.1	s__Streptosporangium minutum	85.0797	1664	2547	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.8736	N/A	N/A	N/A	N/A	1	-
GCF_014203795.1	s__Streptosporangium album	84.5416	1604	2547	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014647935.1	s__Planomonospora parontospora	83.7865	1481	2547	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planomonospora	95.0	97.40	95.90	0.89	0.84	6	-
GCF_014203605.1	s__Planomonospora_A venezuelensis	83.7535	1519	2547	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planomonospora_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015711605.1	s__Planomonospora_A sp015711605	83.6655	1505	2547	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planomonospora_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015711645.1	s__Planomonospora sp015711645	83.5771	1458	2547	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648175.1	s__Planobispora rosea	83.5207	1491	2547	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planobispora	95.0	99.82	99.64	0.97	0.95	3	-
GCF_016863135.1	s__Planobispora longispora	83.3832	1558	2547	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planobispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003236395.1	s__Nonomuraea sp003236395	80.4636	1240	2547	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 11:00:30,642] [INFO] GTDB search result was written to GCF_013409935.1_ASM1340993v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:00:30,643] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:00:30,646] [INFO] DFAST_QC result json was written to GCF_013409935.1_ASM1340993v1_genomic.fna/dqc_result.json
[2024-01-24 11:00:30,646] [INFO] DFAST_QC completed!
[2024-01-24 11:00:30,647] [INFO] Total running time: 0h3m4s