[2024-01-24 11:19:53,649] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:19:53,651] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:19:53,651] [INFO] DQC Reference Directory: /var/lib/cwl/stg1aa01bd7-87c6-4604-be42-d800851d0fe5/dqc_reference
[2024-01-24 11:19:55,078] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:19:55,079] [INFO] Task started: Prodigal
[2024-01-24 11:19:55,079] [INFO] Running command: gunzip -c /var/lib/cwl/stgab7b607b-0cd3-4a2e-8cb9-3f94a1eb795d/GCF_002154415.1_ASM215441v1_genomic.fna.gz | prodigal -d GCF_002154415.1_ASM215441v1_genomic.fna/cds.fna -a GCF_002154415.1_ASM215441v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:13,091] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:13,091] [INFO] Task started: HMMsearch
[2024-01-24 11:20:13,092] [INFO] Running command: hmmsearch --tblout GCF_002154415.1_ASM215441v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1aa01bd7-87c6-4604-be42-d800851d0fe5/dqc_reference/reference_markers.hmm GCF_002154415.1_ASM215441v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:13,443] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:13,445] [INFO] Found 6/6 markers.
[2024-01-24 11:20:13,508] [INFO] Query marker FASTA was written to GCF_002154415.1_ASM215441v1_genomic.fna/markers.fasta
[2024-01-24 11:20:13,509] [INFO] Task started: Blastn
[2024-01-24 11:20:13,509] [INFO] Running command: blastn -query GCF_002154415.1_ASM215441v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1aa01bd7-87c6-4604-be42-d800851d0fe5/dqc_reference/reference_markers.fasta -out GCF_002154415.1_ASM215441v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:14,959] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:14,963] [INFO] Selected 17 target genomes.
[2024-01-24 11:20:14,964] [INFO] Target genome list was writen to GCF_002154415.1_ASM215441v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:14,970] [INFO] Task started: fastANI
[2024-01-24 11:20:14,971] [INFO] Running command: fastANI --query /var/lib/cwl/stgab7b607b-0cd3-4a2e-8cb9-3f94a1eb795d/GCF_002154415.1_ASM215441v1_genomic.fna.gz --refList GCF_002154415.1_ASM215441v1_genomic.fna/target_genomes.txt --output GCF_002154415.1_ASM215441v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:46,536] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:46,538] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1aa01bd7-87c6-4604-be42-d800851d0fe5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:46,538] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1aa01bd7-87c6-4604-be42-d800851d0fe5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:46,555] [INFO] Found 17 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:20:46,556] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:20:46,556] [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 angustmyceticus	strain=NRRL B-2347	GCA_002154415.1	285578	285578	type	True	100.0	2029	2061	95	conclusive
Streptomyces angustmyceticus	strain=JCM 4053	GCA_019933235.1	285578	285578	type	True	99.9752	2057	2061	95	conclusive
Streptomyces angustmyceticus	strain=NBRC 3934	GCA_009176265.1	285578	285578	type	True	99.9607	2051	2061	95	conclusive
Streptomyces caniferus	strain=NBRC 15389	GCA_009811555.1	285557	285557	type	True	92.596	1743	2061	95	below_threshold
Streptomyces decoyicus	strain=NRRL 2666	GCA_001270575.1	249567	249567	type	True	90.9635	1625	2061	95	below_threshold
Streptomyces libani subsp. libani	strain=NBRC 13452	GCA_009811595.1	68044	68043	type	True	89.8337	1670	2061	95	below_threshold
Streptomyces libani subsp. libani	strain=JCM 4322	GCA_014649275.1	68044	68043	type	True	89.8245	1661	2061	95	below_threshold
Streptomyces lydicamycinicus	strain=NBRC 110027	GCA_000829715.2	1546107	1546107	type	True	89.5011	1591	2061	95	below_threshold
Streptomyces tubercidicus	strain=NBRC 13090	GCA_009811635.1	47759	47759	type	True	89.4898	1558	2061	95	below_threshold
Streptomyces platensis	strain=DSM 40041	GCA_002119195.1	58346	58346	type	True	89.4345	1573	2061	95	below_threshold
Streptomyces sioyaensis	strain=DSM 40032	GCA_004122735.1	67364	67364	type	True	89.3724	1547	2061	95	below_threshold
Streptomyces pinistramenti	strain=SF28	GCA_020564935.1	2884812	2884812	type	True	85.9425	1238	2061	95	below_threshold
Streptomyces benahoarensis	strain=MZ03-37	GCA_007280575.1	2595054	2595054	type	True	84.8618	1072	2061	95	below_threshold
Streptomyces monomycini	strain=NRRL B-24309	GCA_022271435.1	371720	371720	type	True	84.1973	1260	2061	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=R7	GCA_022760195.1	132474	1927	type	True	84.137	1290	2061	95	below_threshold
Streptomyces paromomycinus	strain=NBRC 15454	GCA_003865155.1	92743	92743	type	True	84.0473	1289	2061	95	below_threshold
