[2024-01-24 14:55:27,060] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:27,061] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:27,062] [INFO] DQC Reference Directory: /var/lib/cwl/stg2d83c88a-8c5a-4094-8a54-afebe2b3ddbb/dqc_reference
[2024-01-24 14:55:28,409] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:28,424] [INFO] Task started: Prodigal
[2024-01-24 14:55:28,425] [INFO] Running command: gunzip -c /var/lib/cwl/stg34d2689b-f438-4638-b108-e4e38119b038/GCF_007829885.1_ASM782988v1_genomic.fna.gz | prodigal -d GCF_007829885.1_ASM782988v1_genomic.fna/cds.fna -a GCF_007829885.1_ASM782988v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:50,534] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:50,534] [INFO] Task started: HMMsearch
[2024-01-24 14:55:50,534] [INFO] Running command: hmmsearch --tblout GCF_007829885.1_ASM782988v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2d83c88a-8c5a-4094-8a54-afebe2b3ddbb/dqc_reference/reference_markers.hmm GCF_007829885.1_ASM782988v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:50,831] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:50,832] [INFO] Found 6/6 markers.
[2024-01-24 14:55:50,888] [INFO] Query marker FASTA was written to GCF_007829885.1_ASM782988v1_genomic.fna/markers.fasta
[2024-01-24 14:55:50,888] [INFO] Task started: Blastn
[2024-01-24 14:55:50,888] [INFO] Running command: blastn -query GCF_007829885.1_ASM782988v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d83c88a-8c5a-4094-8a54-afebe2b3ddbb/dqc_reference/reference_markers.fasta -out GCF_007829885.1_ASM782988v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:52,253] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:52,257] [INFO] Selected 15 target genomes.
[2024-01-24 14:55:52,257] [INFO] Target genome list was writen to GCF_007829885.1_ASM782988v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:52,266] [INFO] Task started: fastANI
[2024-01-24 14:55:52,266] [INFO] Running command: fastANI --query /var/lib/cwl/stg34d2689b-f438-4638-b108-e4e38119b038/GCF_007829885.1_ASM782988v1_genomic.fna.gz --refList GCF_007829885.1_ASM782988v1_genomic.fna/target_genomes.txt --output GCF_007829885.1_ASM782988v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:56:20,121] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:20,121] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2d83c88a-8c5a-4094-8a54-afebe2b3ddbb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:56:20,121] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2d83c88a-8c5a-4094-8a54-afebe2b3ddbb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:56:20,134] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:56:20,134] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:56:20,135] [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 brevispora	strain=DSM 42059	GCA_007829885.1	887462	887462	type	True	100.0	2512	2512	95	conclusive
Streptomyces poriferorum	strain=P01-B04	GCA_019399235.1	2798799	2798799	type	True	89.0188	1666	2512	95	below_threshold
Streptomyces atratus	strain=JCM 3386	GCA_014648655.1	1893	1893	suspected-type	True	87.0204	1733	2512	95	below_threshold
Streptomyces gelaticus	strain=JCM 4376	GCA_014649535.1	285446	285446	type	True	86.9765	1644	2512	95	below_threshold
Streptomyces fulvorobeus	strain=DSM 41455	GCA_013409565.1	284028	284028	type	True	85.183	1412	2512	95	below_threshold
Streptomyces clavifer	strain=DSM 40843	GCA_017876255.1	68188	68188	type	True	85.0924	1596	2512	95	below_threshold
Streptomyces clavifer	strain=JCM 5059	GCA_014651175.1	68188	68188	type	True	85.0168	1582	2512	95	below_threshold
Streptomyces microflavus	strain=JCM 4496	GCA_014650075.1	1919	1919	type	True	84.8992	1621	2512	95	below_threshold
Streptomyces griseolus	strain=NRRL B-2925	GCA_000721185.1	1909	1909	type	True	84.7671	1502	2512	95	below_threshold
Streptomyces rhizosphaericola	strain=1AS2c	GCA_004794175.1	2564098	2564098	type	True	84.72	1297	2512	95	below_threshold
[Kitasatospora] papulosa	strain=NRRL B-16504	GCA_000717245.1	1464011	1464011	type	True	84.6264	1548	2512	95	below_threshold
Streptomyces nitrosporeus	strain=ATCC 12769	GCA_008704555.1	28894	28894	type	True	84.236	1499	2512	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	82.8579	1389	2512	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	81.8242	1016	2512	95	below_threshold
Streptomyces caniscabiei	strain=NE06-02D	GCA_014930365.1	2746961	2746961	type	True	81.0247	1332	2512	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:56:20,136] [INFO] DFAST Taxonomy check result was written to GCF_007829885.1_ASM782988v1_genomic.fna/tc_result.tsv
[2024-01-24 14:56:20,137] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:56:20,137] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:56:20,137] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2d83c88a-8c5a-4094-8a54-afebe2b3ddbb/dqc_reference/checkm_data
[2024-01-24 14:56:20,138] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:56:20,207] [INFO] Task started: CheckM
[2024-01-24 14:56:20,208] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007829885.1_ASM782988v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007829885.1_ASM782988v1_genomic.fna/checkm_input GCF_007829885.1_ASM782988v1_genomic.fna/checkm_result
[2024-01-24 14:58:17,667] [INFO] Task succeeded: CheckM
[2024-01-24 14:58:17,667] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:58:17,687] [INFO] ===== Completeness check finished =====
[2024-01-24 14:58:17,687] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:58:17,687] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007829885.1_ASM782988v1_genomic.fna/markers.fasta)
[2024-01-24 14:58:17,688] [INFO] Task started: Blastn
[2024-01-24 14:58:17,688] [INFO] Running command: blastn -query GCF_007829885.1_ASM782988v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d83c88a-8c5a-4094-8a54-afebe2b3ddbb/dqc_reference/reference_markers_gtdb.fasta -out GCF_007829885.1_ASM782988v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:58:19,834] [INFO] Task succeeded: Blastn
[2024-01-24 14:58:19,841] [INFO] Selected 6 target genomes.
[2024-01-24 14:58:19,841] [INFO] Target genome list was writen to GCF_007829885.1_ASM782988v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:58:19,848] [INFO] Task started: fastANI
[2024-01-24 14:58:19,849] [INFO] Running command: fastANI --query /var/lib/cwl/stg34d2689b-f438-4638-b108-e4e38119b038/GCF_007829885.1_ASM782988v1_genomic.fna.gz --refList GCF_007829885.1_ASM782988v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007829885.1_ASM782988v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:58:33,099] [INFO] Task succeeded: fastANI
[2024-01-24 14:58:33,106] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:58:33,106] [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_007829885.1	s__Streptomyces brevispora	100.0	2511	2512	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_017353455.1	s__Streptomyces laculatispora	92.7017	1502	2512	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.54	97.53	0.87	0.87	3	-
GCF_001905365.1	s__Streptomyces sp001905365	91.2215	1898	2512	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003751445.1	s__Streptomyces sp003751445	91.1518	1914	2512	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000470535.1	s__Streptomyces sp000470535	91.0893	1696	2512	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008042275.1	s__Streptomyces sp008042275	89.017	1842	2512	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 14:58:33,108] [INFO] GTDB search result was written to GCF_007829885.1_ASM782988v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:58:33,108] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:58:33,111] [INFO] DFAST_QC result json was written to GCF_007829885.1_ASM782988v1_genomic.fna/dqc_result.json
[2024-01-24 14:58:33,112] [INFO] DFAST_QC completed!
[2024-01-24 14:58:33,112] [INFO] Total running time: 0h3m6s