[2024-01-24 13:40:39,896] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:39,897] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:39,897] [INFO] DQC Reference Directory: /var/lib/cwl/stg794eaf3b-a2bc-45ac-a216-fd9ef22da934/dqc_reference
[2024-01-24 13:40:40,980] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:40,981] [INFO] Task started: Prodigal
[2024-01-24 13:40:40,981] [INFO] Running command: gunzip -c /var/lib/cwl/stge4193d6b-3d87-4697-8dac-6ea790384fd1/GCF_003721215.1_ASM372121v1_genomic.fna.gz | prodigal -d GCF_003721215.1_ASM372121v1_genomic.fna/cds.fna -a GCF_003721215.1_ASM372121v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:28,069] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:28,070] [INFO] Task started: HMMsearch
[2024-01-24 13:41:28,070] [INFO] Running command: hmmsearch --tblout GCF_003721215.1_ASM372121v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg794eaf3b-a2bc-45ac-a216-fd9ef22da934/dqc_reference/reference_markers.hmm GCF_003721215.1_ASM372121v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:28,458] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:28,459] [INFO] Found 6/6 markers.
[2024-01-24 13:41:28,541] [INFO] Query marker FASTA was written to GCF_003721215.1_ASM372121v1_genomic.fna/markers.fasta
[2024-01-24 13:41:28,541] [INFO] Task started: Blastn
[2024-01-24 13:41:28,541] [INFO] Running command: blastn -query GCF_003721215.1_ASM372121v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg794eaf3b-a2bc-45ac-a216-fd9ef22da934/dqc_reference/reference_markers.fasta -out GCF_003721215.1_ASM372121v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:29,813] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:29,816] [INFO] Selected 21 target genomes.
[2024-01-24 13:41:29,816] [INFO] Target genome list was writen to GCF_003721215.1_ASM372121v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:29,821] [INFO] Task started: fastANI
[2024-01-24 13:41:29,821] [INFO] Running command: fastANI --query /var/lib/cwl/stge4193d6b-3d87-4697-8dac-6ea790384fd1/GCF_003721215.1_ASM372121v1_genomic.fna.gz --refList GCF_003721215.1_ASM372121v1_genomic.fna/target_genomes.txt --output GCF_003721215.1_ASM372121v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:42:20,745] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:20,745] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg794eaf3b-a2bc-45ac-a216-fd9ef22da934/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:42:20,746] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg794eaf3b-a2bc-45ac-a216-fd9ef22da934/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:42:20,757] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:42:20,758] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:42:20,758] [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 sabulosicollis	strain=PRKS01-29	GCA_016103465.1	2715963	2715963	type	True	86.2627	1740	3248	95	below_threshold
Streptomyces yatensis	strain=DSM 41771	GCA_018069625.1	155177	155177	type	True	86.032	2060	3248	95	below_threshold
Streptomyces iranensis	strain=DSM 41954	GCA_017874715.1	576784	576784	type	True	86.0312	2107	3248	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_003675955.1	1226757	1226757	type	True	85.9889	2148	3248	95	below_threshold
Streptomyces rapamycinicus	strain=DSM 41530	GCA_014205315.1	1226757	1226757	type	True	85.9646	2157	3248	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_000418455.1	1226757	1226757	type	True	85.9236	2161	3248	95	below_threshold
Streptomyces antimycoticus	strain=NBRC 12839	GCA_005405925.1	68175	68175	type	True	85.9087	2102	3248	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_024298965.1	1226757	1226757	type	True	85.8888	2164	3248	95	below_threshold
Streptomyces hygroscopicus subsp. hygroscopicus	strain=NBRC 13472	GCA_001553455.1	68042	1912	type	True	85.8737	1725	3248	95	below_threshold
Streptomyces sparsogenes	strain=DSM 40356	GCA_001969965.1	67365	67365	type	True	84.4572	1597	3248	95	below_threshold
Streptomyces sparsogenes	strain=ATCC 25498	GCA_001704635.1	67365	67365	type	True	84.4133	1641	3248	95	below_threshold
Streptomyces syringium	strain=DSM 41480	GCA_017876625.1	76729	76729	type	True	81.8248	1266	3248	95	below_threshold
Streptomyces netropsis	strain=CECT 3265	GCA_014203545.1	55404	55404	type	True	81.7857	1292	3248	95	below_threshold
Streptomyces netropsis	strain=JCM 4063	GCA_014648835.1	55404	55404	type	True	81.7711	1270	3248	95	below_threshold
Streptomyces pactum	strain=ATCC 27456	GCA_016031615.1	68249	68249	type	True	81.59	1347	3248	95	below_threshold
Streptomyces albireticuli	strain=NRRL B1670	GCA_021228125.1	1940	1940	type	True	81.3759	1293	3248	95	below_threshold
Streptomyces monomycini	strain=NRRL B-24309	GCA_022271435.1	371720	371720	type	True	81.2327	1363	3248	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=R7	GCA_022760195.1	132474	1927	type	True	81.1762	1400	3248	95	below_threshold
Streptomyces huiliensis	strain=SCA2-4	GCA_020037025.1	2876027	2876027	type	True	81.0805	1111	3248	95	below_threshold
