[2024-01-24 15:02:16,335] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:16,337] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:16,338] [INFO] DQC Reference Directory: /var/lib/cwl/stgaf8f1b52-f61e-4fee-8987-a596ea06dde3/dqc_reference
[2024-01-24 15:02:17,605] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:17,606] [INFO] Task started: Prodigal
[2024-01-24 15:02:17,606] [INFO] Running command: gunzip -c /var/lib/cwl/stg5c95d774-22b6-4c30-a38a-549f6c481340/GCF_014648055.1_ASM1464805v1_genomic.fna.gz | prodigal -d GCF_014648055.1_ASM1464805v1_genomic.fna/cds.fna -a GCF_014648055.1_ASM1464805v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:40,038] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:40,038] [INFO] Task started: HMMsearch
[2024-01-24 15:02:40,039] [INFO] Running command: hmmsearch --tblout GCF_014648055.1_ASM1464805v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaf8f1b52-f61e-4fee-8987-a596ea06dde3/dqc_reference/reference_markers.hmm GCF_014648055.1_ASM1464805v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:40,432] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:40,434] [INFO] Found 6/6 markers.
[2024-01-24 15:02:40,502] [INFO] Query marker FASTA was written to GCF_014648055.1_ASM1464805v1_genomic.fna/markers.fasta
[2024-01-24 15:02:40,502] [INFO] Task started: Blastn
[2024-01-24 15:02:40,503] [INFO] Running command: blastn -query GCF_014648055.1_ASM1464805v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf8f1b52-f61e-4fee-8987-a596ea06dde3/dqc_reference/reference_markers.fasta -out GCF_014648055.1_ASM1464805v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:41,910] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:41,914] [INFO] Selected 17 target genomes.
[2024-01-24 15:02:41,915] [INFO] Target genome list was writen to GCF_014648055.1_ASM1464805v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:41,927] [INFO] Task started: fastANI
[2024-01-24 15:02:41,928] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c95d774-22b6-4c30-a38a-549f6c481340/GCF_014648055.1_ASM1464805v1_genomic.fna.gz --refList GCF_014648055.1_ASM1464805v1_genomic.fna/target_genomes.txt --output GCF_014648055.1_ASM1464805v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:20,658] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:20,659] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaf8f1b52-f61e-4fee-8987-a596ea06dde3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:20,660] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaf8f1b52-f61e-4fee-8987-a596ea06dde3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:20,676] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:03:20,676] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 15:03:20,677] [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 pseudovulgare	strain=JCM 3115	GCA_014648055.1	35765	35765	type	True	100.0	2828	2831	95	inconclusive
Streptosporangium sandarakinum	strain=DSM 45763	GCA_013409935.1	1260955	1260955	type	True	96.5264	2319	2831	95	inconclusive
Streptosporangium canum	strain=CGMCC 4.2126	GCA_900113865.1	324952	324952	type	True	85.1463	1829	2831	95	below_threshold
Streptosporangium minutum	strain=M26	GCA_002149035.1	569862	569862	type	True	85.0039	1768	2831	95	below_threshold
Streptosporangium roseum	strain=DSM 43021	GCA_000024865.1	2001	2001	type	True	84.9425	1906	2831	95	below_threshold
Streptosporangium album	strain=DSM 43023	GCA_014203795.1	47479	47479	type	True	84.3264	1696	2831	95	below_threshold
Streptosporangium violaceochromogenes	strain=JCM 3281	GCA_014654615.1	46188	46188	type	True	83.831	1276	2831	95	below_threshold
Planomonospora parontospora subsp. antibiotica	strain=NBRC 15869	GCA_016863235.1	97193	58119	type	True	83.7098	1504	2831	95	below_threshold
Planomonospora parontospora subsp. antibiotica	strain=JCM 3094	GCA_014647955.1	97193	58119	type	True	83.6344	1521	2831	95	below_threshold
Planobispora rosea	strain=NBRC 15558	GCA_016863155.1	35762	35762	type	True	83.403	1527	2831	95	below_threshold
Planobispora rosea	strain=JCM 3166	GCA_014648175.1	35762	35762	type	True	83.3812	1553	2831	95	below_threshold
Planobispora longispora	strain=NBRC 13918	GCA_016863135.1	28887	28887	type	True	83.0872	1645	2831	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	80.6957	1576	2831	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	80.5052	958	2831	95	below_threshold
Nonomuraea phyllanthi	strain=PA1-10	GCA_006334985.2	2219224	2219224	type	True	80.3667	1485	2831	95	below_threshold
