[2024-01-24 10:47:09,748] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:09,759] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:09,760] [INFO] DQC Reference Directory: /var/lib/cwl/stg3407845a-84cd-4cc4-acc6-6c78a810182d/dqc_reference
[2024-01-24 10:47:11,964] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:11,965] [INFO] Task started: Prodigal
[2024-01-24 10:47:11,966] [INFO] Running command: gunzip -c /var/lib/cwl/stga3869add-b8fc-4281-845d-f90c1f66b2c6/GCF_011008945.1_ASM1100894v1_genomic.fna.gz | prodigal -d GCF_011008945.1_ASM1100894v1_genomic.fna/cds.fna -a GCF_011008945.1_ASM1100894v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:31,333] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:31,334] [INFO] Task started: HMMsearch
[2024-01-24 10:47:31,334] [INFO] Running command: hmmsearch --tblout GCF_011008945.1_ASM1100894v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3407845a-84cd-4cc4-acc6-6c78a810182d/dqc_reference/reference_markers.hmm GCF_011008945.1_ASM1100894v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:31,719] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:31,720] [INFO] Found 6/6 markers.
[2024-01-24 10:47:31,781] [INFO] Query marker FASTA was written to GCF_011008945.1_ASM1100894v1_genomic.fna/markers.fasta
[2024-01-24 10:47:31,782] [INFO] Task started: Blastn
[2024-01-24 10:47:31,782] [INFO] Running command: blastn -query GCF_011008945.1_ASM1100894v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3407845a-84cd-4cc4-acc6-6c78a810182d/dqc_reference/reference_markers.fasta -out GCF_011008945.1_ASM1100894v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:33,204] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:33,209] [INFO] Selected 17 target genomes.
[2024-01-24 10:47:33,209] [INFO] Target genome list was writen to GCF_011008945.1_ASM1100894v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:33,539] [INFO] Task started: fastANI
[2024-01-24 10:47:33,539] [INFO] Running command: fastANI --query /var/lib/cwl/stga3869add-b8fc-4281-845d-f90c1f66b2c6/GCF_011008945.1_ASM1100894v1_genomic.fna.gz --refList GCF_011008945.1_ASM1100894v1_genomic.fna/target_genomes.txt --output GCF_011008945.1_ASM1100894v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:09,523] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:09,523] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3407845a-84cd-4cc4-acc6-6c78a810182d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:09,524] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3407845a-84cd-4cc4-acc6-6c78a810182d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:09,537] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:48:09,537] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:09,537] [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
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	100.0	2235	2260	95	conclusive
Streptomyces leeuwenhoekii	strain=C34	GCA_000696595.1	1437453	1437453	type	True	94.7621	1738	2260	95	below_threshold
Streptomyces leeuwenhoekii	strain=C34 (= DSM 42122 = NRRL B-24963)	GCA_001013905.1	1437453	1437453	type	True	94.7412	1921	2260	95	below_threshold
Streptomyces viridiviolaceus	strain=JCM 4855	GCA_014650995.1	68282	68282	type	True	87.1393	1552	2260	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	87.1236	1598	2260	95	below_threshold
Streptomyces flaveolus	strain=JCM 4032	GCA_014648815.1	67297	67297	type	True	86.7462	1566	2260	95	below_threshold
Streptomyces fumanus	strain=JCM 4477	GCA_014655295.1	67302	67302	type	True	86.5758	1572	2260	95	below_threshold
Streptomyces fumigatiscleroticus	strain=JCM 3101	GCA_014647975.1	66371	66371	type	True	86.4644	1554	2260	95	below_threshold
Streptomyces griseostramineus	strain=CECT 3273	GCA_014203535.1	66898	66898	suspected-type	True	86.0176	1553	2260	95	below_threshold
Streptomyces ardesiacus	strain=NBRC 15402	GCA_003112575.1	285564	285564	type	True	85.978	1522	2260	95	below_threshold
Streptomyces daghestanicus	strain=NBRC 12762	GCA_020521275.1	66885	66885	suspected-type	True	85.9258	1531	2260	95	below_threshold
Streptomyces griseostramineus	strain=JCM 4385	GCA_014649635.1	66898	66898	suspected-type	True	85.8964	1577	2260	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	85.8804	1526	2260	95	below_threshold
Streptomyces indiaensis	strain=DSM 43803	GCA_021474405.1	284033	284033	type	True	85.3135	1414	2260	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	85.0132	1352	2260	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	84.4991	1349	2260	95	below_threshold
