[2024-01-24 12:06:24,800] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:24,820] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:24,820] [INFO] DQC Reference Directory: /var/lib/cwl/stg7bf86c7b-874c-48d7-af23-2bbb355a1701/dqc_reference
[2024-01-24 12:06:26,248] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:26,248] [INFO] Task started: Prodigal
[2024-01-24 12:06:26,249] [INFO] Running command: gunzip -c /var/lib/cwl/stg64b1110d-c872-4593-bae1-3c325919972b/GCF_016863395.1_ASM1686339v1_genomic.fna.gz | prodigal -d GCF_016863395.1_ASM1686339v1_genomic.fna/cds.fna -a GCF_016863395.1_ASM1686339v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:47,914] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:47,914] [INFO] Task started: HMMsearch
[2024-01-24 12:06:47,914] [INFO] Running command: hmmsearch --tblout GCF_016863395.1_ASM1686339v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7bf86c7b-874c-48d7-af23-2bbb355a1701/dqc_reference/reference_markers.hmm GCF_016863395.1_ASM1686339v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:48,234] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:48,235] [INFO] Found 6/6 markers.
[2024-01-24 12:06:48,291] [INFO] Query marker FASTA was written to GCF_016863395.1_ASM1686339v1_genomic.fna/markers.fasta
[2024-01-24 12:06:48,292] [INFO] Task started: Blastn
[2024-01-24 12:06:48,292] [INFO] Running command: blastn -query GCF_016863395.1_ASM1686339v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7bf86c7b-874c-48d7-af23-2bbb355a1701/dqc_reference/reference_markers.fasta -out GCF_016863395.1_ASM1686339v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:49,656] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:49,661] [INFO] Selected 13 target genomes.
[2024-01-24 12:06:49,661] [INFO] Target genome list was writen to GCF_016863395.1_ASM1686339v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:49,676] [INFO] Task started: fastANI
[2024-01-24 12:06:49,676] [INFO] Running command: fastANI --query /var/lib/cwl/stg64b1110d-c872-4593-bae1-3c325919972b/GCF_016863395.1_ASM1686339v1_genomic.fna.gz --refList GCF_016863395.1_ASM1686339v1_genomic.fna/target_genomes.txt --output GCF_016863395.1_ASM1686339v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:16,986] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:16,987] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7bf86c7b-874c-48d7-af23-2bbb355a1701/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:16,987] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7bf86c7b-874c-48d7-af23-2bbb355a1701/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:16,998] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:07:16,998] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:07:16,998] [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
Sphaerisporangium rufum	strain=NBRC 109079	GCA_016863395.1	1381558	1381558	type	True	100.0	2519	2524	95	conclusive
Sphaerisporangium melleum	strain=JCM 13064	GCA_014646695.1	321316	321316	type	True	82.633	1540	2524	95	below_threshold
Sphaerisporangium corydalis	strain=NEAU-YHS15	GCA_025506355.1	1441875	1441875	type	True	82.4416	1540	2524	95	below_threshold
Sphaerisporangium album	strain=CCTCC AA 208026	GCA_003323745.1	509200	509200	type	True	82.0776	1461	2524	95	below_threshold
Sphaerisporangium krabiense	strain=NBRC 107571	GCA_016863355.1	763782	763782	type	True	81.919	1415	2524	95	below_threshold
Sphaerisporangium siamense	strain=NBRC 107570	GCA_016863415.1	795645	795645	type	True	81.9164	1417	2524	95	below_threshold
Sphaerisporangium krabiense	strain=DSM 45790	GCA_014200435.1	763782	763782	type	True	81.9044	1446	2524	95	below_threshold
Sphaerisporangium siamense	strain=DSM 45784	GCA_014205275.1	795645	795645	type	True	81.894	1432	2524	95	below_threshold
Sphaerisporangium rubeum	strain=DSM 44936	GCA_014207705.1	321317	321317	type	True	81.6062	1343	2524	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	79.652	860	2524	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	79.606	1340	2524	95	below_threshold
Microbispora oryzae	strain=RL4-1S	GCA_017896165.1	2806554	2806554	type	True	79.5958	1141	2524	95	below_threshold
Nonomuraea basaltis	strain=160415	GCA_005893125.1	2495887	2495887	type	True	78.9641	1278	2524	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:17,001] [INFO] DFAST Taxonomy check result was written to GCF_016863395.1_ASM1686339v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:17,001] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:17,001] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:17,002] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7bf86c7b-874c-48d7-af23-2bbb355a1701/dqc_reference/checkm_data
[2024-01-24 12:07:17,002] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:17,074] [INFO] Task started: CheckM
[2024-01-24 12:07:17,075] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016863395.1_ASM1686339v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016863395.1_ASM1686339v1_genomic.fna/checkm_input GCF_016863395.1_ASM1686339v1_genomic.fna/checkm_result
[2024-01-24 12:08:18,518] [INFO] Task succeeded: CheckM
[2024-01-24 12:08:18,519] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 3.82%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:08:18,539] [INFO] ===== Completeness check finished =====
[2024-01-24 12:08:18,540] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:08:18,540] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016863395.1_ASM1686339v1_genomic.fna/markers.fasta)
[2024-01-24 12:08:18,540] [INFO] Task started: Blastn
[2024-01-24 12:08:18,540] [INFO] Running command: blastn -query GCF_016863395.1_ASM1686339v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7bf86c7b-874c-48d7-af23-2bbb355a1701/dqc_reference/reference_markers_gtdb.fasta -out GCF_016863395.1_ASM1686339v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:08:20,558] [INFO] Task succeeded: Blastn
[2024-01-24 12:08:20,562] [INFO] Selected 9 target genomes.
[2024-01-24 12:08:20,562] [INFO] Target genome list was writen to GCF_016863395.1_ASM1686339v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:08:20,568] [INFO] Task started: fastANI
[2024-01-24 12:08:20,568] [INFO] Running command: fastANI --query /var/lib/cwl/stg64b1110d-c872-4593-bae1-3c325919972b/GCF_016863395.1_ASM1686339v1_genomic.fna.gz --refList GCF_016863395.1_ASM1686339v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016863395.1_ASM1686339v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:39,469] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:39,477] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:08:39,477] [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_016863395.1	s__Sphaerisporangium rufum	100.0	2519	2524	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014646695.1	s__Sphaerisporangium melleum	82.6335	1542	2524	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	99.98	99.98	0.99	0.99	2	-
GCF_003323745.1	s__Sphaerisporangium album	82.0798	1463	2524	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018531465.1	s__Sphaerisporangium sp018531465	81.9738	1554	2524	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014200435.1	s__Sphaerisporangium krabiense	81.9328	1441	2524	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_014205275.1	s__Sphaerisporangium siamense	81.8932	1432	2524	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014207705.1	s__Sphaerisporangium rubeum	81.6157	1341	2524	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003260025.2	s__Microbispora triticiradicis	80.1305	1211	2524	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	98.16	96.98	0.92	0.88	7	-
GCF_016863135.1	s__Planobispora longispora	79.9287	1257	2524	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 12:08:39,479] [INFO] GTDB search result was written to GCF_016863395.1_ASM1686339v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:39,480] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:39,483] [INFO] DFAST_QC result json was written to GCF_016863395.1_ASM1686339v1_genomic.fna/dqc_result.json
[2024-01-24 12:08:39,483] [INFO] DFAST_QC completed!
[2024-01-24 12:08:39,483] [INFO] Total running time: 0h2m15s