[2024-01-24 15:18:25,923] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:25,925] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:25,926] [INFO] DQC Reference Directory: /var/lib/cwl/stg8b2a5257-0cce-4fb6-bfda-4ccb34dfb547/dqc_reference
[2024-01-24 15:18:27,276] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:27,278] [INFO] Task started: Prodigal
[2024-01-24 15:18:27,278] [INFO] Running command: gunzip -c /var/lib/cwl/stgd2638603-a79d-4184-8f69-fa64b0a4ad81/GCF_001552235.1_ASM155223v1_genomic.fna.gz | prodigal -d GCF_001552235.1_ASM155223v1_genomic.fna/cds.fna -a GCF_001552235.1_ASM155223v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:44,940] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:44,940] [INFO] Task started: HMMsearch
[2024-01-24 15:18:44,940] [INFO] Running command: hmmsearch --tblout GCF_001552235.1_ASM155223v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8b2a5257-0cce-4fb6-bfda-4ccb34dfb547/dqc_reference/reference_markers.hmm GCF_001552235.1_ASM155223v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:45,309] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:45,311] [INFO] Found 6/6 markers.
[2024-01-24 15:18:45,366] [INFO] Query marker FASTA was written to GCF_001552235.1_ASM155223v1_genomic.fna/markers.fasta
[2024-01-24 15:18:45,366] [INFO] Task started: Blastn
[2024-01-24 15:18:45,366] [INFO] Running command: blastn -query GCF_001552235.1_ASM155223v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b2a5257-0cce-4fb6-bfda-4ccb34dfb547/dqc_reference/reference_markers.fasta -out GCF_001552235.1_ASM155223v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:46,733] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:46,737] [INFO] Selected 21 target genomes.
[2024-01-24 15:18:46,737] [INFO] Target genome list was writen to GCF_001552235.1_ASM155223v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:46,752] [INFO] Task started: fastANI
[2024-01-24 15:18:46,753] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2638603-a79d-4184-8f69-fa64b0a4ad81/GCF_001552235.1_ASM155223v1_genomic.fna.gz --refList GCF_001552235.1_ASM155223v1_genomic.fna/target_genomes.txt --output GCF_001552235.1_ASM155223v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:32,918] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:32,919] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8b2a5257-0cce-4fb6-bfda-4ccb34dfb547/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:32,920] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8b2a5257-0cce-4fb6-bfda-4ccb34dfb547/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:32,941] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:19:32,942] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:19:32,942] [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 rubrobrunea	strain=NBRC 15275	GCA_001552235.1	115335	115335	type	True	100.0	2109	2121	95	conclusive
Actinomadura viridis	strain=DSM 43175	GCA_015751755.1	58110	58110	type	True	82.2526	1363	2121	95	below_threshold
Actinomadura hibisca	strain=NBRC 15177	GCA_001552635.1	68565	68565	type	True	82.101	1315	2121	95	below_threshold
Actinomadura macrotermitis	strain=RB68	GCA_009604375.1	2585200	2585200	type	True	82.0919	1293	2121	95	below_threshold
Actinomadura montaniterrae	strain=CYP1-1B	GCA_008923365.1	1803903	1803903	type	True	81.9516	1280	2121	95	below_threshold
Actinomadura physcomitrii	strain=LD22	GCA_008923205.2	2650748	2650748	type	True	81.8889	1340	2121	95	below_threshold
Actinomadura meyerae	strain=DSM 44715	GCA_900188445.1	240840	240840	type	True	81.8239	1318	2121	95	below_threshold
Actinomadura coerulea	strain=DSM 43675	GCA_014208105.1	46159	46159	type	True	81.7599	1291	2121	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	81.7104	1378	2121	95	below_threshold
Actinomadura coerulea	strain=JCM 3320	GCA_014648535.1	46159	46159	type	True	81.7036	1280	2121	95	below_threshold
Actinomadura hallensis	strain=DSM 45043	GCA_006716765.1	337895	337895	type	True	81.6836	1224	2121	95	below_threshold
Actinomadura nitritigenes	strain=L46	GCA_017573545.1	134602	134602	type	True	81.6269	1396	2121	95	below_threshold
Actinomadura citrea	strain=DSM 43461	GCA_013409045.1	46158	46158	type	True	81.5891	1304	2121	95	below_threshold
Actinomadura rubrisoli	strain=H3C3	GCA_004349215.1	2530368	2530368	type	True	81.541	1203	2121	95	below_threshold
Actinomadura formosensis	strain=NBRC 14204	GCA_001552155.1	60706	60706	type	True	81.5009	1114	2121	95	below_threshold
Actinomadura graeca	strain=32-07	GCA_019175365.1	2750812	2750812	type	True	81.3292	1239	2121	95	below_threshold
Actinomadura roseirufa		GCA_900659635.1	2094049	2094049	type	True	81.3067	1156	2121	95	below_threshold
Actinomadura parmotrematis	strain=PM05-2	GCA_019458805.1	2864039	2864039	type	True	81.2552	1244	2121	95	below_threshold
Actinomadura soli	strain=14C53	GCA_005889715.1	2508997	2508997	type	True	81.1453	1138	2121	95	below_threshold
