[2024-01-25 17:46:35,800] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:46:35,803] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:46:35,804] [INFO] DQC Reference Directory: /var/lib/cwl/stgc02bf0a0-6ad8-4270-8446-0af193214628/dqc_reference
[2024-01-25 17:46:37,025] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:46:37,026] [INFO] Task started: Prodigal
[2024-01-25 17:46:37,026] [INFO] Running command: gunzip -c /var/lib/cwl/stg1f6f4f2b-eded-4eec-a718-0eaf08dcdaae/GCF_014651155.1_ASM1465115v1_genomic.fna.gz | prodigal -d GCF_014651155.1_ASM1465115v1_genomic.fna/cds.fna -a GCF_014651155.1_ASM1465115v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:46:58,544] [INFO] Task succeeded: Prodigal
[2024-01-25 17:46:58,545] [INFO] Task started: HMMsearch
[2024-01-25 17:46:58,545] [INFO] Running command: hmmsearch --tblout GCF_014651155.1_ASM1465115v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc02bf0a0-6ad8-4270-8446-0af193214628/dqc_reference/reference_markers.hmm GCF_014651155.1_ASM1465115v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:46:58,849] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:46:58,852] [INFO] Found 6/6 markers.
[2024-01-25 17:46:58,918] [INFO] Query marker FASTA was written to GCF_014651155.1_ASM1465115v1_genomic.fna/markers.fasta
[2024-01-25 17:46:58,919] [INFO] Task started: Blastn
[2024-01-25 17:46:58,919] [INFO] Running command: blastn -query GCF_014651155.1_ASM1465115v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc02bf0a0-6ad8-4270-8446-0af193214628/dqc_reference/reference_markers.fasta -out GCF_014651155.1_ASM1465115v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:47:00,183] [INFO] Task succeeded: Blastn
[2024-01-25 17:47:00,186] [INFO] Selected 14 target genomes.
[2024-01-25 17:47:00,186] [INFO] Target genome list was writen to GCF_014651155.1_ASM1465115v1_genomic.fna/target_genomes.txt
[2024-01-25 17:47:00,193] [INFO] Task started: fastANI
[2024-01-25 17:47:00,193] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f6f4f2b-eded-4eec-a718-0eaf08dcdaae/GCF_014651155.1_ASM1465115v1_genomic.fna.gz --refList GCF_014651155.1_ASM1465115v1_genomic.fna/target_genomes.txt --output GCF_014651155.1_ASM1465115v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:47:31,856] [INFO] Task succeeded: fastANI
[2024-01-25 17:47:31,857] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc02bf0a0-6ad8-4270-8446-0af193214628/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:47:31,857] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc02bf0a0-6ad8-4270-8446-0af193214628/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:47:31,866] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:47:31,866] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 17:47:31,867] [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 anthocyanicus	strain=JCM 5058	GCA_014651155.1	68174	68174	type	True	100.0	2702	2702	95	inconclusive
Streptomyces rubrogriseus	strain=NBRC 15455	GCA_003112595.1	194673	194673	type	True	96.891	2468	2702	95	inconclusive
Streptomyces tendae	strain=JCM 4610	GCA_014650435.1	1932	1932	type	True	93.9085	2269	2702	95	below_threshold
Streptomyces hyderabadensis	strain=JCM 17657	GCA_020404845.1	598549	598549	type	True	93.305	2161	2702	95	below_threshold
Streptomyces violaceorubidus	strain=NRRL B-16381	GCA_000717995.1	284042	284042	type	True	93.0918	2020	2702	95	below_threshold
Streptomyces ardesiacus	strain=NBRC 15402	GCA_003112575.1	285564	285564	type	True	91.9957	2122	2702	95	below_threshold
Streptomyces parvulus	strain=JCM 4068	GCA_014648855.1	146923	146923	type	True	89.5969	1999	2702	95	below_threshold
Streptomyces ambofaciens	strain=ATCC 23877	GCA_001267885.1	1889	1889	type	True	89.2714	2005	2702	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	87.9014	1914	2702	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	85.9741	1510	2702	95	below_threshold
Streptomyces indiaensis	strain=DSM 43803	GCA_021474405.1	284033	284033	type	True	85.2358	1608	2702	95	below_threshold
Streptomyces cahuitamycinicus	strain=13K301	GCA_002891435.1	2070367	2070367	type	True	85.1319	1479	2702	95	below_threshold
