[2024-01-24 13:52:10,151] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:52:10,153] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:52:10,153] [INFO] DQC Reference Directory: /var/lib/cwl/stg0571e545-73c9-48aa-ac83-4858461f33ec/dqc_reference
[2024-01-24 13:52:11,400] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:52:11,401] [INFO] Task started: Prodigal
[2024-01-24 13:52:11,401] [INFO] Running command: gunzip -c /var/lib/cwl/stgad61c4e6-9e36-4832-afa7-230ea3eb43ba/GCF_002149035.1_ASM214903v1_genomic.fna.gz | prodigal -d GCF_002149035.1_ASM214903v1_genomic.fna/cds.fna -a GCF_002149035.1_ASM214903v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:52:35,045] [INFO] Task succeeded: Prodigal
[2024-01-24 13:52:35,046] [INFO] Task started: HMMsearch
[2024-01-24 13:52:35,046] [INFO] Running command: hmmsearch --tblout GCF_002149035.1_ASM214903v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0571e545-73c9-48aa-ac83-4858461f33ec/dqc_reference/reference_markers.hmm GCF_002149035.1_ASM214903v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:52:35,427] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:52:35,429] [INFO] Found 6/6 markers.
[2024-01-24 13:52:35,505] [INFO] Query marker FASTA was written to GCF_002149035.1_ASM214903v1_genomic.fna/markers.fasta
[2024-01-24 13:52:35,505] [INFO] Task started: Blastn
[2024-01-24 13:52:35,505] [INFO] Running command: blastn -query GCF_002149035.1_ASM214903v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0571e545-73c9-48aa-ac83-4858461f33ec/dqc_reference/reference_markers.fasta -out GCF_002149035.1_ASM214903v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:52:36,852] [INFO] Task succeeded: Blastn
[2024-01-24 13:52:36,856] [INFO] Selected 15 target genomes.
[2024-01-24 13:52:36,857] [INFO] Target genome list was writen to GCF_002149035.1_ASM214903v1_genomic.fna/target_genomes.txt
[2024-01-24 13:52:36,881] [INFO] Task started: fastANI
[2024-01-24 13:52:36,881] [INFO] Running command: fastANI --query /var/lib/cwl/stgad61c4e6-9e36-4832-afa7-230ea3eb43ba/GCF_002149035.1_ASM214903v1_genomic.fna.gz --refList GCF_002149035.1_ASM214903v1_genomic.fna/target_genomes.txt --output GCF_002149035.1_ASM214903v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:53:09,683] [INFO] Task succeeded: fastANI
[2024-01-24 13:53:09,683] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0571e545-73c9-48aa-ac83-4858461f33ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:53:09,684] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0571e545-73c9-48aa-ac83-4858461f33ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:53:09,706] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:53:09,707] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:53:09,707] [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 minutum	strain=M26	GCA_002149035.1	569862	569862	type	True	100.0	2906	2927	95	inconclusive
Streptosporangium canum	strain=CGMCC 4.2126	GCA_900113865.1	324952	324952	type	True	95.8844	2399	2927	95	inconclusive
Streptosporangium roseum	strain=DSM 43021	GCA_000024865.1	2001	2001	type	True	94.7682	2535	2927	95	below_threshold
Streptosporangium album	strain=DSM 43023	GCA_014203795.1	47479	47479	type	True	88.2218	1805	2927	95	below_threshold
Streptosporangium amethystogenes	strain=NRRL B-2639	GCA_000721075.1	2002	2002	type	True	85.2052	1775	2927	95	below_threshold
Streptosporangium sandarakinum	strain=DSM 45763	GCA_013409935.1	1260955	1260955	type	True	84.8849	1680	2927	95	below_threshold
Planomonospora parontospora subsp. antibiotica	strain=NBRC 15869	GCA_016863235.1	97193	58119	type	True	84.6332	1541	2927	95	below_threshold
Planomonospora sphaerica	strain=JCM 9374	GCA_001653075.1	161355	161355	type	True	84.4401	1608	2927	95	below_threshold
Planobispora longispora	strain=NBRC 13918	GCA_016863135.1	28887	28887	type	True	84.2557	1681	2927	95	below_threshold
Planobispora rosea	strain=NBRC 15558	GCA_016863155.1	35762	35762	type	True	84.0709	1609	2927	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	80.6206	961	2927	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	80.5578	1481	2927	95	below_threshold
Nonomuraea aurantiaca	strain=NEAU-L178	GCA_020215705.1	2878562	2878562	type	True	80.3451	1485	2927	95	below_threshold
