[2024-01-24 13:51:10,227] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:51:10,230] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:51:10,230] [INFO] DQC Reference Directory: /var/lib/cwl/stg18d9f282-a991-4f65-bc04-ffa857b1d7cf/dqc_reference
[2024-01-24 13:51:11,431] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:51:11,432] [INFO] Task started: Prodigal
[2024-01-24 13:51:11,433] [INFO] Running command: gunzip -c /var/lib/cwl/stga9e8d084-d722-4665-81d9-e197b37ea06a/GCF_030135485.1_ASM3013548v1_genomic.fna.gz | prodigal -d GCF_030135485.1_ASM3013548v1_genomic.fna/cds.fna -a GCF_030135485.1_ASM3013548v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:51:31,104] [INFO] Task succeeded: Prodigal
[2024-01-24 13:51:31,105] [INFO] Task started: HMMsearch
[2024-01-24 13:51:31,105] [INFO] Running command: hmmsearch --tblout GCF_030135485.1_ASM3013548v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg18d9f282-a991-4f65-bc04-ffa857b1d7cf/dqc_reference/reference_markers.hmm GCF_030135485.1_ASM3013548v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:51:31,444] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:51:31,445] [INFO] Found 6/6 markers.
[2024-01-24 13:51:31,503] [INFO] Query marker FASTA was written to GCF_030135485.1_ASM3013548v1_genomic.fna/markers.fasta
[2024-01-24 13:51:31,504] [INFO] Task started: Blastn
[2024-01-24 13:51:31,504] [INFO] Running command: blastn -query GCF_030135485.1_ASM3013548v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg18d9f282-a991-4f65-bc04-ffa857b1d7cf/dqc_reference/reference_markers.fasta -out GCF_030135485.1_ASM3013548v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:32,838] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:32,850] [INFO] Selected 19 target genomes.
[2024-01-24 13:51:32,850] [INFO] Target genome list was writen to GCF_030135485.1_ASM3013548v1_genomic.fna/target_genomes.txt
[2024-01-24 13:51:32,864] [INFO] Task started: fastANI
[2024-01-24 13:51:32,865] [INFO] Running command: fastANI --query /var/lib/cwl/stga9e8d084-d722-4665-81d9-e197b37ea06a/GCF_030135485.1_ASM3013548v1_genomic.fna.gz --refList GCF_030135485.1_ASM3013548v1_genomic.fna/target_genomes.txt --output GCF_030135485.1_ASM3013548v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:52:08,315] [INFO] Task succeeded: fastANI
[2024-01-24 13:52:08,315] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg18d9f282-a991-4f65-bc04-ffa857b1d7cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:52:08,316] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg18d9f282-a991-4f65-bc04-ffa857b1d7cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:52:08,337] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:52:08,337] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:52:08,337] [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 fragilis	strain=NBRC 12862	GCA_003112515.1	67301	67301	type	True	99.9283	2267	2289	95	conclusive
Streptomyces chilikensis	strain=RC 1830	GCA_001642695.2	1194079	1194079	type	True	89.4574	1709	2289	95	below_threshold
Streptomyces abyssomicinicus	strain=CHI39	GCA_008974245.1	574929	574929	type	True	89.083	1777	2289	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	82.7618	1197	2289	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	82.5466	1248	2289	95	below_threshold
Streptomyces calvus	strain=JCM 4326	GCA_014649315.1	67282	67282	type	True	82.5186	1348	2289	95	below_threshold
Streptomyces griseosporeus	strain=JCM 4766	GCA_014656055.1	1910	1910	type	True	82.5178	1351	2289	95	below_threshold
Streptomyces calvus	strain=CECT 3271	GCA_014138735.1	67282	67282	type	True	82.4994	1365	2289	95	below_threshold
Streptomyces galbus	strain=JCM 4639	GCA_014650535.1	33898	33898	type	True	82.492	1333	2289	95	below_threshold
Streptomyces longwoodensis	strain=DSM 41677	GCA_001514125.1	68231	68231	type	True	82.4385	1377	2289	95	below_threshold
Streptomyces viridosporus	strain=NRRL 2414	GCA_002078235.1	67581	67581	type	True	82.3909	1162	2289	95	below_threshold
Streptomyces bauhiniae	strain=Bv016	GCA_004784475.1	2340725	2340725	type	True	82.2631	1202	2289	95	below_threshold
Streptomyces indiaensis	strain=DSM 43803	GCA_021474405.1	284033	284033	type	True	82.1033	1232	2289	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	81.7896	1298	2289	95	below_threshold
Streptomyces monashensis	strain=MUSC 1	GCA_001866665.1	1678012	1678012	type	True	81.67	1294	2289	95	below_threshold
Streptomyces avermitilis	strain=MA-4680	GCA_000009765.2	33903	33903	type	True	81.5924	1278	2289	95	below_threshold
Streptomyces avermitilis	strain=DSM 46492	GCA_001514135.1	33903	33903	type	True	81.571	1267	2289	95	below_threshold
Streptomyces avermitilis	strain=NBRC 14893	GCA_005405965.1	33903	33903	type	True	81.5329	1301	2289	95	below_threshold
