[2024-01-24 12:14:33,573] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:33,575] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:33,575] [INFO] DQC Reference Directory: /var/lib/cwl/stg7ccadbe5-7234-4949-bcb4-02d40f4488ab/dqc_reference
[2024-01-24 12:14:34,939] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:34,940] [INFO] Task started: Prodigal
[2024-01-24 12:14:34,940] [INFO] Running command: gunzip -c /var/lib/cwl/stg8aec625d-0648-4262-ac42-4fd0489ccf87/GCF_014650655.1_ASM1465065v1_genomic.fna.gz | prodigal -d GCF_014650655.1_ASM1465065v1_genomic.fna/cds.fna -a GCF_014650655.1_ASM1465065v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:57,504] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:57,505] [INFO] Task started: HMMsearch
[2024-01-24 12:14:57,505] [INFO] Running command: hmmsearch --tblout GCF_014650655.1_ASM1465065v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7ccadbe5-7234-4949-bcb4-02d40f4488ab/dqc_reference/reference_markers.hmm GCF_014650655.1_ASM1465065v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:57,858] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:57,860] [INFO] Found 6/6 markers.
[2024-01-24 12:14:57,929] [INFO] Query marker FASTA was written to GCF_014650655.1_ASM1465065v1_genomic.fna/markers.fasta
[2024-01-24 12:14:57,930] [INFO] Task started: Blastn
[2024-01-24 12:14:57,930] [INFO] Running command: blastn -query GCF_014650655.1_ASM1465065v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ccadbe5-7234-4949-bcb4-02d40f4488ab/dqc_reference/reference_markers.fasta -out GCF_014650655.1_ASM1465065v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:59,323] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:59,326] [INFO] Selected 18 target genomes.
[2024-01-24 12:14:59,327] [INFO] Target genome list was writen to GCF_014650655.1_ASM1465065v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:59,334] [INFO] Task started: fastANI
[2024-01-24 12:14:59,335] [INFO] Running command: fastANI --query /var/lib/cwl/stg8aec625d-0648-4262-ac42-4fd0489ccf87/GCF_014650655.1_ASM1465065v1_genomic.fna.gz --refList GCF_014650655.1_ASM1465065v1_genomic.fna/target_genomes.txt --output GCF_014650655.1_ASM1465065v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:39,563] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:39,564] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7ccadbe5-7234-4949-bcb4-02d40f4488ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:39,564] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7ccadbe5-7234-4949-bcb4-02d40f4488ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:39,580] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:15:39,580] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:39,581] [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 anandii	strain=JCM 4720	GCA_014650655.1	285454	285454	type	True	100.0	2589	2590	95	conclusive
Streptomyces naganishii	strain=JCM 4654	GCA_014650575.1	285447	285447	type	True	94.598	2178	2590	95	below_threshold
Streptomyces spiralis	strain=JCM 3302	GCA_014654675.1	66376	66376	type	True	87.7024	1868	2590	95	below_threshold
Streptomyces triticisoli	strain=NEAU-DSCPA1-4-4	GCA_003270085.1	2182797	2182797	type	True	87.6543	1479	2590	95	below_threshold
Streptomyces carpinensis	strain=NRRL B-16921	GCA_002154505.1	66369	66369	type	True	87.654	1651	2590	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	87.5217	1637	2590	95	below_threshold
Streptomyces thermodiastaticus	strain=DSM 40573	GCA_021394575.1	44061	44061	type	True	85.7594	1488	2590	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	85.5426	1641	2590	95	below_threshold
Streptomyces cellostaticus	strain=DSM 40189	GCA_001513965.1	67285	67285	type	True	85.5412	1761	2590	95	below_threshold
Streptomyces bungoensis	strain=DSM 41781	GCA_001514215.1	285568	285568	type	True	85.4981	1776	2590	95	below_threshold
Streptomyces griseostramineus	strain=JCM 4385	GCA_014649635.1	66898	66898	suspected-type	True	85.4258	1618	2590	95	below_threshold
Streptomyces viridiviolaceus	strain=JCM 4855	GCA_014650995.1	68282	68282	type	True	85.3565	1646	2590	95	below_threshold
Streptomyces griseostramineus	strain=CECT 3273	GCA_014203535.1	66898	66898	suspected-type	True	85.3552	1629	2590	95	below_threshold
Streptomyces griseochromogenes	strain=ATCC 14511	GCA_001542625.2	68214	68214	type	True	85.3425	1788	2590	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	85.3178	1778	2590	95	below_threshold
