[2024-01-24 11:19:48,994] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:19:48,996] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:19:48,996] [INFO] DQC Reference Directory: /var/lib/cwl/stgf0148ea9-9f07-44cd-a5b4-fafb02283c03/dqc_reference
[2024-01-24 11:19:50,155] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:19:50,156] [INFO] Task started: Prodigal
[2024-01-24 11:19:50,156] [INFO] Running command: gunzip -c /var/lib/cwl/stgb804d5e6-18e1-4cef-9115-7cca2ebc8d1e/GCF_014873935.1_ASM1487393v1_genomic.fna.gz | prodigal -d GCF_014873935.1_ASM1487393v1_genomic.fna/cds.fna -a GCF_014873935.1_ASM1487393v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:14,370] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:14,371] [INFO] Task started: HMMsearch
[2024-01-24 11:20:14,371] [INFO] Running command: hmmsearch --tblout GCF_014873935.1_ASM1487393v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf0148ea9-9f07-44cd-a5b4-fafb02283c03/dqc_reference/reference_markers.hmm GCF_014873935.1_ASM1487393v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:14,751] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:14,752] [INFO] Found 6/6 markers.
[2024-01-24 11:20:14,820] [INFO] Query marker FASTA was written to GCF_014873935.1_ASM1487393v1_genomic.fna/markers.fasta
[2024-01-24 11:20:14,821] [INFO] Task started: Blastn
[2024-01-24 11:20:14,821] [INFO] Running command: blastn -query GCF_014873935.1_ASM1487393v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0148ea9-9f07-44cd-a5b4-fafb02283c03/dqc_reference/reference_markers.fasta -out GCF_014873935.1_ASM1487393v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:16,115] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:16,120] [INFO] Selected 18 target genomes.
[2024-01-24 11:20:16,121] [INFO] Target genome list was writen to GCF_014873935.1_ASM1487393v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:16,131] [INFO] Task started: fastANI
[2024-01-24 11:20:16,131] [INFO] Running command: fastANI --query /var/lib/cwl/stgb804d5e6-18e1-4cef-9115-7cca2ebc8d1e/GCF_014873935.1_ASM1487393v1_genomic.fna.gz --refList GCF_014873935.1_ASM1487393v1_genomic.fna/target_genomes.txt --output GCF_014873935.1_ASM1487393v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:21:02,011] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:02,012] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf0148ea9-9f07-44cd-a5b4-fafb02283c03/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:21:02,012] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf0148ea9-9f07-44cd-a5b4-fafb02283c03/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:21:02,026] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:21:02,026] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:21:02,027] [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 algeriensis	strain=DSM 46744	GCA_014873935.1	1679523	1679523	type	True	100.0	2869	2870	95	conclusive
Actinomadura cremea	strain=JCM 3308	GCA_014648495.1	1991	1991	type	True	91.16	2274	2870	95	below_threshold
Actinomadura rifamycini	strain=DSM 43936	GCA_000425065.1	31962	31962	type	True	90.5313	2171	2870	95	below_threshold
Actinomadura bangladeshensis	strain=DSM 45347	GCA_004348335.1	453573	453573	type	True	83.8781	1560	2870	95	below_threshold
Actinomadura latina	strain=ATCC BAA-277	GCA_012396395.1	163603	163603	type	True	83.6457	1618	2870	95	below_threshold
Actinomadura physcomitrii	strain=LD22	GCA_008923205.2	2650748	2650748	type	True	83.6135	1739	2870	95	below_threshold
Actinomadura montaniterrae	strain=CYP1-1B	GCA_008923365.1	1803903	1803903	type	True	83.5841	1736	2870	95	below_threshold
Actinomadura formosensis	strain=NBRC 14204	GCA_001552155.1	60706	60706	type	True	83.5463	1383	2870	95	below_threshold
Actinomadura nitritigenes	strain=L46	GCA_017573545.1	134602	134602	type	True	83.4132	1840	2870	95	below_threshold
Actinomadura darangshiensis	strain=DSM 45941	GCA_004349235.1	705336	705336	type	True	83.4001	1669	2870	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	83.3956	1879	2870	95	below_threshold
Actinomadura madurae	strain=DSM 43067	GCA_900115095.1	1993	1993	type	True	83.2569	1769	2870	95	below_threshold
Actinomadura citrea	strain=DSM 43461	GCA_013409045.1	46158	46158	type	True	83.2532	1764	2870	95	below_threshold
Actinomadura citrea	strain=JCM 3295	GCA_014648455.1	46158	46158	type	True	83.2127	1728	2870	95	below_threshold
