[2024-01-24 11:05:25,347] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:25,351] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:25,352] [INFO] DQC Reference Directory: /var/lib/cwl/stg37368653-4461-4e6d-91ec-eaba2bec92ae/dqc_reference
[2024-01-24 11:05:26,738] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:26,739] [INFO] Task started: Prodigal
[2024-01-24 11:05:26,739] [INFO] Running command: gunzip -c /var/lib/cwl/stg38b8f2bc-aa18-450a-813f-f3943eb998e2/GCF_003323735.1_ASM332373v1_genomic.fna.gz | prodigal -d GCF_003323735.1_ASM332373v1_genomic.fna/cds.fna -a GCF_003323735.1_ASM332373v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:49,083] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:49,084] [INFO] Task started: HMMsearch
[2024-01-24 11:05:49,084] [INFO] Running command: hmmsearch --tblout GCF_003323735.1_ASM332373v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg37368653-4461-4e6d-91ec-eaba2bec92ae/dqc_reference/reference_markers.hmm GCF_003323735.1_ASM332373v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:49,429] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:49,431] [INFO] Found 6/6 markers.
[2024-01-24 11:05:49,488] [INFO] Query marker FASTA was written to GCF_003323735.1_ASM332373v1_genomic.fna/markers.fasta
[2024-01-24 11:05:49,489] [INFO] Task started: Blastn
[2024-01-24 11:05:49,489] [INFO] Running command: blastn -query GCF_003323735.1_ASM332373v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg37368653-4461-4e6d-91ec-eaba2bec92ae/dqc_reference/reference_markers.fasta -out GCF_003323735.1_ASM332373v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:50,844] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:50,848] [INFO] Selected 19 target genomes.
[2024-01-24 11:05:50,849] [INFO] Target genome list was writen to GCF_003323735.1_ASM332373v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:50,857] [INFO] Task started: fastANI
[2024-01-24 11:05:50,858] [INFO] Running command: fastANI --query /var/lib/cwl/stg38b8f2bc-aa18-450a-813f-f3943eb998e2/GCF_003323735.1_ASM332373v1_genomic.fna.gz --refList GCF_003323735.1_ASM332373v1_genomic.fna/target_genomes.txt --output GCF_003323735.1_ASM332373v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:25,718] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:25,719] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg37368653-4461-4e6d-91ec-eaba2bec92ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:25,719] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg37368653-4461-4e6d-91ec-eaba2bec92ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:25,739] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:06:25,739] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:06:25,739] [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 reniochalinae	strain=LHW50302	GCA_003323735.1	2250578	2250578	type	True	100.0	2527	2531	95	conclusive
Streptomyces diacarni	strain=LHW51701	GCA_003323715.1	2800381	2800381	type	True	94.3207	2143	2531	95	below_threshold
Streptomyces albus	strain=NBRC 13014	GCA_000813365.1	1888	1888	suspected-type	True	85.7424	1661	2531	95	below_threshold
Streptomyces albus subsp. albus	strain=NRRL B-1811	GCA_000725885.1	67257	1888	suspected-type	True	85.6665	1683	2531	95	below_threshold
Streptomyces smyrnaeus	strain=DSM 42105	GCA_017676345.1	1387713	1387713	type	True	85.15	1728	2531	95	below_threshold
Streptomyces oryzae	strain=S16-07	GCA_017676365.1	1434886	1434886	type	True	85.125	1511	2531	95	below_threshold
Streptomyces spirodelae	strain=DW4-2	GCA_017676385.1	2812904	2812904	type	True	84.9862	1580	2531	95	below_threshold
Streptomyces qinglanensis	strain=CGMCC 4.6825	GCA_900111245.1	943816	943816	type	True	84.7068	1585	2531	95	below_threshold
Streptomyces qinglanensis	strain=172205	GCA_003265665.1	943816	943816	type	True	84.6768	1593	2531	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=R7	GCA_022760195.1	132474	1927	type	True	80.1703	1236	2531	95	below_threshold
Streptomyces monomycini	strain=NRRL B-24309	GCA_022271435.1	371720	371720	type	True	80.1498	1192	2531	95	below_threshold
Streptomyces paromomycinus	strain=NBRC 15454	GCA_003865155.1	92743	92743	type	True	80.116	1234	2531	95	below_threshold
Streptomyces gobiensis	strain=1_25	GCA_021216675.1	2875706	2875706	type	True	80.0616	868	2531	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_024298965.1	1226757	1226757	type	True	79.7595	1221	2531	95	below_threshold
Streptomyces bungoensis	strain=DSM 41781	GCA_001514215.1	285568	285568	type	True	79.6825	1120	2531	95	below_threshold
Streptomyces nymphaeiformis	strain=SFB5A	GCA_014203895.1	2663842	2663842	type	True	79.5614	1103	2531	95	below_threshold
