[2024-01-24 11:59:35,587] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:35,591] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:35,591] [INFO] DQC Reference Directory: /var/lib/cwl/stgbaffa0fd-bf0c-429c-bac6-7329e5e913ca/dqc_reference
[2024-01-24 11:59:36,805] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:36,806] [INFO] Task started: Prodigal
[2024-01-24 11:59:36,806] [INFO] Running command: gunzip -c /var/lib/cwl/stga29f2175-a435-4254-a59c-392ea4bf4629/GCF_900659635.1_LMG30035_FinalContigs.fasta.gz_genomic.fna.gz | prodigal -d GCF_900659635.1_LMG30035_FinalContigs.fasta.gz_genomic.fna/cds.fna -a GCF_900659635.1_LMG30035_FinalContigs.fasta.gz_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:58,191] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:58,192] [INFO] Task started: HMMsearch
[2024-01-24 11:59:58,192] [INFO] Running command: hmmsearch --tblout GCF_900659635.1_LMG30035_FinalContigs.fasta.gz_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbaffa0fd-bf0c-429c-bac6-7329e5e913ca/dqc_reference/reference_markers.hmm GCF_900659635.1_LMG30035_FinalContigs.fasta.gz_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:58,669] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:58,671] [INFO] Found 6/6 markers.
[2024-01-24 11:59:58,742] [INFO] Query marker FASTA was written to GCF_900659635.1_LMG30035_FinalContigs.fasta.gz_genomic.fna/markers.fasta
[2024-01-24 11:59:58,743] [INFO] Task started: Blastn
[2024-01-24 11:59:58,743] [INFO] Running command: blastn -query GCF_900659635.1_LMG30035_FinalContigs.fasta.gz_genomic.fna/markers.fasta -db /var/lib/cwl/stgbaffa0fd-bf0c-429c-bac6-7329e5e913ca/dqc_reference/reference_markers.fasta -out GCF_900659635.1_LMG30035_FinalContigs.fasta.gz_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:00,063] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:00,068] [INFO] Selected 19 target genomes.
[2024-01-24 12:00:00,068] [INFO] Target genome list was writen to GCF_900659635.1_LMG30035_FinalContigs.fasta.gz_genomic.fna/target_genomes.txt
[2024-01-24 12:00:00,091] [INFO] Task started: fastANI
[2024-01-24 12:00:00,092] [INFO] Running command: fastANI --query /var/lib/cwl/stga29f2175-a435-4254-a59c-392ea4bf4629/GCF_900659635.1_LMG30035_FinalContigs.fasta.gz_genomic.fna.gz --refList GCF_900659635.1_LMG30035_FinalContigs.fasta.gz_genomic.fna/target_genomes.txt --output GCF_900659635.1_LMG30035_FinalContigs.fasta.gz_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:00:43,816] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:43,817] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbaffa0fd-bf0c-429c-bac6-7329e5e913ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:00:43,817] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbaffa0fd-bf0c-429c-bac6-7329e5e913ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:00:43,844] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:00:43,844] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:00:43,845] [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 roseirufa		GCA_900659635.1	2094049	2094049	type	True	100.0	2682	2713	95	conclusive
Actinomadura rubrisoli	strain=H3C3	GCA_004349215.1	2530368	2530368	type	True	85.0442	1588	2713	95	below_threshold
Actinomadura graeca	strain=32-07	GCA_019175365.1	2750812	2750812	type	True	84.6819	1643	2713	95	below_threshold
Actinomadura litoris	strain=NEAU-AAG5	GCA_009733595.1	2678616	2678616	type	True	84.5299	1714	2713	95	below_threshold
Actinomadura macra	strain=NBRC 14102	GCA_001552215.1	46164	46164	type	True	84.3555	1646	2713	95	below_threshold
Actinomadura physcomitrii	strain=LD22	GCA_008923205.2	2650748	2650748	type	True	83.7216	1507	2713	95	below_threshold
Actinomadura montaniterrae	strain=CYP1-1B	GCA_008923365.1	1803903	1803903	type	True	83.6091	1588	2713	95	below_threshold
Actinomadura latina	strain=ATCC BAA-277	GCA_012396395.1	163603	163603	type	True	83.6031	1369	2713	95	below_threshold
Actinomadura formosensis	strain=NBRC 14204	GCA_001552155.1	60706	60706	type	True	83.5511	1236	2713	95	below_threshold
Actinomadura bangladeshensis	strain=DSM 45347	GCA_004348335.1	453573	453573	type	True	83.4953	1335	2713	95	below_threshold
Actinomadura mexicana	strain=DSM 44485	GCA_900188105.1	134959	134959	type	True	83.4915	1502	2713	95	below_threshold
Actinomadura citrea	strain=DSM 43461	GCA_013409045.1	46158	46158	type	True	83.485	1542	2713	95	below_threshold
Actinomadura nitritigenes	strain=L46	GCA_017573545.1	134602	134602	type	True	83.4579	1649	2713	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	83.4411	1629	2713	95	below_threshold
Actinomadura meyerae	strain=DSM 44715	GCA_900188445.1	240840	240840	type	True	83.3667	1477	2713	95	below_threshold
Actinomadura geliboluensis	strain=A8036	GCA_005889745.1	882440	882440	type	True	83.2758	1318	2713	95	below_threshold
Actinomadura spongiicola	strain=LHW52907	GCA_003432485.1	2303421	2303421	type	True	82.7119	1361	2713	95	below_threshold
