[2024-01-24 15:10:54,342] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:54,344] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:54,344] [INFO] DQC Reference Directory: /var/lib/cwl/stge0195c28-43d3-4a19-b362-5d82ec978709/dqc_reference
[2024-01-24 15:10:56,635] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:56,637] [INFO] Task started: Prodigal
[2024-01-24 15:10:56,638] [INFO] Running command: gunzip -c /var/lib/cwl/stgae3841c2-ed21-4505-b002-2d2014437f1e/GCF_005889745.1_ASM588974v1_genomic.fna.gz | prodigal -d GCF_005889745.1_ASM588974v1_genomic.fna/cds.fna -a GCF_005889745.1_ASM588974v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:11:19,955] [INFO] Task succeeded: Prodigal
[2024-01-24 15:11:19,956] [INFO] Task started: HMMsearch
[2024-01-24 15:11:19,956] [INFO] Running command: hmmsearch --tblout GCF_005889745.1_ASM588974v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge0195c28-43d3-4a19-b362-5d82ec978709/dqc_reference/reference_markers.hmm GCF_005889745.1_ASM588974v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:11:20,368] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:11:20,370] [INFO] Found 6/6 markers.
[2024-01-24 15:11:20,449] [INFO] Query marker FASTA was written to GCF_005889745.1_ASM588974v1_genomic.fna/markers.fasta
[2024-01-24 15:11:20,450] [INFO] Task started: Blastn
[2024-01-24 15:11:20,450] [INFO] Running command: blastn -query GCF_005889745.1_ASM588974v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge0195c28-43d3-4a19-b362-5d82ec978709/dqc_reference/reference_markers.fasta -out GCF_005889745.1_ASM588974v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:21,809] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:21,813] [INFO] Selected 17 target genomes.
[2024-01-24 15:11:21,814] [INFO] Target genome list was writen to GCF_005889745.1_ASM588974v1_genomic.fna/target_genomes.txt
[2024-01-24 15:11:21,862] [INFO] Task started: fastANI
[2024-01-24 15:11:21,862] [INFO] Running command: fastANI --query /var/lib/cwl/stgae3841c2-ed21-4505-b002-2d2014437f1e/GCF_005889745.1_ASM588974v1_genomic.fna.gz --refList GCF_005889745.1_ASM588974v1_genomic.fna/target_genomes.txt --output GCF_005889745.1_ASM588974v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:12:04,538] [INFO] Task succeeded: fastANI
[2024-01-24 15:12:04,539] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge0195c28-43d3-4a19-b362-5d82ec978709/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:12:04,539] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge0195c28-43d3-4a19-b362-5d82ec978709/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:12:04,552] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:12:04,552] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:12:04,553] [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
Actinomadura geliboluensis	strain=A8036	GCA_005889745.1	882440	882440	type	True	100.0	2722	2752	95	conclusive
Actinomadura meyerae	strain=DSM 44715	GCA_900188445.1	240840	240840	type	True	92.9305	1987	2752	95	below_threshold
Actinomadura bangladeshensis	strain=DSM 45347	GCA_004348335.1	453573	453573	type	True	89.8069	1760	2752	95	below_threshold
Actinomadura latina	strain=NBRC 106108	GCA_001552195.1	163603	163603	type	True	89.0643	1779	2752	95	below_threshold
Actinomadura latina	strain=ATCC BAA-277	GCA_012396395.1	163603	163603	type	True	89.03	1771	2752	95	below_threshold
Actinomadura darangshiensis	strain=DSM 45941	GCA_004349235.1	705336	705336	type	True	87.2783	1729	2752	95	below_threshold
Actinomadura madurae	strain=DSM 43067	GCA_900115095.1	1993	1993	type	True	86.8741	1830	2752	95	below_threshold
Actinomadura coerulea	strain=DSM 43675	GCA_014208105.1	46159	46159	type	True	86.7197	1676	2752	95	below_threshold
Actinomadura coerulea	strain=JCM 3320	GCA_014648535.1	46159	46159	type	True	86.7009	1691	2752	95	below_threshold
Actinomadura citrea	strain=JCM 3295	GCA_014648455.1	46158	46158	type	True	86.6186	1756	2752	95	below_threshold
Actinomadura citrea	strain=DSM 43461	GCA_013409045.1	46158	46158	type	True	86.5018	1776	2752	95	below_threshold
Actinomadura nitritigenes	strain=L46	GCA_017573545.1	134602	134602	type	True	84.8343	1805	2752	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	84.8329	1820	2752	95	below_threshold
