[2024-01-24 14:06:30,201] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:30,202] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:30,202] [INFO] DQC Reference Directory: /var/lib/cwl/stg310a5680-a2a9-455e-9fcb-14823b072fd2/dqc_reference
[2024-01-24 14:06:31,558] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:31,559] [INFO] Task started: Prodigal
[2024-01-24 14:06:31,560] [INFO] Running command: gunzip -c /var/lib/cwl/stg3a53a8d0-5ce7-47c8-a9a8-5a1b7843912f/GCF_003429565.1_ASM342956v1_genomic.fna.gz | prodigal -d GCF_003429565.1_ASM342956v1_genomic.fna/cds.fna -a GCF_003429565.1_ASM342956v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:52,328] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:52,328] [INFO] Task started: HMMsearch
[2024-01-24 14:06:52,328] [INFO] Running command: hmmsearch --tblout GCF_003429565.1_ASM342956v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg310a5680-a2a9-455e-9fcb-14823b072fd2/dqc_reference/reference_markers.hmm GCF_003429565.1_ASM342956v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:52,627] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:52,628] [INFO] Found 6/6 markers.
[2024-01-24 14:06:52,686] [INFO] Query marker FASTA was written to GCF_003429565.1_ASM342956v1_genomic.fna/markers.fasta
[2024-01-24 14:06:52,686] [INFO] Task started: Blastn
[2024-01-24 14:06:52,686] [INFO] Running command: blastn -query GCF_003429565.1_ASM342956v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg310a5680-a2a9-455e-9fcb-14823b072fd2/dqc_reference/reference_markers.fasta -out GCF_003429565.1_ASM342956v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:53,909] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:53,912] [INFO] Selected 29 target genomes.
[2024-01-24 14:06:53,912] [INFO] Target genome list was writen to GCF_003429565.1_ASM342956v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:53,923] [INFO] Task started: fastANI
[2024-01-24 14:06:53,923] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a53a8d0-5ce7-47c8-a9a8-5a1b7843912f/GCF_003429565.1_ASM342956v1_genomic.fna.gz --refList GCF_003429565.1_ASM342956v1_genomic.fna/target_genomes.txt --output GCF_003429565.1_ASM342956v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:07:46,181] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:46,181] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg310a5680-a2a9-455e-9fcb-14823b072fd2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:07:46,182] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg310a5680-a2a9-455e-9fcb-14823b072fd2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:07:46,205] [INFO] Found 29 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:07:46,205] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:07:46,205] [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 triticagri	strain=NEAU-YY421	GCA_003429565.1	2293568	2293568	type	True	100.0	2344	2370	95	conclusive
Streptomyces boluensis	strain=YC537	GCA_009908195.1	1775135	1775135	type	True	83.0874	1282	2370	95	below_threshold
Streptomyces silaceus	strain=NRRL B-24166	GCA_001419745.1	545123	545123	type	True	82.4318	1266	2370	95	below_threshold
Streptomyces apocyni	strain=TRM 66233	GCA_009739465.1	2654677	2654677	type	True	82.3895	1232	2370	95	below_threshold
Streptomyces mesophilus	strain=YC504	GCA_011044995.1	1775132	1775132	type	True	82.0267	1365	2370	95	below_threshold
Streptomyces polyasparticus	strain=TRM66268-LWL	GCA_014493765.1	2767826	2767826	type	True	81.9372	1438	2370	95	below_threshold
Streptomyces spectabilis	strain=KCTC9218	GCA_022698305.1	68270	68270	type	True	81.8467	1403	2370	95	below_threshold
Streptomyces longispororuber	strain=JCM 4784	GCA_014656095.1	68230	68230	type	True	81.7115	1312	2370	95	below_threshold
Streptomyces himalayensis subsp. himalayensis	strain=PSKA28	GCA_013778455.1	2756131	2820085	type	True	81.6939	1255	2370	95	below_threshold