Actinomadura parmotrematis	strain=PM05-2	GCA_019458805.1	2864039	2864039	type	True	81.3698	1343	2713	95	below_threshold
Actinomadura rupiterrae	strain=DSM 45251	GCA_024172125.1	559627	559627	type	True	80.8981	1339	2713	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:00:43,846] [INFO] DFAST Taxonomy check result was written to GCF_900659635.1_LMG30035_FinalContigs.fasta.gz_genomic.fna/tc_result.tsv
[2024-01-24 12:00:43,847] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:00:43,847] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:00:43,847] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbaffa0fd-bf0c-429c-bac6-7329e5e913ca/dqc_reference/checkm_data
[2024-01-24 12:00:43,848] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:00:43,932] [INFO] Task started: CheckM
[2024-01-24 12:00:43,932] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900659635.1_LMG30035_FinalContigs.fasta.gz_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900659635.1_LMG30035_FinalContigs.fasta.gz_genomic.fna/checkm_input GCF_900659635.1_LMG30035_FinalContigs.fasta.gz_genomic.fna/checkm_result
[2024-01-24 12:01:50,020] [INFO] Task succeeded: CheckM
[2024-01-24 12:01:50,021] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 12.04%
Strain heterogeneity: 61.54%
--------------------------------------------------------------------------------
[2024-01-24 12:01:50,054] [INFO] ===== Completeness check finished =====
[2024-01-24 12:01:50,055] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:01:50,055] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900659635.1_LMG30035_FinalContigs.fasta.gz_genomic.fna/markers.fasta)
[2024-01-24 12:01:50,055] [INFO] Task started: Blastn
[2024-01-24 12:01:50,056] [INFO] Running command: blastn -query GCF_900659635.1_LMG30035_FinalContigs.fasta.gz_genomic.fna/markers.fasta -db /var/lib/cwl/stgbaffa0fd-bf0c-429c-bac6-7329e5e913ca/dqc_reference/reference_markers_gtdb.fasta -out GCF_900659635.1_LMG30035_FinalContigs.fasta.gz_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:01:52,160] [INFO] Task succeeded: Blastn
[2024-01-24 12:01:52,165] [INFO] Selected 14 target genomes.
[2024-01-24 12:01:52,165] [INFO] Target genome list was writen to GCF_900659635.1_LMG30035_FinalContigs.fasta.gz_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:01:52,178] [INFO] Task started: fastANI
[2024-01-24 12:01:52,178] [INFO] Running command: fastANI --query /var/lib/cwl/stga29f2175-a435-4254-a59c-392ea4bf4629/GCF_900659635.1_LMG30035_FinalContigs.fasta.gz_genomic.fna.gz --refList GCF_900659635.1_LMG30035_FinalContigs.fasta.gz_genomic.fna/target_genomes_gtdb.txt --output GCF_900659635.1_LMG30035_FinalContigs.fasta.gz_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:02:25,891] [INFO] Task succeeded: fastANI
[2024-01-24 12:02:25,907] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:02:25,907] [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_900659635.1	s__Spirillospora roseirufa	100.0	2682	2713	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_004349215.1	s__Spirillospora rubrisoli	85.0209	1592	2713	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	84.5632	1708	2713	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	99.22	99.22	0.97	0.97	2	-
GCF_001552215.1	s__Spirillospora macra	84.3587	1646	2713	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	84.2013	1605	2713	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	83.6443	1521	2713	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	83.5996	1591	2713	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	83.5844	1609	2713	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	95.82	95.82	0.89	0.89	2	-
GCF_001552155.1	s__Spirillospora formosensis	83.5502	1236	2713	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	99.99	99.99	0.99	0.99	2	-
GCF_013409365.1	s__Spirillospora luteofluorescens	83.5328	1529	2713	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	83.5008	1641	2713	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	95.12	95.12	0.83	0.83	2	-
GCF_013409045.1	s__Spirillospora citrea	83.4637	1546	2713	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004348335.1	s__Spirillospora bangladeshensis	83.4304	1345	2713	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188445.1	s__Spirillospora meyerae	83.4156	1469	2713	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 12:02:25,909] [INFO] GTDB search result was written to GCF_900659635.1_LMG30035_FinalContigs.fasta.gz_genomic.fna/result_gtdb.tsv
[2024-01-24 12:02:25,909] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:02:25,913] [INFO] DFAST_QC result json was written to GCF_900659635.1_LMG30035_FinalContigs.fasta.gz_genomic.fna/dqc_result.json
[2024-01-24 12:02:25,913] [INFO] DFAST_QC completed!
[2024-01-24 12:02:25,913] [INFO] Total running time: 0h2m50s