Nonomuraea phyllanthi	strain=WYY166	GCA_009497075.1	2219224	2219224	type	True	80.3589	1488	2831	95	below_threshold
Nonomuraea aurantiaca	strain=NEAU-L178	GCA_020215705.1	2878562	2878562	type	True	80.1727	1439	2831	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:20,680] [INFO] DFAST Taxonomy check result was written to GCF_014648055.1_ASM1464805v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:20,680] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:20,681] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:20,681] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaf8f1b52-f61e-4fee-8987-a596ea06dde3/dqc_reference/checkm_data
[2024-01-24 15:03:20,682] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:20,769] [INFO] Task started: CheckM
[2024-01-24 15:03:20,769] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014648055.1_ASM1464805v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014648055.1_ASM1464805v1_genomic.fna/checkm_input GCF_014648055.1_ASM1464805v1_genomic.fna/checkm_result
[2024-01-24 15:05:06,728] [INFO] Task succeeded: CheckM
[2024-01-24 15:05:06,729] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 7.99%
Strain heterogeneity: 55.56%
--------------------------------------------------------------------------------
[2024-01-24 15:05:06,759] [INFO] ===== Completeness check finished =====
[2024-01-24 15:05:06,759] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:05:06,760] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014648055.1_ASM1464805v1_genomic.fna/markers.fasta)
[2024-01-24 15:05:06,760] [INFO] Task started: Blastn
[2024-01-24 15:05:06,760] [INFO] Running command: blastn -query GCF_014648055.1_ASM1464805v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf8f1b52-f61e-4fee-8987-a596ea06dde3/dqc_reference/reference_markers_gtdb.fasta -out GCF_014648055.1_ASM1464805v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:05:09,004] [INFO] Task succeeded: Blastn
[2024-01-24 15:05:09,008] [INFO] Selected 12 target genomes.
[2024-01-24 15:05:09,008] [INFO] Target genome list was writen to GCF_014648055.1_ASM1464805v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:05:09,019] [INFO] Task started: fastANI
[2024-01-24 15:05:09,019] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c95d774-22b6-4c30-a38a-549f6c481340/GCF_014648055.1_ASM1464805v1_genomic.fna.gz --refList GCF_014648055.1_ASM1464805v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014648055.1_ASM1464805v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:05:37,402] [INFO] Task succeeded: fastANI
[2024-01-24 15:05:37,413] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:05:37,413] [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_014648055.1	s__Streptosporangium pseudovulgare	100.0	2828	2831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	96.6013	N/A	N/A	N/A	N/A	1	conclusive
GCF_013409935.1	s__Streptosporangium sandarakinum	96.5265	2319	2831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	96.6013	N/A	N/A	N/A	N/A	1	-
GCF_900113865.1	s__Streptosporangium canum	85.1415	1828	2831	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	85.0053	1768	2831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.8736	N/A	N/A	N/A	N/A	1	-
GCF_000024865.1	s__Streptosporangium roseum	84.9391	1908	2831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203795.1	s__Streptosporangium album	84.2907	1702	2831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014654615.1	s__Streptosporangium violaceochromogenes	83.8202	1278	2831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203605.1	s__Planomonospora_A venezuelensis	83.6337	1573	2831	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	83.4891	1583	2831	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	83.4579	1488	2831	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	83.4008	1549	2831	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	83.0916	1645	2831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planobispora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:05:37,415] [INFO] GTDB search result was written to GCF_014648055.1_ASM1464805v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:05:37,415] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:05:37,422] [INFO] DFAST_QC result json was written to GCF_014648055.1_ASM1464805v1_genomic.fna/dqc_result.json
[2024-01-24 15:05:37,422] [INFO] DFAST_QC completed!
[2024-01-24 15:05:37,423] [INFO] Total running time: 0h3m21s