[2024-01-24 13:27:40,504] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:40,506] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:40,506] [INFO] DQC Reference Directory: /var/lib/cwl/stgc1bc7cf8-f44d-48a8-a8cf-1e0f87aa2400/dqc_reference
[2024-01-24 13:27:41,734] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:41,735] [INFO] Task started: Prodigal
[2024-01-24 13:27:41,735] [INFO] Running command: gunzip -c /var/lib/cwl/stg4562923d-bcce-448c-82f4-653914abbbe9/GCF_019175365.1_ASM1917536v1_genomic.fna.gz | prodigal -d GCF_019175365.1_ASM1917536v1_genomic.fna/cds.fna -a GCF_019175365.1_ASM1917536v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:16,713] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:16,713] [INFO] Task started: HMMsearch
[2024-01-24 13:28:16,714] [INFO] Running command: hmmsearch --tblout GCF_019175365.1_ASM1917536v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc1bc7cf8-f44d-48a8-a8cf-1e0f87aa2400/dqc_reference/reference_markers.hmm GCF_019175365.1_ASM1917536v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:17,101] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:17,102] [INFO] Found 6/6 markers.
[2024-01-24 13:28:17,180] [INFO] Query marker FASTA was written to GCF_019175365.1_ASM1917536v1_genomic.fna/markers.fasta
[2024-01-24 13:28:17,181] [INFO] Task started: Blastn
[2024-01-24 13:28:17,181] [INFO] Running command: blastn -query GCF_019175365.1_ASM1917536v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1bc7cf8-f44d-48a8-a8cf-1e0f87aa2400/dqc_reference/reference_markers.fasta -out GCF_019175365.1_ASM1917536v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:18,515] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:18,520] [INFO] Selected 17 target genomes.
[2024-01-24 13:28:18,520] [INFO] Target genome list was writen to GCF_019175365.1_ASM1917536v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:18,612] [INFO] Task started: fastANI
[2024-01-24 13:28:18,612] [INFO] Running command: fastANI --query /var/lib/cwl/stg4562923d-bcce-448c-82f4-653914abbbe9/GCF_019175365.1_ASM1917536v1_genomic.fna.gz --refList GCF_019175365.1_ASM1917536v1_genomic.fna/target_genomes.txt --output GCF_019175365.1_ASM1917536v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:29:00,082] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:00,083] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc1bc7cf8-f44d-48a8-a8cf-1e0f87aa2400/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:29:00,083] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc1bc7cf8-f44d-48a8-a8cf-1e0f87aa2400/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:29:00,098] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:29:00,099] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:29:00,099] [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 graeca	strain=32-07	GCA_019175365.1	2750812	2750812	type	True	100.0	2991	2992	95	conclusive
Actinomadura macra	strain=NBRC 14102	GCA_001552215.1	46164	46164	type	True	89.6841	2298	2992	95	below_threshold
Actinomadura litoris	strain=NEAU-AAG5	GCA_009733595.1	2678616	2678616	type	True	86.3784	1964	2992	95	below_threshold
Actinomadura rubrisoli	strain=H3C3	GCA_004349215.1	2530368	2530368	type	True	85.7573	1789	2992	95	below_threshold
Actinomadura roseirufa		GCA_900659635.1	2094049	2094049	type	True	84.7702	1632	2992	95	below_threshold
Actinomadura mexicana	strain=DSM 44485	GCA_900188105.1	134959	134959	type	True	83.9362	1678	2992	95	below_threshold
Actinomadura bangladeshensis	strain=DSM 45347	GCA_004348335.1	453573	453573	type	True	83.9302	1473	2992	95	below_threshold
Actinomadura darangshiensis	strain=DSM 45941	GCA_004349235.1	705336	705336	type	True	83.8039	1571	2992	95	below_threshold
Actinomadura chibensis	strain=JCM 14158	GCA_008085895.1	392828	392828	type	True	83.78	1831	2992	95	below_threshold
Actinomadura nitritigenes	strain=L46	GCA_017573545.1	134602	134602	type	True	83.7062	1755	2992	95	below_threshold
Actinomadura syzygii	strain=GKU157	GCA_008085905.1	1427538	1427538	type	True	83.6815	1787	2992	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	83.6648	1779	2992	95	below_threshold
Actinomadura chibensis	strain=NBRC 106107	GCA_001552135.1	392828	392828	type	True	83.6598	1802	2992	95	below_threshold
Actinomadura geliboluensis	strain=A8036	GCA_005889745.1	882440	882440	type	True	83.5837	1462	2992	95	below_threshold
Actinomadura spongiicola	strain=LHW52907	GCA_003432485.1	2303421	2303421	type	True	83.2918	1566	2992	95	below_threshold
Actinomadura parmotrematis	strain=PM05-2	GCA_019458805.1	2864039	2864039	type	True	81.1601	1430	2992	95	below_threshold