Streptomyces galbus	strain=JCM 4639	GCA_014650535.1	33898	33898	type	True	80.5339	1271	3248	95	below_threshold
Streptomyces spectabilis	strain=KCTC9218	GCA_022698305.1	68270	68270	type	True	80.5309	1381	3248	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:42:20,759] [INFO] DFAST Taxonomy check result was written to GCF_003721215.1_ASM372121v1_genomic.fna/tc_result.tsv
[2024-01-24 13:42:20,759] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:42:20,760] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:42:20,760] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg794eaf3b-a2bc-45ac-a216-fd9ef22da934/dqc_reference/checkm_data
[2024-01-24 13:42:20,761] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:42:20,860] [INFO] Task started: CheckM
[2024-01-24 13:42:20,860] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003721215.1_ASM372121v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003721215.1_ASM372121v1_genomic.fna/checkm_input GCF_003721215.1_ASM372121v1_genomic.fna/checkm_result
[2024-01-24 13:45:19,385] [INFO] Task succeeded: CheckM
[2024-01-24 13:45:19,386] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:45:19,406] [INFO] ===== Completeness check finished =====
[2024-01-24 13:45:19,406] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:45:19,406] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003721215.1_ASM372121v1_genomic.fna/markers.fasta)
[2024-01-24 13:45:19,406] [INFO] Task started: Blastn
[2024-01-24 13:45:19,406] [INFO] Running command: blastn -query GCF_003721215.1_ASM372121v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg794eaf3b-a2bc-45ac-a216-fd9ef22da934/dqc_reference/reference_markers_gtdb.fasta -out GCF_003721215.1_ASM372121v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:45:21,406] [INFO] Task succeeded: Blastn
[2024-01-24 13:45:21,409] [INFO] Selected 16 target genomes.
[2024-01-24 13:45:21,409] [INFO] Target genome list was writen to GCF_003721215.1_ASM372121v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:45:21,484] [INFO] Task started: fastANI
[2024-01-24 13:45:21,484] [INFO] Running command: fastANI --query /var/lib/cwl/stge4193d6b-3d87-4697-8dac-6ea790384fd1/GCF_003721215.1_ASM372121v1_genomic.fna.gz --refList GCF_003721215.1_ASM372121v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003721215.1_ASM372121v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:46:03,417] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:03,427] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:46:03,427] [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_000158915.1	s__Streptomyces himastatinicus	95.4132	2651	3248	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.59	95.41	0.86	0.82	5	conclusive
GCF_001417735.1	s__Streptomyces sp001417735	92.3845	2122	3248	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005405945.1	s__Streptomyces violaceusniger	86.1678	2114	3248	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.67	97.67	0.85	0.85	2	-
GCF_018138715.1	s__Streptomyces asiaticus	86.0367	2144	3248	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.17	95.36	0.90	0.81	10	-
GCF_003675955.1	s__Streptomyces rapamycinicus	85.97	2154	3248	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.67	99.95	99.91	0.99	0.99	3	-
GCF_016741935.1	s__Streptomyces sp016741935	85.94	2130	3248	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0488	N/A	N/A	N/A	N/A	1	-
GCF_005405925.1	s__Streptomyces antimycoticus	85.9224	2097	3248	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.0185	97.28	96.80	0.85	0.81	7	-
GCF_000147815.2	s__Streptomyces violaceusniger_A	85.8841	2048	3248	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3301	95.69	95.54	0.80	0.80	4	-
GCF_001553455.1	s__Streptomyces hygroscopicus	85.8574	1728	3248	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.24	98.00	0.92	0.90	7	-
GCF_013364155.1	s__Streptomyces sp013364155	85.5806	1722	3248	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016741875.1	s__Streptomyces coffeae	85.1938	1789	3248	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001704635.1	s__Streptomyces sparsogenes	84.4703	1630	3248	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.81	99.81	0.87	0.87	2	-
GCF_018614525.1	s__Streptomyces sp018614525	81.8567	1119	3248	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876625.1	s__Streptomyces syringium	81.7904	1273	3248	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.60	99.60	0.98	0.98	2	-
GCF_014203545.1	s__Streptomyces netropsis	81.7887	1292	3248	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001590865.1	s__Streptomyces sp001590865	81.0883	1195	3248	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 13:46:03,429] [INFO] GTDB search result was written to GCF_003721215.1_ASM372121v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:46:03,430] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:46:03,433] [INFO] DFAST_QC result json was written to GCF_003721215.1_ASM372121v1_genomic.fna/dqc_result.json
[2024-01-24 13:46:03,434] [INFO] DFAST_QC completed!
[2024-01-24 13:46:03,434] [INFO] Total running time: 0h5m24s