[2024-01-24 14:30:59,489] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:59,490] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:59,491] [INFO] DQC Reference Directory: /var/lib/cwl/stg420ab1d7-48f1-4c4e-b928-fd479150bef0/dqc_reference
[2024-01-24 14:31:00,771] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:00,772] [INFO] Task started: Prodigal
[2024-01-24 14:31:00,772] [INFO] Running command: gunzip -c /var/lib/cwl/stg157e938d-5210-4c9c-857b-29eb6085cb59/GCF_002911665.1_ASM291166v1_genomic.fna.gz | prodigal -d GCF_002911665.1_ASM291166v1_genomic.fna/cds.fna -a GCF_002911665.1_ASM291166v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:19,149] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:19,150] [INFO] Task started: HMMsearch
[2024-01-24 14:31:19,150] [INFO] Running command: hmmsearch --tblout GCF_002911665.1_ASM291166v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg420ab1d7-48f1-4c4e-b928-fd479150bef0/dqc_reference/reference_markers.hmm GCF_002911665.1_ASM291166v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:19,496] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:19,497] [INFO] Found 6/6 markers.
[2024-01-24 14:31:19,552] [INFO] Query marker FASTA was written to GCF_002911665.1_ASM291166v1_genomic.fna/markers.fasta
[2024-01-24 14:31:19,552] [INFO] Task started: Blastn
[2024-01-24 14:31:19,552] [INFO] Running command: blastn -query GCF_002911665.1_ASM291166v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg420ab1d7-48f1-4c4e-b928-fd479150bef0/dqc_reference/reference_markers.fasta -out GCF_002911665.1_ASM291166v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:21,046] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:21,051] [INFO] Selected 15 target genomes.
[2024-01-24 14:31:21,051] [INFO] Target genome list was writen to GCF_002911665.1_ASM291166v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:21,064] [INFO] Task started: fastANI
[2024-01-24 14:31:21,065] [INFO] Running command: fastANI --query /var/lib/cwl/stg157e938d-5210-4c9c-857b-29eb6085cb59/GCF_002911665.1_ASM291166v1_genomic.fna.gz --refList GCF_002911665.1_ASM291166v1_genomic.fna/target_genomes.txt --output GCF_002911665.1_ASM291166v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:58,220] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:58,221] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg420ab1d7-48f1-4c4e-b928-fd479150bef0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:58,222] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg420ab1d7-48f1-4c4e-b928-fd479150bef0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:58,240] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:31:58,240] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:58,240] [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 rubteroloni	strain=RB29	GCA_002911665.1	1926885	1926885	type	True	100.0	2152	2152	95	conclusive
Actinomadura rayongensis	strain=DSM 102126	GCA_009831215.1	1429076	1429076	type	True	94.4411	1883	2152	95	below_threshold
Actinomadura atramentaria	strain=SF2197	GCA_000381885.1	1990	1990	type	True	85.5078	1486	2152	95	below_threshold
Actinomadura flavalba	strain=DSM 45200	GCA_000374305.1	1120938	1120938	type	True	82.8925	1319	2152	95	below_threshold
Actinomadura parmotrematis	strain=PM05-2	GCA_019458805.1	2864039	2864039	type	True	81.8878	1295	2152	95	below_threshold
Actinomadura macrotermitis	strain=RB68	GCA_009604375.1	2585200	2585200	type	True	81.8695	1379	2152	95	below_threshold
Actinomadura bangladeshensis	strain=DSM 45347	GCA_004348335.1	453573	453573	type	True	81.5816	1140	2152	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	81.544	1371	2152	95	below_threshold
Actinomadura nitritigenes	strain=L46	GCA_017573545.1	134602	134602	type	True	81.3905	1358	2152	95	below_threshold
Actinomadura hibisca	strain=NBRC 15177	GCA_001552635.1	68565	68565	type	True	81.38	1295	2152	95	below_threshold
Actinomadura geliboluensis	strain=A8036	GCA_005889745.1	882440	882440	type	True	81.2042	1151	2152	95	below_threshold
Actinomadura graeca	strain=32-07	GCA_019175365.1	2750812	2750812	type	True	81.0683	1233	2152	95	below_threshold
Actinomadura rifamycini	strain=DSM 43936	GCA_000425065.1	31962	31962	type	True	81.0565	1278	2152	95	below_threshold