Streptomyces fodineus	strain=TW1S1	GCA_001735805.1	1904616	1904616	type	True	84.2734	1438	2260	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:09,539] [INFO] DFAST Taxonomy check result was written to GCF_011008945.1_ASM1100894v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:09,539] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:09,539] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:09,539] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3407845a-84cd-4cc4-acc6-6c78a810182d/dqc_reference/checkm_data
[2024-01-24 10:48:09,540] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:09,616] [INFO] Task started: CheckM
[2024-01-24 10:48:09,616] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011008945.1_ASM1100894v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011008945.1_ASM1100894v1_genomic.fna/checkm_input GCF_011008945.1_ASM1100894v1_genomic.fna/checkm_result
[2024-01-24 10:49:41,567] [INFO] Task succeeded: CheckM
[2024-01-24 10:49:41,569] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:49:41,602] [INFO] ===== Completeness check finished =====
[2024-01-24 10:49:41,603] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:49:41,603] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011008945.1_ASM1100894v1_genomic.fna/markers.fasta)
[2024-01-24 10:49:41,604] [INFO] Task started: Blastn
[2024-01-24 10:49:41,604] [INFO] Running command: blastn -query GCF_011008945.1_ASM1100894v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3407845a-84cd-4cc4-acc6-6c78a810182d/dqc_reference/reference_markers_gtdb.fasta -out GCF_011008945.1_ASM1100894v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:43,868] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:43,873] [INFO] Selected 18 target genomes.
[2024-01-24 10:49:43,873] [INFO] Target genome list was writen to GCF_011008945.1_ASM1100894v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:49:43,887] [INFO] Task started: fastANI
[2024-01-24 10:49:43,887] [INFO] Running command: fastANI --query /var/lib/cwl/stga3869add-b8fc-4281-845d-f90c1f66b2c6/GCF_011008945.1_ASM1100894v1_genomic.fna.gz --refList GCF_011008945.1_ASM1100894v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011008945.1_ASM1100894v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:50:20,720] [INFO] Task succeeded: fastANI
[2024-01-24 10:50:20,738] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 10:50:20,738] [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_000931445.1	s__Streptomyces cyaneogriseus	94.9889	2001	2260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.603	N/A	N/A	N/A	N/A	1	-
GCF_001013905.1	s__Streptomyces leeuwenhoekii	94.7854	1916	2260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.603	99.67	99.36	0.97	0.94	3	-
GCF_014650995.1	s__Streptomyces viridiviolaceus	87.0969	1557	2260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014534645.1	s__Streptomyces sp014534645	87.059	1606	2260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003248315.1	s__Streptomyces sp003248315	86.7929	1518	2260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648815.1	s__Streptomyces flaveolus	86.7345	1567	2260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002005565.1	s__Streptomyces sp002005565	86.6845	1459	2260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014655295.1	s__Streptomyces fumanus	86.6115	1567	2260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647975.1	s__Streptomyces fumigatiscleroticus	86.4486	1557	2260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002005225.1	s__Streptomyces pactum_A	86.4007	1581	2260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.96	0.98	0.98	2	-
GCF_009852415.1	s__Streptomyces sp009852415	86.1121	1604	2260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014649155.1	s__Streptomyces griseoviridis	86.0059	1513	2260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.52	99.48	0.96	0.96	3	-
GCF_014203535.1	s__Streptomyces griseostramineus	85.9675	1559	2260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.88	99.76	0.99	0.98	3	-
GCF_006782915.1	s__Streptomyces calvus	85.7675	1547	2260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.66	99.31	0.97	0.96	5	-
GCF_002920535.1	s__Streptomyces sp002920535	85.473	1438	2260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018604545.1	s__Streptomyces sp018604545	85.3563	1497	2260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014257025.1	s__Streptomyces sp014257025	84.9154	1429	2260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001735805.1	s__Streptomyces fodineus	84.2654	1437	2260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:50:20,740] [INFO] GTDB search result was written to GCF_011008945.1_ASM1100894v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:50:20,740] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:50:20,744] [INFO] DFAST_QC result json was written to GCF_011008945.1_ASM1100894v1_genomic.fna/dqc_result.json
[2024-01-24 10:50:20,744] [INFO] DFAST_QC completed!
[2024-01-24 10:50:20,744] [INFO] Total running time: 0h3m11s