Streptomyces deccanensis	strain=KCTC 19241	GCA_022385335.1	424188	424188	type	True	81.383	1328	2289	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:52:08,338] [INFO] DFAST Taxonomy check result was written to GCF_030135485.1_ASM3013548v1_genomic.fna/tc_result.tsv
[2024-01-24 13:52:08,339] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:52:08,339] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:52:08,339] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg18d9f282-a991-4f65-bc04-ffa857b1d7cf/dqc_reference/checkm_data
[2024-01-24 13:52:08,340] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:52:08,402] [INFO] Task started: CheckM
[2024-01-24 13:52:08,403] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030135485.1_ASM3013548v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030135485.1_ASM3013548v1_genomic.fna/checkm_input GCF_030135485.1_ASM3013548v1_genomic.fna/checkm_result
[2024-01-24 13:53:35,931] [INFO] Task succeeded: CheckM
[2024-01-24 13:53:35,933] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.48%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:53:35,957] [INFO] ===== Completeness check finished =====
[2024-01-24 13:53:35,958] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:53:35,958] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030135485.1_ASM3013548v1_genomic.fna/markers.fasta)
[2024-01-24 13:53:35,958] [INFO] Task started: Blastn
[2024-01-24 13:53:35,959] [INFO] Running command: blastn -query GCF_030135485.1_ASM3013548v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg18d9f282-a991-4f65-bc04-ffa857b1d7cf/dqc_reference/reference_markers_gtdb.fasta -out GCF_030135485.1_ASM3013548v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:53:38,176] [INFO] Task succeeded: Blastn
[2024-01-24 13:53:38,180] [INFO] Selected 17 target genomes.
[2024-01-24 13:53:38,180] [INFO] Target genome list was writen to GCF_030135485.1_ASM3013548v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:53:38,194] [INFO] Task started: fastANI
[2024-01-24 13:53:38,194] [INFO] Running command: fastANI --query /var/lib/cwl/stga9e8d084-d722-4665-81d9-e197b37ea06a/GCF_030135485.1_ASM3013548v1_genomic.fna.gz --refList GCF_030135485.1_ASM3013548v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030135485.1_ASM3013548v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:54:10,896] [INFO] Task succeeded: fastANI
[2024-01-24 13:54:10,913] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:54:10,913] [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_003112515.1	s__Streptomyces fragilis	99.9283	2267	2289	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001642695.1	s__Streptomyces chilikensis	89.4986	1702	2289	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008974245.1	s__Streptomyces abyssomicinicus	89.05	1781	2289	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000761215.1	s__Streptomyces glaucescens	82.5465	1362	2289	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	82.4806	1333	2289	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001514125.1	s__Streptomyces longwoodensis	82.4691	1370	2289	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.95	95.95	0.86	0.86	2	-
GCF_000383935.1	s__Streptomyces sp000383935	82.4161	1321	2289	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.62	97.70	0.92	0.84	4	-
GCF_013364255.1	s__Streptomyces seoulensis_A	82.4067	1369	2289	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004784475.1	s__Streptomyces bauhiniae	82.2429	1205	2289	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3953	95.70	95.47	0.88	0.84	6	-
GCF_000720185.1	s__Streptomyces sp000720185	82.232	1268	2289	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000373625.1	s__Streptomyces sp000373625	82.0817	1201	2289	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001280015.1	s__Streptomyces sp001280015	81.9036	1252	2289	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900236475.1	s__Streptomyces chartreusis_D	81.8721	1299	2289	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.98	1.00	1.00	4	-
GCF_004346005.1	s__Streptomyces sp004346005	81.7793	1342	2289	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000009765.2	s__Streptomyces avermitilis	81.5772	1280	2289	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.91	0.98	0.92	9	-
GCF_016598615.1	s__Streptomyces sp016598615	81.1174	1294	2289	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000317595.1	s__Streptomyces ipomoeae	81.1018	1158	2289	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.29	98.81	0.89	0.87	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:54:10,915] [INFO] GTDB search result was written to GCF_030135485.1_ASM3013548v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:54:10,915] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:54:10,919] [INFO] DFAST_QC result json was written to GCF_030135485.1_ASM3013548v1_genomic.fna/dqc_result.json
[2024-01-24 13:54:10,919] [INFO] DFAST_QC completed!
[2024-01-24 13:54:10,919] [INFO] Total running time: 0h3m1s