Actinomadura spongiicola	strain=LHW52907	GCA_003432485.1	2303421	2303421	type	True	84.374	1400	2752	95	below_threshold
Actinomadura graeca	strain=32-07	GCA_019175365.1	2750812	2750812	type	True	83.6247	1458	2752	95	below_threshold
Actinomadura parmotrematis	strain=PM05-2	GCA_019458805.1	2864039	2864039	type	True	81.5749	1376	2752	95	below_threshold
Actinomadura rupiterrae	strain=DSM 45251	GCA_024172125.1	559627	559627	type	True	81.1182	1402	2752	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:12:04,555] [INFO] DFAST Taxonomy check result was written to GCF_005889745.1_ASM588974v1_genomic.fna/tc_result.tsv
[2024-01-24 15:12:04,555] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:12:04,555] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:12:04,556] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge0195c28-43d3-4a19-b362-5d82ec978709/dqc_reference/checkm_data
[2024-01-24 15:12:04,557] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:12:04,640] [INFO] Task started: CheckM
[2024-01-24 15:12:04,640] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005889745.1_ASM588974v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005889745.1_ASM588974v1_genomic.fna/checkm_input GCF_005889745.1_ASM588974v1_genomic.fna/checkm_result
[2024-01-24 15:13:10,876] [INFO] Task succeeded: CheckM
[2024-01-24 15:13:10,878] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 10.42%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2024-01-24 15:13:10,905] [INFO] ===== Completeness check finished =====
[2024-01-24 15:13:10,906] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:13:10,906] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005889745.1_ASM588974v1_genomic.fna/markers.fasta)
[2024-01-24 15:13:10,907] [INFO] Task started: Blastn
[2024-01-24 15:13:10,907] [INFO] Running command: blastn -query GCF_005889745.1_ASM588974v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge0195c28-43d3-4a19-b362-5d82ec978709/dqc_reference/reference_markers_gtdb.fasta -out GCF_005889745.1_ASM588974v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:13:13,039] [INFO] Task succeeded: Blastn
[2024-01-24 15:13:13,043] [INFO] Selected 9 target genomes.
[2024-01-24 15:13:13,043] [INFO] Target genome list was writen to GCF_005889745.1_ASM588974v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:13:13,052] [INFO] Task started: fastANI
[2024-01-24 15:13:13,052] [INFO] Running command: fastANI --query /var/lib/cwl/stgae3841c2-ed21-4505-b002-2d2014437f1e/GCF_005889745.1_ASM588974v1_genomic.fna.gz --refList GCF_005889745.1_ASM588974v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005889745.1_ASM588974v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:13:38,295] [INFO] Task succeeded: fastANI
[2024-01-24 15:13:38,311] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:13:38,312] [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_005889745.1	s__Spirillospora geliboluensis	100.0	2722	2752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013364275.1	s__Spirillospora sp013364275	94.5038	2200	2752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188445.1	s__Spirillospora meyerae	93.0396	1976	2752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348335.1	s__Spirillospora bangladeshensis	89.7962	1761	2752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013372625.1	s__Spirillospora sp013372625	89.2631	1609	2752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552195.1	s__Spirillospora latina	89.0253	1783	2752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	99.98	99.98	0.98	0.98	2	-
GCF_004349235.1	s__Spirillospora darangshiensis	87.2622	1731	2752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115095.1	s__Spirillospora madurae	86.8746	1830	2752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	99.34	99.27	0.95	0.95	3	-
GCF_008327685.1	s__Spirillospora sp008327685	86.528	1846	2752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:13:38,314] [INFO] GTDB search result was written to GCF_005889745.1_ASM588974v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:13:38,315] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:13:38,320] [INFO] DFAST_QC result json was written to GCF_005889745.1_ASM588974v1_genomic.fna/dqc_result.json
[2024-01-24 15:13:38,321] [INFO] DFAST_QC completed!
[2024-01-24 15:13:38,321] [INFO] Total running time: 0h2m44s