Actinomadura rupiterrae	strain=DSM 45251	GCA_024172125.1	559627	559627	type	True	80.8563	1287	2152	95	below_threshold
Actinomadura spongiicola	strain=LHW52907	GCA_003432485.1	2303421	2303421	type	True	80.7754	1087	2152	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:58,242] [INFO] DFAST Taxonomy check result was written to GCF_002911665.1_ASM291166v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:58,243] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:58,243] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:58,243] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg420ab1d7-48f1-4c4e-b928-fd479150bef0/dqc_reference/checkm_data
[2024-01-24 14:31:58,244] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:58,304] [INFO] Task started: CheckM
[2024-01-24 14:31:58,304] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002911665.1_ASM291166v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002911665.1_ASM291166v1_genomic.fna/checkm_input GCF_002911665.1_ASM291166v1_genomic.fna/checkm_result
[2024-01-24 14:33:19,503] [INFO] Task succeeded: CheckM
[2024-01-24 14:33:19,505] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:33:19,527] [INFO] ===== Completeness check finished =====
[2024-01-24 14:33:19,528] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:33:19,528] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002911665.1_ASM291166v1_genomic.fna/markers.fasta)
[2024-01-24 14:33:19,528] [INFO] Task started: Blastn
[2024-01-24 14:33:19,529] [INFO] Running command: blastn -query GCF_002911665.1_ASM291166v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg420ab1d7-48f1-4c4e-b928-fd479150bef0/dqc_reference/reference_markers_gtdb.fasta -out GCF_002911665.1_ASM291166v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:33:22,096] [INFO] Task succeeded: Blastn
[2024-01-24 14:33:22,101] [INFO] Selected 14 target genomes.
[2024-01-24 14:33:22,102] [INFO] Target genome list was writen to GCF_002911665.1_ASM291166v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:33:22,119] [INFO] Task started: fastANI
[2024-01-24 14:33:22,119] [INFO] Running command: fastANI --query /var/lib/cwl/stg157e938d-5210-4c9c-857b-29eb6085cb59/GCF_002911665.1_ASM291166v1_genomic.fna.gz --refList GCF_002911665.1_ASM291166v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002911665.1_ASM291166v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:33:57,563] [INFO] Task succeeded: fastANI
[2024-01-24 14:33:57,580] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:33:57,581] [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_002911665.1	s__Spirillospora rubteroloni	100.0	2152	2152	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_009831215.1	s__Spirillospora rayongensis	94.4736	1879	2152	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000381885.1	s__Spirillospora atramentaria	85.5276	1484	2152	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374305.1	s__Spirillospora flavalba	82.9344	1313	2152	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	81.9118	1371	2152	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	81.6304	1294	2152	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	81.5411	1146	2152	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	81.4965	1306	2152	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	81.4585	1075	2152	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009793335.1	s__Spirillospora sp009793335	81.4531	1370	2152	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	81.3239	1372	2152	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	95.12	95.12	0.83	0.83	2	-
GCF_900659615.1	s__Spirillospora fibrosa	81.2012	1302	2152	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	81.1147	1106	2152	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	81.0746	1274	2152	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	99.13	99.13	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:33:57,585] [INFO] GTDB search result was written to GCF_002911665.1_ASM291166v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:33:57,586] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:33:57,590] [INFO] DFAST_QC result json was written to GCF_002911665.1_ASM291166v1_genomic.fna/dqc_result.json
[2024-01-24 14:33:57,590] [INFO] DFAST_QC completed!
[2024-01-24 14:33:57,590] [INFO] Total running time: 0h2m58s