Streptomyces alanosinicus	strain=JCM 4714	GCA_014650595.1	68171	68171	type	True	79.2997	1130	2531	95	below_threshold
Microtetraspora niveoalba	strain=NBRC 15239	GCA_001570405.1	46175	46175	type	True	76.5953	643	2531	95	below_threshold
Microbispora cellulosiformans	strain=Gxj-6	GCA_008728085.1	2614688	2614688	type	True	76.5212	578	2531	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:25,741] [INFO] DFAST Taxonomy check result was written to GCF_003323735.1_ASM332373v1_genomic.fna/tc_result.tsv
[2024-01-24 11:06:25,741] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:25,742] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:25,742] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg37368653-4461-4e6d-91ec-eaba2bec92ae/dqc_reference/checkm_data
[2024-01-24 11:06:25,743] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:25,816] [INFO] Task started: CheckM
[2024-01-24 11:06:25,817] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003323735.1_ASM332373v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003323735.1_ASM332373v1_genomic.fna/checkm_input GCF_003323735.1_ASM332373v1_genomic.fna/checkm_result
[2024-01-24 11:08:16,886] [INFO] Task succeeded: CheckM
[2024-01-24 11:08:16,889] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 9.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:08:16,916] [INFO] ===== Completeness check finished =====
[2024-01-24 11:08:16,917] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:08:16,917] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003323735.1_ASM332373v1_genomic.fna/markers.fasta)
[2024-01-24 11:08:16,917] [INFO] Task started: Blastn
[2024-01-24 11:08:16,918] [INFO] Running command: blastn -query GCF_003323735.1_ASM332373v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg37368653-4461-4e6d-91ec-eaba2bec92ae/dqc_reference/reference_markers_gtdb.fasta -out GCF_003323735.1_ASM332373v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:08:19,123] [INFO] Task succeeded: Blastn
[2024-01-24 11:08:19,129] [INFO] Selected 12 target genomes.
[2024-01-24 11:08:19,129] [INFO] Target genome list was writen to GCF_003323735.1_ASM332373v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:08:19,158] [INFO] Task started: fastANI
[2024-01-24 11:08:19,159] [INFO] Running command: fastANI --query /var/lib/cwl/stg38b8f2bc-aa18-450a-813f-f3943eb998e2/GCF_003323735.1_ASM332373v1_genomic.fna.gz --refList GCF_003323735.1_ASM332373v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003323735.1_ASM332373v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:08:41,765] [INFO] Task succeeded: fastANI
[2024-01-24 11:08:41,782] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:08:41,782] [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_003323735.1	s__Streptomyces reniochalinae	100.0	2527	2531	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_003323715.1	s__Streptomyces diacarni	94.3115	2144	2531	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000424785.1	s__Streptomyces sp000424785	87.209	1901	2531	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013302895.1	s__Streptomyces chlorinus	86.3319	1701	2531	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000725885.1	s__Streptomyces albus	85.6703	1683	2531	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.54	97.77	0.97	0.92	14	-
GCF_017676345.1	s__Streptomyces smyrnaeus	85.168	1725	2531	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.11	97.08	0.90	0.88	5	-
GCF_000424765.1	s__Streptomyces sp000424765	84.7028	1564	2531	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.13	98.98	0.93	0.92	5	-
GCF_900111245.1	s__Streptomyces qinglanensis	84.6957	1588	2531	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.98	99.98	0.99	0.99	2	-
GCF_900104815.1	s__Streptomyces misionensis	79.8886	1119	2531	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.36	97.46	0.91	0.87	3	-
GCF_013387495.1	s__Streptomyces sp013387495	79.7597	1014	2531	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008704425.1	s__Streptomyces fradiae	79.6268	1081	2531	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.82	99.37	0.98	0.97	5	-
GCF_000717185.1	s__Kitasatospora phosalacinea_A	78.2121	959	2531	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:08:41,784] [INFO] GTDB search result was written to GCF_003323735.1_ASM332373v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:08:41,784] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:08:41,788] [INFO] DFAST_QC result json was written to GCF_003323735.1_ASM332373v1_genomic.fna/dqc_result.json
[2024-01-24 11:08:41,788] [INFO] DFAST_QC completed!
[2024-01-24 11:08:41,788] [INFO] Total running time: 0h3m16s