Actinomadura graeca	strain=32-07	GCA_019175365.1	2750812	2750812	type	True	82.5599	1535	2870	95	below_threshold
Actinomadura spongiicola	strain=LHW52907	GCA_003432485.1	2303421	2303421	type	True	82.3778	1400	2870	95	below_threshold
Actinomadura parmotrematis	strain=PM05-2	GCA_019458805.1	2864039	2864039	type	True	81.0623	1518	2870	95	below_threshold
Actinomadura rupiterrae	strain=DSM 45251	GCA_024172125.1	559627	559627	type	True	80.7198	1481	2870	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:21:02,028] [INFO] DFAST Taxonomy check result was written to GCF_014873935.1_ASM1487393v1_genomic.fna/tc_result.tsv
[2024-01-24 11:21:02,029] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:21:02,029] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:21:02,029] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf0148ea9-9f07-44cd-a5b4-fafb02283c03/dqc_reference/checkm_data
[2024-01-24 11:21:02,030] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:21:02,106] [INFO] Task started: CheckM
[2024-01-24 11:21:02,106] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014873935.1_ASM1487393v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014873935.1_ASM1487393v1_genomic.fna/checkm_input GCF_014873935.1_ASM1487393v1_genomic.fna/checkm_result
[2024-01-24 11:22:41,509] [INFO] Task succeeded: CheckM
[2024-01-24 11:22:41,510] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:22:41,538] [INFO] ===== Completeness check finished =====
[2024-01-24 11:22:41,538] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:22:41,538] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014873935.1_ASM1487393v1_genomic.fna/markers.fasta)
[2024-01-24 11:22:41,539] [INFO] Task started: Blastn
[2024-01-24 11:22:41,539] [INFO] Running command: blastn -query GCF_014873935.1_ASM1487393v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0148ea9-9f07-44cd-a5b4-fafb02283c03/dqc_reference/reference_markers_gtdb.fasta -out GCF_014873935.1_ASM1487393v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:22:43,571] [INFO] Task succeeded: Blastn
[2024-01-24 11:22:43,575] [INFO] Selected 11 target genomes.
[2024-01-24 11:22:43,576] [INFO] Target genome list was writen to GCF_014873935.1_ASM1487393v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:22:43,585] [INFO] Task started: fastANI
[2024-01-24 11:22:43,586] [INFO] Running command: fastANI --query /var/lib/cwl/stgb804d5e6-18e1-4cef-9115-7cca2ebc8d1e/GCF_014873935.1_ASM1487393v1_genomic.fna.gz --refList GCF_014873935.1_ASM1487393v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014873935.1_ASM1487393v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:23:13,738] [INFO] Task succeeded: fastANI
[2024-01-24 11:23:13,748] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:23:13,749] [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_014873935.1	s__Spirillospora algeriensis	100.0	2869	2870	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001942465.1	s__Spirillospora sp001942465	92.5977	2183	2870	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648495.1	s__Spirillospora cremea	91.1942	2269	2870	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425065.1	s__Spirillospora rifamycini	90.5092	2174	2870	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	99.13	99.13	0.92	0.92	2	-
GCF_008824145.1	s__Spirillospora sp008824145	90.2608	2241	2870	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	83.8789	1561	2870	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	83.6993	1443	2870	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552155.1	s__Spirillospora formosensis	83.5798	1378	2870	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	99.99	99.99	0.99	0.99	2	-
GCF_008923365.1	s__Spirillospora montaniterrae	83.5236	1748	2870	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	83.3895	1845	2870	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	95.12	95.12	0.83	0.83	2	-
GCF_013409365.1	s__Spirillospora luteofluorescens	83.3157	1752	2870	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 11:23:13,750] [INFO] GTDB search result was written to GCF_014873935.1_ASM1487393v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:23:13,751] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:23:13,754] [INFO] DFAST_QC result json was written to GCF_014873935.1_ASM1487393v1_genomic.fna/dqc_result.json
[2024-01-24 11:23:13,755] [INFO] DFAST_QC completed!
[2024-01-24 11:23:13,755] [INFO] Total running time: 0h3m25s