Actinomadura rupiterrae	strain=DSM 45251	GCA_024172125.1	559627	559627	type	True	80.8862	1237	2121	95	below_threshold
Actinomadura spongiicola	strain=LHW52907	GCA_003432485.1	2303421	2303421	type	True	80.7411	1108	2121	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:32,943] [INFO] DFAST Taxonomy check result was written to GCF_001552235.1_ASM155223v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:32,944] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:32,944] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:32,945] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8b2a5257-0cce-4fb6-bfda-4ccb34dfb547/dqc_reference/checkm_data
[2024-01-24 15:19:32,946] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:33,008] [INFO] Task started: CheckM
[2024-01-24 15:19:33,008] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001552235.1_ASM155223v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001552235.1_ASM155223v1_genomic.fna/checkm_input GCF_001552235.1_ASM155223v1_genomic.fna/checkm_result
[2024-01-24 15:20:53,124] [INFO] Task succeeded: CheckM
[2024-01-24 15:20:53,126] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 6.48%
Strain heterogeneity: 37.50%
--------------------------------------------------------------------------------
[2024-01-24 15:20:53,154] [INFO] ===== Completeness check finished =====
[2024-01-24 15:20:53,154] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:20:53,155] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001552235.1_ASM155223v1_genomic.fna/markers.fasta)
[2024-01-24 15:20:53,155] [INFO] Task started: Blastn
[2024-01-24 15:20:53,155] [INFO] Running command: blastn -query GCF_001552235.1_ASM155223v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b2a5257-0cce-4fb6-bfda-4ccb34dfb547/dqc_reference/reference_markers_gtdb.fasta -out GCF_001552235.1_ASM155223v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:20:55,287] [INFO] Task succeeded: Blastn
[2024-01-24 15:20:55,291] [INFO] Selected 16 target genomes.
[2024-01-24 15:20:55,291] [INFO] Target genome list was writen to GCF_001552235.1_ASM155223v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:20:55,302] [INFO] Task started: fastANI
[2024-01-24 15:20:55,302] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2638603-a79d-4184-8f69-fa64b0a4ad81/GCF_001552235.1_ASM155223v1_genomic.fna.gz --refList GCF_001552235.1_ASM155223v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001552235.1_ASM155223v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:21:27,405] [INFO] Task succeeded: fastANI
[2024-01-24 15:21:27,420] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:21:27,420] [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
GCA_003001795.1	s__Actinomadura_B viridilutea	99.9982	2103	2121	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Actinomadura_B	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_015751755.1	s__Spirillospora viridis	82.2444	1366	2121	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009604375.1	s__Spirillospora macrotermitis	82.0886	1294	2121	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552635.1	s__Spirillospora hibisca	82.0845	1318	2121	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	81.8993	1337	2121	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008923365.1	s__Spirillospora montaniterrae	81.8793	1293	2121	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013211575.1	s__Spirillospora verrucosospora	81.8372	1373	2121	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	95.82	95.82	0.89	0.89	2	-
GCF_006716765.1	s__Spirillospora hallensis	81.688	1223	2121	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	81.5947	1403	2121	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	95.12	95.12	0.83	0.83	2	-
GCF_004349215.1	s__Spirillospora rubrisoli	81.5398	1205	2121	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	81.4715	1118	2121	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900659615.1	s__Spirillospora fibrosa	81.3648	1345	2121	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	81.3238	1154	2121	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348535.1	s__Spirillospora sp004348535	81.241	1105	2121	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005889715.1	s__Spirillospora sp005889715	81.0811	1148	2121	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008923185.1	s__Spirillospora rudentiformis	81.0611	1291	2121	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 15:21:27,422] [INFO] GTDB search result was written to GCF_001552235.1_ASM155223v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:21:27,423] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:21:27,427] [INFO] DFAST_QC result json was written to GCF_001552235.1_ASM155223v1_genomic.fna/dqc_result.json
[2024-01-24 15:21:27,427] [INFO] DFAST_QC completed!
[2024-01-24 15:21:27,427] [INFO] Total running time: 0h3m2s