Streptomyces prasinopilosus	strain=NRRL B-2711	GCA_001419695.1	67344	67344	type	True	85.065	1090	2702	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	84.4662	1584	2702	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:47:31,870] [INFO] DFAST Taxonomy check result was written to GCF_014651155.1_ASM1465115v1_genomic.fna/tc_result.tsv
[2024-01-25 17:47:31,871] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:47:31,871] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:47:31,872] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc02bf0a0-6ad8-4270-8446-0af193214628/dqc_reference/checkm_data
[2024-01-25 17:47:31,873] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:47:31,946] [INFO] Task started: CheckM
[2024-01-25 17:47:31,947] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014651155.1_ASM1465115v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014651155.1_ASM1465115v1_genomic.fna/checkm_input GCF_014651155.1_ASM1465115v1_genomic.fna/checkm_result
[2024-01-25 17:49:30,426] [INFO] Task succeeded: CheckM
[2024-01-25 17:49:30,427] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:49:30,455] [INFO] ===== Completeness check finished =====
[2024-01-25 17:49:30,455] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:49:30,456] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014651155.1_ASM1465115v1_genomic.fna/markers.fasta)
[2024-01-25 17:49:30,456] [INFO] Task started: Blastn
[2024-01-25 17:49:30,456] [INFO] Running command: blastn -query GCF_014651155.1_ASM1465115v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc02bf0a0-6ad8-4270-8446-0af193214628/dqc_reference/reference_markers_gtdb.fasta -out GCF_014651155.1_ASM1465115v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:49:32,556] [INFO] Task succeeded: Blastn
[2024-01-25 17:49:32,558] [INFO] Selected 10 target genomes.
[2024-01-25 17:49:32,559] [INFO] Target genome list was writen to GCF_014651155.1_ASM1465115v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:49:32,564] [INFO] Task started: fastANI
[2024-01-25 17:49:32,564] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f6f4f2b-eded-4eec-a718-0eaf08dcdaae/GCF_014651155.1_ASM1465115v1_genomic.fna.gz --refList GCF_014651155.1_ASM1465115v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014651155.1_ASM1465115v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:49:55,386] [INFO] Task succeeded: fastANI
[2024-01-25 17:49:55,393] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:49:55,393] [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_014651155.1	s__Streptomyces anthocyanicus	100.0	2702	2702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.9168	99.40	98.26	0.96	0.83	31	conclusive
GCF_003112595.1	s__Streptomyces rubrogriseus	96.8819	2469	2702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.9168	N/A	N/A	N/A	N/A	1	-
GCF_003369795.1	s__Streptomyces sp003369795	95.1623	2150	2702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3499	N/A	N/A	N/A	N/A	1	-
GCF_014650435.1	s__Streptomyces tendae	93.9085	2269	2702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.72	95.62	0.85	0.82	7	-
GCF_002939385.1	s__Streptomyces sp002939385	93.5914	2152	2702	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	93.4173	2185	2702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000717995.1	s__Streptomyces violaceorubidus	93.1104	2018	2702	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	92.7765	2204	2702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.84	97.03	0.90	0.86	6	-
GCF_003112575.1	s__Streptomyces ardesiacus	92.0169	2118	2702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.97	95.84	0.93	0.82	10	-
GCF_003947455.1	s__Streptomyces sp003947455	90.1512	1886	2702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.68	96.68	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:49:55,394] [INFO] GTDB search result was written to GCF_014651155.1_ASM1465115v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:49:55,395] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:49:55,398] [INFO] DFAST_QC result json was written to GCF_014651155.1_ASM1465115v1_genomic.fna/dqc_result.json
[2024-01-25 17:49:55,398] [INFO] DFAST_QC completed!
[2024-01-25 17:49:55,398] [INFO] Total running time: 0h3m20s