[2024-01-24 13:22:31,769] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:31,772] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:31,772] [INFO] DQC Reference Directory: /var/lib/cwl/stg2ae7cf31-23c7-4bdc-bb8f-9096044a33c0/dqc_reference
[2024-01-24 13:22:33,125] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:33,126] [INFO] Task started: Prodigal
[2024-01-24 13:22:33,126] [INFO] Running command: gunzip -c /var/lib/cwl/stg1da9c133-a0bc-4917-a8c4-8f9d5254711f/GCF_014138835.1_ASM1413883v1_genomic.fna.gz | prodigal -d GCF_014138835.1_ASM1413883v1_genomic.fna/cds.fna -a GCF_014138835.1_ASM1413883v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:54,884] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:54,885] [INFO] Task started: HMMsearch
[2024-01-24 13:22:54,885] [INFO] Running command: hmmsearch --tblout GCF_014138835.1_ASM1413883v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2ae7cf31-23c7-4bdc-bb8f-9096044a33c0/dqc_reference/reference_markers.hmm GCF_014138835.1_ASM1413883v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:55,249] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:55,251] [INFO] Found 6/6 markers.
[2024-01-24 13:22:55,308] [INFO] Query marker FASTA was written to GCF_014138835.1_ASM1413883v1_genomic.fna/markers.fasta
[2024-01-24 13:22:55,309] [INFO] Task started: Blastn
[2024-01-24 13:22:55,309] [INFO] Running command: blastn -query GCF_014138835.1_ASM1413883v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ae7cf31-23c7-4bdc-bb8f-9096044a33c0/dqc_reference/reference_markers.fasta -out GCF_014138835.1_ASM1413883v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:56,675] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:56,679] [INFO] Selected 18 target genomes.
[2024-01-24 13:22:56,679] [INFO] Target genome list was writen to GCF_014138835.1_ASM1413883v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:57,809] [INFO] Task started: fastANI
[2024-01-24 13:22:57,809] [INFO] Running command: fastANI --query /var/lib/cwl/stg1da9c133-a0bc-4917-a8c4-8f9d5254711f/GCF_014138835.1_ASM1413883v1_genomic.fna.gz --refList GCF_014138835.1_ASM1413883v1_genomic.fna/target_genomes.txt --output GCF_014138835.1_ASM1413883v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:23:33,625] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:33,626] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2ae7cf31-23c7-4bdc-bb8f-9096044a33c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:23:33,626] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2ae7cf31-23c7-4bdc-bb8f-9096044a33c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:23:33,646] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:23:33,646] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:23:33,647] [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
Thermomonospora catenispora	strain=3-22-3	GCA_006363815.1	2493090	2493090	type	True	90.3983	1493	2459	95	below_threshold
Thermomonospora echinospora	strain=DSM 43163	GCA_900108175.1	1992	1992	type	True	85.8651	1675	2459	95	below_threshold
Thermomonospora curvata	strain=DSM 43183	GCA_000024385.1	2020	2020	type	True	84.7361	1308	2459	95	below_threshold
Thermomonospora umbrina	strain=DSM 43927	GCA_003386555.1	111806	111806	type	True	83.9327	1394	2459	95	below_threshold
Actinomadura rubrobrunea	strain=NBRC 15275	GCA_001552235.1	115335	115335	type	True	81.9488	1167	2459	95	below_threshold
Actinomadura viridis	strain=DSM 43175	GCA_015751755.1	58110	58110	type	True	81.384	1357	2459	95	below_threshold
Actinomadura macrotermitis	strain=RB68	GCA_009604375.1	2585200	2585200	type	True	81.2527	1333	2459	95	below_threshold
Actinomadura physcomitrii	strain=LD22	GCA_008923205.2	2650748	2650748	type	True	80.7136	1312	2459	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	80.669	1365	2459	95	below_threshold
Actinomadura parmotrematis	strain=PM05-2	GCA_019458805.1	2864039	2864039	type	True	80.6205	1249	2459	95	below_threshold
Actinomadura montaniterrae	strain=CYP1-1B	GCA_008923365.1	1803903	1803903	type	True	80.6091	1299	2459	95	below_threshold
Actinomadura nitritigenes	strain=L46	GCA_017573545.1	134602	134602	type	True	80.4681	1378	2459	95	below_threshold
Actinomadura graeca	strain=32-07	GCA_019175365.1	2750812	2750812	type	True	80.2342	1205	2459	95	below_threshold
Actinomadura rupiterrae	strain=DSM 45251	GCA_024172125.1	559627	559627	type	True	80.1063	1211	2459	95	below_threshold
Actinomadura decatromicini	strain=CYP1-5	GCA_008121305.1	2604572	2604572	type	True	79.8078	1215	2459	95	below_threshold