Streptomyces minutiscleroticus	strain=JCM 4790	GCA_014650875.1	68238	68238	type	True	81.5862	1298	2370	95	below_threshold
Streptomyces murinus	strain=NRRL B-2286	GCA_002154555.1	33900	33900	type	True	81.5381	1003	2370	95	below_threshold
Streptomyces galbus	strain=DSM 40089	GCA_005280195.1	33898	33898	type	True	81.4215	1232	2370	95	below_threshold
Streptomyces griseoluteus	strain=JCM 4765	GCA_004784465.1	29306	29306	type	True	81.4093	1110	2370	95	below_threshold
Streptomyces longwoodensis	strain=DSM 41677	GCA_001514125.1	68231	68231	type	True	81.3924	1250	2370	95	below_threshold
Streptomyces galbus	strain=JCM 4639	GCA_014650535.1	33898	33898	type	True	81.3887	1230	2370	95	below_threshold
Streptomyces griseoluteus	strain=JCM 4765	GCA_014656035.1	29306	29306	type	True	81.3804	1112	2370	95	below_threshold
Streptomyces spinoverrucosus	strain=NBRC 14228	GCA_006539505.1	284043	284043	type	True	81.3798	1277	2370	95	below_threshold
Streptomyces spinoverrucosus	strain=JCM 5077	GCA_014651195.1	284043	284043	type	True	81.3417	1312	2370	95	below_threshold
Streptomyces kebangsaanensis	strain=SUK12	GCA_001906585.1	864058	864058	type	True	81.3163	1175	2370	95	below_threshold
Streptomyces brasiliensis	strain=JCM 3086	GCA_014647875.1	1954	1954	type	True	81.2801	1231	2370	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	81.2545	1131	2370	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	81.2352	1192	2370	95	below_threshold
Streptomyces diastaticus subsp. diastaticus	strain=JCM 4128	GCA_014648935.1	68040	1956	suspected-type	True	81.2102	1131	2370	95	below_threshold
Streptomyces griseofuscus	strain=NRRL B-5429	GCA_000718315.1	146922	146922	type	True	81.2074	1205	2370	95	below_threshold
Streptomyces torulosus	strain=NRRL B-3889	GCA_001419765.1	68276	68276	type	True	81.1885	1095	2370	95	below_threshold
Streptomyces gougerotii	strain=NBRC 13043	GCA_011170145.1	53448	53448	suspected-type	True	81.1656	1146	2370	95	below_threshold
Streptomyces gougerotii	strain=JCM 4136	GCA_014648955.1	53448	53448	suspected-type	True	81.165	1143	2370	95	below_threshold
Streptomyces rishiriensis	strain=NBRC 13407	GCA_003112535.1	68264	68264	type	True	81.1645	1218	2370	95	below_threshold
Streptomyces filipinensis	strain=JCM 4369	GCA_014649495.1	66887	66887	type	True	81.1524	1252	2370	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:07:46,207] [INFO] DFAST Taxonomy check result was written to GCF_003429565.1_ASM342956v1_genomic.fna/tc_result.tsv
[2024-01-24 14:07:46,207] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:07:46,207] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:07:46,207] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg310a5680-a2a9-455e-9fcb-14823b072fd2/dqc_reference/checkm_data
[2024-01-24 14:07:46,209] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:07:46,282] [INFO] Task started: CheckM
[2024-01-24 14:07:46,283] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003429565.1_ASM342956v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003429565.1_ASM342956v1_genomic.fna/checkm_input GCF_003429565.1_ASM342956v1_genomic.fna/checkm_result
[2024-01-24 14:09:31,084] [INFO] Task succeeded: CheckM
[2024-01-24 14:09:31,085] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:09:31,107] [INFO] ===== Completeness check finished =====
[2024-01-24 14:09:31,107] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:09:31,108] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003429565.1_ASM342956v1_genomic.fna/markers.fasta)
[2024-01-24 14:09:31,108] [INFO] Task started: Blastn
[2024-01-24 14:09:31,108] [INFO] Running command: blastn -query GCF_003429565.1_ASM342956v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg310a5680-a2a9-455e-9fcb-14823b072fd2/dqc_reference/reference_markers_gtdb.fasta -out GCF_003429565.1_ASM342956v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:09:33,045] [INFO] Task succeeded: Blastn
[2024-01-24 14:09:33,049] [INFO] Selected 21 target genomes.