Nonomuraea typhae	strain=p1410	GCA_009760925.1	2603600	2603600	type	True	80.0515	1450	2927	95	below_threshold
Nonomuraea phyllanthi	strain=WYY166	GCA_009497075.1	2219224	2219224	type	True	80.0192	1417	2927	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:53:09,709] [INFO] DFAST Taxonomy check result was written to GCF_002149035.1_ASM214903v1_genomic.fna/tc_result.tsv
[2024-01-24 13:53:09,709] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:53:09,709] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:53:09,710] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0571e545-73c9-48aa-ac83-4858461f33ec/dqc_reference/checkm_data
[2024-01-24 13:53:09,711] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:53:09,800] [INFO] Task started: CheckM
[2024-01-24 13:53:09,801] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002149035.1_ASM214903v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002149035.1_ASM214903v1_genomic.fna/checkm_input GCF_002149035.1_ASM214903v1_genomic.fna/checkm_result
[2024-01-24 13:54:19,283] [INFO] Task succeeded: CheckM
[2024-01-24 13:54:19,285] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.89%
Strain heterogeneity: 83.33%
--------------------------------------------------------------------------------
[2024-01-24 13:54:19,311] [INFO] ===== Completeness check finished =====
[2024-01-24 13:54:19,312] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:54:19,312] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002149035.1_ASM214903v1_genomic.fna/markers.fasta)
[2024-01-24 13:54:19,312] [INFO] Task started: Blastn
[2024-01-24 13:54:19,313] [INFO] Running command: blastn -query GCF_002149035.1_ASM214903v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0571e545-73c9-48aa-ac83-4858461f33ec/dqc_reference/reference_markers_gtdb.fasta -out GCF_002149035.1_ASM214903v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:54:21,479] [INFO] Task succeeded: Blastn
[2024-01-24 13:54:21,483] [INFO] Selected 9 target genomes.
[2024-01-24 13:54:21,484] [INFO] Target genome list was writen to GCF_002149035.1_ASM214903v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:54:21,503] [INFO] Task started: fastANI
[2024-01-24 13:54:21,504] [INFO] Running command: fastANI --query /var/lib/cwl/stgad61c4e6-9e36-4832-afa7-230ea3eb43ba/GCF_002149035.1_ASM214903v1_genomic.fna.gz --refList GCF_002149035.1_ASM214903v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002149035.1_ASM214903v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:54:42,855] [INFO] Task succeeded: fastANI
[2024-01-24 13:54:42,869] [INFO] Found 9 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 13:54:42,869] [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_002149035.1	s__Streptosporangium minutum	100.0	2906	2927	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.8736	N/A	N/A	N/A	N/A	1	inconclusive
GCF_900113865.1	s__Streptosporangium canum	95.8805	2399	2927	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.8736	96.48	96.48	0.86	0.86	2	inconclusive
GCF_000024865.1	s__Streptosporangium roseum	94.7692	2533	2927	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	88.2249	1804	2927	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188345.1	s__Streptosporangium subroseum	85.9556	1770	2927	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	95.81	95.81	0.87	0.87	2	-
GCF_000721075.1	s__Streptosporangium amethystogenes	85.2044	1774	2927	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015711605.1	s__Planomonospora_A sp015711605	84.7927	1616	2927	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_014203605.1	s__Planomonospora_A venezuelensis	84.7566	1628	2927	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_014648175.1	s__Planobispora rosea	84.1833	1603	2927	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planobispora	95.0	99.82	99.64	0.97	0.95	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:54:42,871] [INFO] GTDB search result was written to GCF_002149035.1_ASM214903v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:54:42,871] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:54:42,875] [INFO] DFAST_QC result json was written to GCF_002149035.1_ASM214903v1_genomic.fna/dqc_result.json
[2024-01-24 13:54:42,875] [INFO] DFAST_QC completed!
[2024-01-24 13:54:42,875] [INFO] Total running time: 0h2m33s