Actinomadura spongiicola	strain=LHW52907	GCA_003432485.1	2303421	2303421	type	True	79.7651	1050	2459	95	below_threshold
Actinoallomurus spadix	strain=KCTC 9252	GCA_024055725.1	79912	79912	type	True	79.1119	1017	2459	95	below_threshold
Actinoallomurus bryophytorum	strain=DSM 102200	GCA_006716425.1	1490222	1490222	type	True	78.5341	960	2459	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:23:33,649] [INFO] DFAST Taxonomy check result was written to GCF_014138835.1_ASM1413883v1_genomic.fna/tc_result.tsv
[2024-01-24 13:23:33,649] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:23:33,649] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:23:33,650] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2ae7cf31-23c7-4bdc-bb8f-9096044a33c0/dqc_reference/checkm_data
[2024-01-24 13:23:33,651] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:23:33,721] [INFO] Task started: CheckM
[2024-01-24 13:23:33,721] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014138835.1_ASM1413883v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014138835.1_ASM1413883v1_genomic.fna/checkm_input GCF_014138835.1_ASM1413883v1_genomic.fna/checkm_result
[2024-01-24 13:25:44,051] [INFO] Task succeeded: CheckM
[2024-01-24 13:25:44,052] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:25:44,073] [INFO] ===== Completeness check finished =====
[2024-01-24 13:25:44,073] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:25:44,074] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014138835.1_ASM1413883v1_genomic.fna/markers.fasta)
[2024-01-24 13:25:44,074] [INFO] Task started: Blastn
[2024-01-24 13:25:44,075] [INFO] Running command: blastn -query GCF_014138835.1_ASM1413883v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ae7cf31-23c7-4bdc-bb8f-9096044a33c0/dqc_reference/reference_markers_gtdb.fasta -out GCF_014138835.1_ASM1413883v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:46,222] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:46,226] [INFO] Selected 11 target genomes.
[2024-01-24 13:25:46,226] [INFO] Target genome list was writen to GCF_014138835.1_ASM1413883v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:25:46,247] [INFO] Task started: fastANI
[2024-01-24 13:25:46,247] [INFO] Running command: fastANI --query /var/lib/cwl/stg1da9c133-a0bc-4917-a8c4-8f9d5254711f/GCF_014138835.1_ASM1413883v1_genomic.fna.gz --refList GCF_014138835.1_ASM1413883v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014138835.1_ASM1413883v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:26:08,871] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:08,883] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:26:08,883] [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_003589885.1	s__Thermomonospora amylolytica	98.3638	2093	2459	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermomonospora	95.0	98.39	98.39	0.92	0.92	2	conclusive
GCF_006363815.1	s__Thermomonospora catenispora	90.3706	1496	2459	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108175.1	s__Thermomonospora echinospora	85.9114	1668	2459	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024385.1	s__Thermomonospora curvata	84.6735	1314	2459	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermomonospora	95.0	99.63	99.63	0.99	0.99	2	-
GCF_003386555.1	s__Thermomonospora umbrina	83.9975	1384	2459	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003001795.1	s__Actinomadura_B viridilutea	81.9279	1207	2459	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Actinomadura_B	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003289645.1	s__Actinomadura_D craniellae	81.3759	1252	2459	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Actinomadura_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015751755.1	s__Spirillospora viridis	81.3473	1367	2459	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	81.2615	1330	2459	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	80.4588	1381	2459	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	95.12	95.12	0.83	0.83	2	-
GCF_002995495.1	s__Actinocorallia populi	79.7425	1081	2459	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Actinocorallia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:26:08,885] [INFO] GTDB search result was written to GCF_014138835.1_ASM1413883v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:26:08,885] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:26:08,889] [INFO] DFAST_QC result json was written to GCF_014138835.1_ASM1413883v1_genomic.fna/dqc_result.json
[2024-01-24 13:26:08,889] [INFO] DFAST_QC completed!
[2024-01-24 13:26:08,889] [INFO] Total running time: 0h3m37s