[2024-01-24 13:55:48,425] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:48,433] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:48,434] [INFO] DQC Reference Directory: /var/lib/cwl/stg29015f18-5210-40a8-8cf4-581a9fa71a47/dqc_reference
[2024-01-24 13:55:49,826] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:49,827] [INFO] Task started: Prodigal
[2024-01-24 13:55:49,827] [INFO] Running command: gunzip -c /var/lib/cwl/stgcd995aec-5ce6-402f-a587-207b729e17b1/GCF_008704795.1_ASM870479v1_genomic.fna.gz | prodigal -d GCF_008704795.1_ASM870479v1_genomic.fna/cds.fna -a GCF_008704795.1_ASM870479v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:22,409] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:22,409] [INFO] Task started: HMMsearch
[2024-01-24 13:56:22,410] [INFO] Running command: hmmsearch --tblout GCF_008704795.1_ASM870479v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg29015f18-5210-40a8-8cf4-581a9fa71a47/dqc_reference/reference_markers.hmm GCF_008704795.1_ASM870479v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:22,801] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:22,802] [INFO] Found 6/6 markers.
[2024-01-24 13:56:22,876] [INFO] Query marker FASTA was written to GCF_008704795.1_ASM870479v1_genomic.fna/markers.fasta
[2024-01-24 13:56:22,876] [INFO] Task started: Blastn
[2024-01-24 13:56:22,876] [INFO] Running command: blastn -query GCF_008704795.1_ASM870479v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg29015f18-5210-40a8-8cf4-581a9fa71a47/dqc_reference/reference_markers.fasta -out GCF_008704795.1_ASM870479v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:24,128] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:24,138] [INFO] Selected 13 target genomes.
[2024-01-24 13:56:24,139] [INFO] Target genome list was writen to GCF_008704795.1_ASM870479v1_genomic.fna/target_genomes.txt
[2024-01-24 13:56:24,152] [INFO] Task started: fastANI
[2024-01-24 13:56:24,152] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd995aec-5ce6-402f-a587-207b729e17b1/GCF_008704795.1_ASM870479v1_genomic.fna.gz --refList GCF_008704795.1_ASM870479v1_genomic.fna/target_genomes.txt --output GCF_008704795.1_ASM870479v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:00,604] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:00,605] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg29015f18-5210-40a8-8cf4-581a9fa71a47/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:00,605] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg29015f18-5210-40a8-8cf4-581a9fa71a47/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:00,622] [INFO] Found 13 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:57:00,623] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:00,623] [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 spectabilis	strain=ATCC 27465	GCA_008704795.1	68270	68270	type	True	100.0	3268	3269	95	conclusive
Streptomyces spectabilis	strain=KCTC9218	GCA_022698305.1	68270	68270	type	True	99.9989	3263	3269	95	conclusive
Streptomyces spectabilis	strain=CECT 3146	GCA_014203475.1	68270	68270	type	True	99.9903	3230	3269	95	conclusive
Streptomyces spectabilis	strain=JCM 4308	GCA_014649235.1	68270	68270	type	True	99.9837	3222	3269	95	conclusive
Streptomyces longispororuber	strain=JCM 4784	GCA_014656095.1	68230	68230	type	True	88.5292	2136	3269	95	below_threshold
Streptomyces aureoverticillatus	strain=JCM 4347	GCA_014649395.1	66871	66871	type	True	86.858	2229	3269	95	below_threshold
Streptomyces atriruber	strain=NRRL B-24165	GCA_001418325.1	545121	545121	type	True	84.3875	1767	3269	95	below_threshold
Streptomyces durmitorensis	strain=MS405	GCA_023498005.1	319947	319947	type	True	84.0013	2000	3269	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	82.218	1372	3269	95	below_threshold
Streptomyces ardesiacus	strain=NBRC 15402	GCA_003112575.1	285564	285564	type	True	82.2085	1552	3269	95	below_threshold
Streptomyces fumigatiscleroticus	strain=JCM 3101	GCA_014647975.1	66371	66371	type	True	82.1192	1581	3269	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	81.9287	1463	3269	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	81.8189	1710	3269	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:00,627] [INFO] DFAST Taxonomy check result was written to GCF_008704795.1_ASM870479v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:00,630] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:00,631] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:00,631] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg29015f18-5210-40a8-8cf4-581a9fa71a47/dqc_reference/checkm_data
[2024-01-24 13:57:00,633] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:00,726] [INFO] Task started: CheckM
[2024-01-24 13:57:00,726] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008704795.1_ASM870479v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008704795.1_ASM870479v1_genomic.fna/checkm_input GCF_008704795.1_ASM870479v1_genomic.fna/checkm_result
[2024-01-24 13:59:37,905] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:37,906] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 9.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:37,935] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:37,936] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:37,937] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008704795.1_ASM870479v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:37,937] [INFO] Task started: Blastn
[2024-01-24 13:59:37,937] [INFO] Running command: blastn -query GCF_008704795.1_ASM870479v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg29015f18-5210-40a8-8cf4-581a9fa71a47/dqc_reference/reference_markers_gtdb.fasta -out GCF_008704795.1_ASM870479v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:40,072] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:40,076] [INFO] Selected 14 target genomes.
[2024-01-24 13:59:40,076] [INFO] Target genome list was writen to GCF_008704795.1_ASM870479v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:40,106] [INFO] Task started: fastANI
[2024-01-24 13:59:40,106] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd995aec-5ce6-402f-a587-207b729e17b1/GCF_008704795.1_ASM870479v1_genomic.fna.gz --refList GCF_008704795.1_ASM870479v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008704795.1_ASM870479v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:19,541] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:19,556] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:19,557] [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_008704795.1	s__Streptomyces spectabilis	100.0	3268	3269	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.73	96.21	0.96	0.90	4	conclusive
GCF_000720325.1	s__Streptomyces sp000720325	94.4241	2735	3269	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006088715.1	s__Streptomyces sp006088715	93.0635	2803	3269	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.04	98.04	0.88	0.88	2	-
GCF_014656095.1	s__Streptomyces longispororuber	88.4965	2140	3269	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649395.1	s__Streptomyces aureoverticillatus	86.8202	2236	3269	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000414115.1	s__Streptomyces aurantiacus_A	86.8151	2005	3269	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418325.1	s__Streptomyces atriruber	84.4199	1759	3269	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008642355.1	s__Streptomyces venezuelae_B	84.3708	1861	3269	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.58	99.56	0.88	0.87	4	-
GCA_000720845.1	s__Streptomyces sp000720845	82.346	1545	3269	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003112575.1	s__Streptomyces ardesiacus	82.2367	1546	3269	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.97	95.84	0.93	0.82	10	-
GCF_001513975.1	s__Streptomyces curacoi	82.1303	1601	3269	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.35	97.22	0.89	0.84	4	-
GCF_007176755.1	s__Streptomyces sp007176755	82.1229	1495	3269	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	82.1126	1582	3269	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016919245.1	s__Streptomyces zhihengii	81.3319	1573	3269	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 14:00:19,559] [INFO] GTDB search result was written to GCF_008704795.1_ASM870479v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:19,559] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:19,585] [INFO] DFAST_QC result json was written to GCF_008704795.1_ASM870479v1_genomic.fna/dqc_result.json
[2024-01-24 14:00:19,585] [INFO] DFAST_QC completed!
[2024-01-24 14:00:19,585] [INFO] Total running time: 0h4m31s