[2024-01-25 19:52:35,681] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:52:35,683] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:52:35,683] [INFO] DQC Reference Directory: /var/lib/cwl/stg857e5a24-f359-4dba-a473-9cda4bf83a06/dqc_reference
[2024-01-25 19:52:36,858] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:52:36,859] [INFO] Task started: Prodigal
[2024-01-25 19:52:36,859] [INFO] Running command: gunzip -c /var/lib/cwl/stgfbc0fd70-663d-4b34-9ed2-2086a6f2e7a7/GCF_014648855.1_ASM1464885v1_genomic.fna.gz | prodigal -d GCF_014648855.1_ASM1464885v1_genomic.fna/cds.fna -a GCF_014648855.1_ASM1464885v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:52:55,159] [INFO] Task succeeded: Prodigal
[2024-01-25 19:52:55,159] [INFO] Task started: HMMsearch
[2024-01-25 19:52:55,159] [INFO] Running command: hmmsearch --tblout GCF_014648855.1_ASM1464885v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg857e5a24-f359-4dba-a473-9cda4bf83a06/dqc_reference/reference_markers.hmm GCF_014648855.1_ASM1464885v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:52:55,497] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:52:55,498] [INFO] Found 6/6 markers.
[2024-01-25 19:52:55,557] [INFO] Query marker FASTA was written to GCF_014648855.1_ASM1464885v1_genomic.fna/markers.fasta
[2024-01-25 19:52:55,557] [INFO] Task started: Blastn
[2024-01-25 19:52:55,557] [INFO] Running command: blastn -query GCF_014648855.1_ASM1464885v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg857e5a24-f359-4dba-a473-9cda4bf83a06/dqc_reference/reference_markers.fasta -out GCF_014648855.1_ASM1464885v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:52:56,851] [INFO] Task succeeded: Blastn
[2024-01-25 19:52:56,853] [INFO] Selected 22 target genomes.
[2024-01-25 19:52:56,854] [INFO] Target genome list was writen to GCF_014648855.1_ASM1464885v1_genomic.fna/target_genomes.txt
[2024-01-25 19:52:56,870] [INFO] Task started: fastANI
[2024-01-25 19:52:56,870] [INFO] Running command: fastANI --query /var/lib/cwl/stgfbc0fd70-663d-4b34-9ed2-2086a6f2e7a7/GCF_014648855.1_ASM1464885v1_genomic.fna.gz --refList GCF_014648855.1_ASM1464885v1_genomic.fna/target_genomes.txt --output GCF_014648855.1_ASM1464885v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:53:39,724] [INFO] Task succeeded: fastANI
[2024-01-25 19:53:39,724] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg857e5a24-f359-4dba-a473-9cda4bf83a06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:53:39,725] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg857e5a24-f359-4dba-a473-9cda4bf83a06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:53:39,737] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:53:39,738] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:53:39,738] [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 parvulus	strain=JCM 4068	GCA_014648855.1	146923	146923	type	True	100.0	2536	2536	95	conclusive
Streptomyces hyderabadensis	strain=JCM 17657	GCA_020404845.1	598549	598549	type	True	89.7945	1932	2536	95	below_threshold
Streptomyces anthocyanicus	strain=JCM 5058	GCA_014651155.1	68174	68174	type	True	89.7656	1963	2536	95	below_threshold
Streptomyces rubrogriseus	strain=NBRC 15455	GCA_003112595.1	194673	194673	type	True	89.6608	1978	2536	95	below_threshold
Streptomyces tendae	strain=JCM 4610	GCA_014650435.1	1932	1932	type	True	89.6454	2017	2536	95	below_threshold
Streptomyces violaceorubidus	strain=NRRL B-16381	GCA_000717995.1	284042	284042	type	True	89.6149	1882	2536	95	below_threshold
Streptomyces ardesiacus	strain=NBRC 15402	GCA_003112575.1	285564	285564	type	True	89.3698	1886	2536	95	below_threshold
Streptomyces ambofaciens	strain=ATCC 23877	GCA_001267885.1	1889	1889	type	True	89.1505	1930	2536	95	below_threshold
Streptomyces mutabilis	strain=JCM 4400	GCA_014649815.1	67332	67332	type	True	88.9688	1820	2536	95	below_threshold
Streptomyces flaveolus	strain=JCM 4032	GCA_014648815.1	67297	67297	type	True	88.8023	1801	2536	95	below_threshold
Streptomyces solaniscabiei	strain=FS70	GCA_020312315.1	2683255	2683255	type	True	88.5498	1805	2536	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	87.6367	1833	2536	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	86.0183	1465	2536	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	85.6157	1691	2536	95	below_threshold
Streptomyces purpurascens	strain=DSM 40310	GCA_021390235.1	1924	1924	type	True	85.3565	1721	2536	95	below_threshold
Streptomyces cahuitamycinicus	strain=13K301	GCA_002891435.1	2070367	2070367	type	True	85.2806	1415	2536	95	below_threshold
Streptomyces hirsutus	strain=NRRL B-2713	GCA_001418415.1	35620	35620	type	True	84.8508	1378	2536	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	84.5213	1512	2536	95	below_threshold
Streptomyces barkulensis	strain=RC 1831	GCA_002811705.2	1257026	1257026	type	True	80.7255	1103	2536	95	below_threshold
Streptomyces xinghaiensis	strain=S187	GCA_000220705.2	1038928	1038928	type	True	80.7185	1200	2536	95	below_threshold
Streptomyces barkulensis	strain=RC 1831	GCA_002843305.1	1257026	1257026	type	True	80.6839	1128	2536	95	below_threshold
