[2024-01-24 14:46:35,356] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:35,358] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:35,358] [INFO] DQC Reference Directory: /var/lib/cwl/stgdf229a25-b4c9-4b3a-a6ca-4215b3576289/dqc_reference
[2024-01-24 14:46:36,575] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:36,575] [INFO] Task started: Prodigal
[2024-01-24 14:46:36,576] [INFO] Running command: gunzip -c /var/lib/cwl/stgd0ccd2f7-931a-4962-ba1f-a3fab468d984/GCF_017876325.1_ASM1787632v1_genomic.fna.gz | prodigal -d GCF_017876325.1_ASM1787632v1_genomic.fna/cds.fna -a GCF_017876325.1_ASM1787632v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:09,512] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:09,512] [INFO] Task started: HMMsearch
[2024-01-24 14:47:09,513] [INFO] Running command: hmmsearch --tblout GCF_017876325.1_ASM1787632v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdf229a25-b4c9-4b3a-a6ca-4215b3576289/dqc_reference/reference_markers.hmm GCF_017876325.1_ASM1787632v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:09,922] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:09,923] [INFO] Found 6/6 markers.
[2024-01-24 14:47:09,983] [INFO] Query marker FASTA was written to GCF_017876325.1_ASM1787632v1_genomic.fna/markers.fasta
[2024-01-24 14:47:09,983] [INFO] Task started: Blastn
[2024-01-24 14:47:09,984] [INFO] Running command: blastn -query GCF_017876325.1_ASM1787632v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf229a25-b4c9-4b3a-a6ca-4215b3576289/dqc_reference/reference_markers.fasta -out GCF_017876325.1_ASM1787632v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:11,374] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:11,378] [INFO] Selected 15 target genomes.
[2024-01-24 14:47:11,378] [INFO] Target genome list was writen to GCF_017876325.1_ASM1787632v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:11,385] [INFO] Task started: fastANI
[2024-01-24 14:47:11,385] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0ccd2f7-931a-4962-ba1f-a3fab468d984/GCF_017876325.1_ASM1787632v1_genomic.fna.gz --refList GCF_017876325.1_ASM1787632v1_genomic.fna/target_genomes.txt --output GCF_017876325.1_ASM1787632v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:47,626] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:47,626] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdf229a25-b4c9-4b3a-a6ca-4215b3576289/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:47,627] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdf229a25-b4c9-4b3a-a6ca-4215b3576289/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:47,639] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:47:47,639] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:47,639] [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
Saccharothrix coeruleofusca	strain=DSM 43679	GCA_017876325.1	33919	33919	type	True	100.0	2592	2592	95	conclusive
Saccharothrix coeruleofusca	strain=JCM 3313	GCA_014648515.1	33919	33919	type	True	99.3657	2439	2592	95	conclusive
Saccharothrix syringae	strain=NRRL B-16468	GCA_009498035.1	103733	103733	type	True	84.2714	1774	2592	95	below_threshold
Saccharothrix algeriensis	strain=DSM 44581	GCA_016907655.1	173560	173560	type	True	84.2276	1434	2592	95	below_threshold
Saccharothrix syringae	strain=NRRL B-16468	GCA_000716755.1	103733	103733	type	True	84.157	1764	2592	95	below_threshold
Saccharothrix saharensis	strain=DSM 45456	GCA_006716745.1	571190	571190	type	True	83.876	1628	2592	95	below_threshold
Saccharothrix carnea	strain=CGMCC 4.7097	GCA_003014735.1	1280637	1280637	type	True	83.6849	1605	2592	95	below_threshold
Saccharothrix texasensis	strain=DSM 44231	GCA_003752005.1	103734	103734	type	True	83.6519	1648	2592	95	below_threshold
Saccharothrix australiensis	strain=DSM 43800	GCA_003634935.1	2072	2072	type	True	83.4132	1496	2592	95	below_threshold
Saccharothrix variisporea	strain=DSM 43911	GCA_003634995.1	543527	543527	type	True	83.3212	1541	2592	95	below_threshold
Lentzea aerocolonigenes	strain=DSM 40034	GCA_024171805.1	68170	68170	type	True	80.0722	1255	2592	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	79.3451	993	2592	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	79.0245	959	2592	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	78.2727	1113	2592	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	76.8914	866	2592	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:47,641] [INFO] DFAST Taxonomy check result was written to GCF_017876325.1_ASM1787632v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:47,642] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:47,642] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:47,642] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdf229a25-b4c9-4b3a-a6ca-4215b3576289/dqc_reference/checkm_data