[2024-01-24 14:09:33,049] [INFO] Target genome list was writen to GCF_003429565.1_ASM342956v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:09:33,071] [INFO] Task started: fastANI
[2024-01-24 14:09:33,071] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a53a8d0-5ce7-47c8-a9a8-5a1b7843912f/GCF_003429565.1_ASM342956v1_genomic.fna.gz --refList GCF_003429565.1_ASM342956v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003429565.1_ASM342956v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:10:11,280] [INFO] Task succeeded: fastANI
[2024-01-24 14:10:11,296] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:10:11,297] [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_003429565.1	s__Streptomyces triticagri	100.0	2344	2370	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_003574445.1	s__Streptomyces sp003574445	89.2927	1939	2370	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009908195.1	s__Streptomyces boluensis	83.0713	1285	2370	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001419745.1	s__Streptomyces silaceus	82.4542	1263	2370	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.58	99.58	0.96	0.96	2	-
GCF_900100315.1	s__Streptomyces indicus	82.214	1466	2370	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004127445.1	s__Streptomyces alfalfae	82.0688	1343	2370	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.46	98.55	0.94	0.88	8	-
GCF_014493765.1	s__Streptomyces polyasparticus	81.9471	1434	2370	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014655195.1	s__Streptomyces cellulosae	81.6882	1233	2370	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.05	95.87	0.87	0.85	11	-
GCF_003403055.1	s__Streptomyces sp003403055	81.6757	1439	2370	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009755605.1	s__Streptomyces typhae	81.6431	1391	2370	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.66	98.66	0.93	0.93	2	-
GCF_014650875.1	s__Streptomyces minutiscleroticus	81.5647	1302	2370	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.56	98.56	0.90	0.90	2	-
GCF_002154555.1	s__Streptomyces murinus	81.5513	1001	2370	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	97.0065	97.48	97.10	0.91	0.89	7	-
GCA_014649355.1	s__Streptomyces althioticus	81.5428	1271	2370	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.374	98.43	96.72	0.91	0.83	9	-
GCF_000444875.1	s__Streptomyces collinus_A	81.5293	1228	2370	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.10	97.10	0.84	0.84	2	-
GCF_007679425.1	s__Streptomyces incarnatus_A	81.4865	1154	2370	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.50	99.00	0.97	0.94	3	-
GCF_900091725.1	s__Streptomyces sp900091725	81.3728	1277	2370	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_019090105.1	s__Streptomyces sp019090105	81.3713	1133	2370	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857135.1	s__Streptomyces sp009857135	81.3689	1235	2370	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105245.1	s__Streptomyces sp900105245	81.3125	1269	2370	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.80	95.98	0.93	0.89	5	-
GCF_009604455.1	s__Streptomyces sp009604455	81.2353	1276	2370	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011170125.1	s__Streptomyces diastaticus	81.1708	1159	2370	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.51	98.72	0.93	0.90	11	-
--------------------------------------------------------------------------------
[2024-01-24 14:10:11,298] [INFO] GTDB search result was written to GCF_003429565.1_ASM342956v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:10:11,299] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:10:11,303] [INFO] DFAST_QC result json was written to GCF_003429565.1_ASM342956v1_genomic.fna/dqc_result.json
[2024-01-24 14:10:11,303] [INFO] DFAST_QC completed!
[2024-01-24 14:10:11,303] [INFO] Total running time: 0h3m41s