Actinomadura rupiterrae	strain=DSM 45251	GCA_024172125.1	559627	559627	type	True	80.9909	1463	2992	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:29:00,100] [INFO] DFAST Taxonomy check result was written to GCF_019175365.1_ASM1917536v1_genomic.fna/tc_result.tsv
[2024-01-24 13:29:00,101] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:29:00,101] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:29:00,101] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc1bc7cf8-f44d-48a8-a8cf-1e0f87aa2400/dqc_reference/checkm_data
[2024-01-24 13:29:00,102] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:29:00,188] [INFO] Task started: CheckM
[2024-01-24 13:29:00,188] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019175365.1_ASM1917536v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019175365.1_ASM1917536v1_genomic.fna/checkm_input GCF_019175365.1_ASM1917536v1_genomic.fna/checkm_result
[2024-01-24 13:30:57,974] [INFO] Task succeeded: CheckM
[2024-01-24 13:30:57,975] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 10.65%
Strain heterogeneity: 71.43%
--------------------------------------------------------------------------------
[2024-01-24 13:30:58,008] [INFO] ===== Completeness check finished =====
[2024-01-24 13:30:58,008] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:30:58,009] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019175365.1_ASM1917536v1_genomic.fna/markers.fasta)
[2024-01-24 13:30:58,009] [INFO] Task started: Blastn
[2024-01-24 13:30:58,009] [INFO] Running command: blastn -query GCF_019175365.1_ASM1917536v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1bc7cf8-f44d-48a8-a8cf-1e0f87aa2400/dqc_reference/reference_markers_gtdb.fasta -out GCF_019175365.1_ASM1917536v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:00,234] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:00,239] [INFO] Selected 16 target genomes.
[2024-01-24 13:31:00,239] [INFO] Target genome list was writen to GCF_019175365.1_ASM1917536v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:31:00,252] [INFO] Task started: fastANI
[2024-01-24 13:31:00,252] [INFO] Running command: fastANI --query /var/lib/cwl/stg4562923d-bcce-448c-82f4-653914abbbe9/GCF_019175365.1_ASM1917536v1_genomic.fna.gz --refList GCF_019175365.1_ASM1917536v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019175365.1_ASM1917536v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:31:38,415] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:38,435] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:31:38,435] [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_001552215.1	s__Spirillospora macra	89.6981	2295	2992	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009733595.1	s__Spirillospora litoris	86.3724	1966	2992	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	99.22	99.22	0.97	0.97	2	-
GCF_004349215.1	s__Spirillospora rubrisoli	85.7392	1793	2992	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900659635.1	s__Spirillospora roseirufa	84.7602	1633	2992	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900659615.1	s__Spirillospora fibrosa	84.6797	1717	2992	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008327685.1	s__Spirillospora sp008327685	83.9277	1692	2992	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	83.9231	1475	2992	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348515.1	s__Spirillospora sp004348515	83.8709	1369	2992	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013364275.1	s__Spirillospora sp013364275	83.8577	1740	2992	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006547145.1	s__Spirillospora sp006547145	83.825	1704	2992	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004349235.1	s__Spirillospora darangshiensis	83.802	1570	2992	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008923205.2	s__Spirillospora physcomitrii	83.7313	1673	2992	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017573545.1	s__Spirillospora nitritigenes	83.7117	1754	2992	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	95.12	95.12	0.83	0.83	2	-
GCF_005889745.1	s__Spirillospora geliboluensis	83.5708	1464	2992	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648675.1	s__Spirillospora livida	83.5182	1537	2992	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	98.54	97.09	0.95	0.91	3	-
GCF_004348425.1	s__Spirillospora sp004348425	83.4411	1498	2992	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 13:31:38,437] [INFO] GTDB search result was written to GCF_019175365.1_ASM1917536v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:31:38,437] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:31:38,441] [INFO] DFAST_QC result json was written to GCF_019175365.1_ASM1917536v1_genomic.fna/dqc_result.json
[2024-01-24 13:31:38,442] [INFO] DFAST_QC completed!
[2024-01-24 13:31:38,442] [INFO] Total running time: 0h3m58s