[2024-01-24 14:47:47,643] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:47,734] [INFO] Task started: CheckM
[2024-01-24 14:47:47,734] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017876325.1_ASM1787632v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017876325.1_ASM1787632v1_genomic.fna/checkm_input GCF_017876325.1_ASM1787632v1_genomic.fna/checkm_result
[2024-01-24 14:50:36,091] [INFO] Task succeeded: CheckM
[2024-01-24 14:50:36,094] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:50:36,119] [INFO] ===== Completeness check finished =====
[2024-01-24 14:50:36,119] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:50:36,120] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017876325.1_ASM1787632v1_genomic.fna/markers.fasta)
[2024-01-24 14:50:36,120] [INFO] Task started: Blastn
[2024-01-24 14:50:36,120] [INFO] Running command: blastn -query GCF_017876325.1_ASM1787632v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf229a25-b4c9-4b3a-a6ca-4215b3576289/dqc_reference/reference_markers_gtdb.fasta -out GCF_017876325.1_ASM1787632v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:50:38,260] [INFO] Task succeeded: Blastn
[2024-01-24 14:50:38,267] [INFO] Selected 15 target genomes.
[2024-01-24 14:50:38,267] [INFO] Target genome list was writen to GCF_017876325.1_ASM1787632v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:50:38,279] [INFO] Task started: fastANI
[2024-01-24 14:50:38,279] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0ccd2f7-931a-4962-ba1f-a3fab468d984/GCF_017876325.1_ASM1787632v1_genomic.fna.gz --refList GCF_017876325.1_ASM1787632v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017876325.1_ASM1787632v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:51:14,937] [INFO] Task succeeded: fastANI
[2024-01-24 14:51:14,955] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:51:14,955] [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_014648515.1	s__Actinosynnema coeruleofuscum	99.3657	2439	2592	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	99.37	99.37	0.97	0.97	2	conclusive
GCF_009498035.1	s__Actinosynnema syringae	84.2908	1772	2592	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	99.98	99.98	1.00	1.00	2	-
GCF_016907655.1	s__Actinosynnema algeriensis	84.2445	1432	2592	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716745.1	s__Actinosynnema saharense	83.9587	1613	2592	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003014735.1	s__Actinosynnema carneum	83.7285	1597	2592	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	95.10	95.10	0.83	0.83	2	-
GCF_003752005.1	s__Actinosynnema texasense	83.6565	1647	2592	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	98.51	98.51	0.92	0.92	2	-
GCF_003634935.1	s__Actinosynnema australiense	83.4512	1489	2592	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000328705.1	s__Actinosynnema espanaense	83.3786	1514	2592	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634995.1	s__Actinosynnema variisporeum	83.3511	1539	2592	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001280085.1	s__Actinosynnema sp001280085	83.3277	1671	2592	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001984175.1	s__Actinosynnema sp001984175	83.3253	1558	2592	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002354875.1	s__Actinosynnema auranticum	82.8162	1489	2592	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	96.4703	100.00	100.00	1.00	1.00	2	-
GCF_014203755.1	s__Actinosynnema violaceirubrum	81.9065	1276	2592	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016464305.1	s__REN6 sp016464305	81.9021	1336	2592	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__REN6	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003312875.1	s__Amycolatopsis albispora	78.7769	1160	2592	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:51:14,957] [INFO] GTDB search result was written to GCF_017876325.1_ASM1787632v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:51:14,958] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:51:14,962] [INFO] DFAST_QC result json was written to GCF_017876325.1_ASM1787632v1_genomic.fna/dqc_result.json
[2024-01-24 14:51:14,962] [INFO] DFAST_QC completed!
[2024-01-24 14:51:14,962] [INFO] Total running time: 0h4m40s