Streptomyces griseochromogenes	strain=DSM 40499	GCA_017874495.1	68214	68214	type	True	85.2571	1808	2590	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	85.146	1386	2590	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	84.4935	1554	2590	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:39,583] [INFO] DFAST Taxonomy check result was written to GCF_014650655.1_ASM1465065v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:39,584] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:39,584] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:39,584] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7ccadbe5-7234-4949-bcb4-02d40f4488ab/dqc_reference/checkm_data
[2024-01-24 12:15:39,585] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:39,669] [INFO] Task started: CheckM
[2024-01-24 12:15:39,669] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014650655.1_ASM1465065v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014650655.1_ASM1465065v1_genomic.fna/checkm_input GCF_014650655.1_ASM1465065v1_genomic.fna/checkm_result
[2024-01-24 12:17:25,922] [INFO] Task succeeded: CheckM
[2024-01-24 12:17:25,923] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:17:25,949] [INFO] ===== Completeness check finished =====
[2024-01-24 12:17:25,950] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:17:25,950] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014650655.1_ASM1465065v1_genomic.fna/markers.fasta)
[2024-01-24 12:17:25,950] [INFO] Task started: Blastn
[2024-01-24 12:17:25,951] [INFO] Running command: blastn -query GCF_014650655.1_ASM1465065v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ccadbe5-7234-4949-bcb4-02d40f4488ab/dqc_reference/reference_markers_gtdb.fasta -out GCF_014650655.1_ASM1465065v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:17:28,084] [INFO] Task succeeded: Blastn
[2024-01-24 12:17:28,088] [INFO] Selected 16 target genomes.
[2024-01-24 12:17:28,088] [INFO] Target genome list was writen to GCF_014650655.1_ASM1465065v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:17:28,101] [INFO] Task started: fastANI
[2024-01-24 12:17:28,101] [INFO] Running command: fastANI --query /var/lib/cwl/stg8aec625d-0648-4262-ac42-4fd0489ccf87/GCF_014650655.1_ASM1465065v1_genomic.fna.gz --refList GCF_014650655.1_ASM1465065v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014650655.1_ASM1465065v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:18:03,107] [INFO] Task succeeded: fastANI
[2024-01-24 12:18:03,126] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:18:03,127] [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_014650655.1	s__Streptomyces anandii	100.0	2589	2590	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_014650575.1	s__Streptomyces naganishii	94.598	2178	2590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014654675.1	s__Streptomyces spiralis	87.7206	1865	2590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.07	98.07	0.87	0.87	2	-
GCF_002154505.1	s__Streptomyces carpinensis	87.6301	1654	2590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006540305.1	s__Streptomyces sp006540305	87.296	1744	2590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000383935.1	s__Streptomyces sp000383935	87.2616	1753	2590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.62	97.70	0.92	0.84	4	-
GCF_902506575.1	s__Streptomyces mexicanus	86.9914	1692	2590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.95	96.19	0.87	0.78	3	-
GCF_000720185.1	s__Streptomyces sp000720185	86.9756	1752	2590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009852415.1	s__Streptomyces sp009852415	85.5857	1664	2590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001513965.1	s__Streptomyces cellostaticus	85.5412	1761	2590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203535.1	s__Streptomyces griseostramineus	85.3551	1629	2590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.88	99.76	0.99	0.98	3	-
GCF_001542625.1	s__Streptomyces griseochromogenes	85.3417	1789	2590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001905845.1	s__Streptomyces sp001905845	85.2283	1680	2590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649375.1	s__Streptomyces aurantiogriseus	85.0988	1739	2590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539505.1	s__Streptomyces spinoverrucosus	85.0435	1635	2590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.41	95.17	0.85	0.79	5	-
GCF_001507435.1	s__Streptomyces sp001507435	83.7989	1645	2590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.91	96.23	0.91	0.88	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:18:03,128] [INFO] GTDB search result was written to GCF_014650655.1_ASM1465065v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:18:03,129] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:18:03,134] [INFO] DFAST_QC result json was written to GCF_014650655.1_ASM1465065v1_genomic.fna/dqc_result.json
[2024-01-24 12:18:03,135] [INFO] DFAST_QC completed!
[2024-01-24 12:18:03,135] [INFO] Total running time: 0h3m30s