Neomegalonema perideroedes	strain=DSM 15528	GCA_000374145.1	217219	217219	type	True	74.8846	88	2061	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:46,558] [INFO] DFAST Taxonomy check result was written to GCF_002154415.1_ASM215441v1_genomic.fna/tc_result.tsv
[2024-01-24 11:20:46,558] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:46,558] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:46,559] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1aa01bd7-87c6-4604-be42-d800851d0fe5/dqc_reference/checkm_data
[2024-01-24 11:20:46,559] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:46,636] [INFO] Task started: CheckM
[2024-01-24 11:20:46,637] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002154415.1_ASM215441v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002154415.1_ASM215441v1_genomic.fna/checkm_input GCF_002154415.1_ASM215441v1_genomic.fna/checkm_result
[2024-01-24 11:21:43,911] [INFO] Task succeeded: CheckM
[2024-01-24 11:21:43,913] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 9.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:21:43,939] [INFO] ===== Completeness check finished =====
[2024-01-24 11:21:43,940] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:21:43,940] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002154415.1_ASM215441v1_genomic.fna/markers.fasta)
[2024-01-24 11:21:43,941] [INFO] Task started: Blastn
[2024-01-24 11:21:43,941] [INFO] Running command: blastn -query GCF_002154415.1_ASM215441v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1aa01bd7-87c6-4604-be42-d800851d0fe5/dqc_reference/reference_markers_gtdb.fasta -out GCF_002154415.1_ASM215441v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:46,146] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:46,151] [INFO] Selected 13 target genomes.
[2024-01-24 11:21:46,151] [INFO] Target genome list was writen to GCF_002154415.1_ASM215441v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:21:46,162] [INFO] Task started: fastANI
[2024-01-24 11:21:46,162] [INFO] Running command: fastANI --query /var/lib/cwl/stgab7b607b-0cd3-4a2e-8cb9-3f94a1eb795d/GCF_002154415.1_ASM215441v1_genomic.fna.gz --refList GCF_002154415.1_ASM215441v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002154415.1_ASM215441v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:22:10,503] [INFO] Task succeeded: fastANI
[2024-01-24 11:22:10,526] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:22:10,527] [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_009176265.1	s__Streptomyces angustmyceticus	99.9607	2051	2061	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.96	1.00	1.00	2	conclusive
GCF_009811555.1	s__Streptomyces caniferus	92.5816	1745	2061	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004125265.1	s__Streptomyces lydicus_C	91.5054	1642	2061	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187385.1	s__Streptomyces sp900187385	91.4447	1661	2061	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.81	99.51	0.98	0.96	9	-
GCF_001270575.1	s__Streptomyces decoyicus	90.9622	1625	2061	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.25	96.25	0.87	0.87	2	-
GCF_009811595.1	s__Streptomyces libani	89.8427	1669	2061	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.04	96.45	0.91	0.86	12	-
GCF_009811635.1	s__Streptomyces tubercidicus	89.4441	1562	2061	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008704855.1	s__Streptomyces platensis	89.4192	1598	2061	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.55	95.21	0.91	0.87	7	-
GCF_004122735.1	s__Streptomyces sioyaensis	89.4128	1543	2061	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.26	95.36	0.89	0.84	9	-
GCF_014203555.1	s__Streptomyces olivoverticillatus	82.3989	969	2061	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008705135.1	s__Streptomyces coeruleorubidus	80.9071	1072	2061	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.68	95.03	0.91	0.83	4	-
GCF_002846355.1	s__Kitasatospora sp002846355	79.2384	859	2061	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	96.05	96.05	0.83	0.83	2	-
GCA_015478825.1	s__Patulibacter sp015478825	75.3736	166	2061	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Patulibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:22:10,531] [INFO] GTDB search result was written to GCF_002154415.1_ASM215441v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:22:10,531] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:22:10,535] [INFO] DFAST_QC result json was written to GCF_002154415.1_ASM215441v1_genomic.fna/dqc_result.json
[2024-01-24 11:22:10,535] [INFO] DFAST_QC completed!
[2024-01-24 11:22:10,535] [INFO] Total running time: 0h2m17s