Actinomadura rubrobrunea	strain=NBRC 15275	GCA_001552235.1	115335	115335	type	True	76.8014	711	2536	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:53:39,739] [INFO] DFAST Taxonomy check result was written to GCF_014648855.1_ASM1464885v1_genomic.fna/tc_result.tsv
[2024-01-25 19:53:39,740] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:53:39,740] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:53:39,740] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg857e5a24-f359-4dba-a473-9cda4bf83a06/dqc_reference/checkm_data
[2024-01-25 19:53:39,741] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:53:39,810] [INFO] Task started: CheckM
[2024-01-25 19:53:39,811] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014648855.1_ASM1464885v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014648855.1_ASM1464885v1_genomic.fna/checkm_input GCF_014648855.1_ASM1464885v1_genomic.fna/checkm_result
[2024-01-25 19:55:24,529] [INFO] Task succeeded: CheckM
[2024-01-25 19:55:24,530] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 17.71%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:55:24,551] [INFO] ===== Completeness check finished =====
[2024-01-25 19:55:24,552] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:55:24,553] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014648855.1_ASM1464885v1_genomic.fna/markers.fasta)
[2024-01-25 19:55:24,553] [INFO] Task started: Blastn
[2024-01-25 19:55:24,553] [INFO] Running command: blastn -query GCF_014648855.1_ASM1464885v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg857e5a24-f359-4dba-a473-9cda4bf83a06/dqc_reference/reference_markers_gtdb.fasta -out GCF_014648855.1_ASM1464885v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:55:26,757] [INFO] Task succeeded: Blastn
[2024-01-25 19:55:26,760] [INFO] Selected 18 target genomes.
[2024-01-25 19:55:26,760] [INFO] Target genome list was writen to GCF_014648855.1_ASM1464885v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:55:26,776] [INFO] Task started: fastANI
[2024-01-25 19:55:26,776] [INFO] Running command: fastANI --query /var/lib/cwl/stgfbc0fd70-663d-4b34-9ed2-2086a6f2e7a7/GCF_014648855.1_ASM1464885v1_genomic.fna.gz --refList GCF_014648855.1_ASM1464885v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014648855.1_ASM1464885v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:56:06,647] [INFO] Task succeeded: fastANI
[2024-01-25 19:56:06,659] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:56:06,659] [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_014648855.1	s__Streptomyces parvulus	100.0	2536	2536	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.39	95.93	0.93	0.87	4	conclusive
GCF_003947455.1	s__Streptomyces sp003947455	92.8657	1948	2536	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.68	96.68	0.84	0.84	2	-
GCF_002939385.1	s__Streptomyces sp002939385	90.0346	1909	2536	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.14	95.04	0.81	0.78	6	-
GCA_000720845.1	s__Streptomyces sp000720845	89.8556	1943	2536	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651155.1	s__Streptomyces anthocyanicus	89.7413	1965	2536	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.9168	99.40	98.26	0.96	0.83	31	-
GCF_014650435.1	s__Streptomyces tendae	89.669	2014	2536	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.72	95.62	0.85	0.82	7	-
GCF_019049325.1	s__Streptomyces sp019049325	89.6625	1934	2536	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003112595.1	s__Streptomyces rubrogriseus	89.659	1979	2536	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.9168	N/A	N/A	N/A	N/A	1	-
GCF_000717995.1	s__Streptomyces violaceorubidus	89.6353	1879	2536	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003112555.1	s__Streptomyces coelicoflavus	89.5659	1971	2536	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.84	97.03	0.90	0.86	6	-
GCF_004364245.1	s__Streptomyces sp004364245	89.4254	1937	2536	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003671715.1	s__Streptomyces sp003671715	89.385	1924	2536	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.92	95.92	0.81	0.81	2	-
GCF_001267885.1	s__Streptomyces ambofaciens	89.1482	1930	2536	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.23	99.23	0.92	0.92	2	-
GCA_002155895.1	s__Streptomyces rochei	88.9974	1642	2536	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.80	98.25	0.91	0.79	28	-
GCF_014648815.1	s__Streptomyces flaveolus	88.8157	1799	2536	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002005565.1	s__Streptomyces sp002005565	88.517	1674	2536	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000761215.1	s__Streptomyces glaucescens	85.3112	1604	2536	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143855.1	s__Streptomyces sp003143855	84.8707	1586	2536	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.17	95.17	0.79	0.79	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:56:06,661] [INFO] GTDB search result was written to GCF_014648855.1_ASM1464885v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:56:06,661] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:56:06,666] [INFO] DFAST_QC result json was written to GCF_014648855.1_ASM1464885v1_genomic.fna/dqc_result.json
[2024-01-25 19:56:06,666] [INFO] DFAST_QC completed!
[2024-01-25 19:56:06,666] [INFO] Total running time: 0h3m31s