[2024-01-25 17:37:05,687] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:37:05,688] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:37:05,688] [INFO] DQC Reference Directory: /var/lib/cwl/stg40594fcd-89ac-4bf2-a1a0-6b08c724ffa4/dqc_reference
[2024-01-25 17:37:06,858] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:37:06,859] [INFO] Task started: Prodigal
[2024-01-25 17:37:06,859] [INFO] Running command: gunzip -c /var/lib/cwl/stgcf28d077-d065-4366-9973-5f70425faa87/GCF_011044995.1_ASM1104499v1_genomic.fna.gz | prodigal -d GCF_011044995.1_ASM1104499v1_genomic.fna/cds.fna -a GCF_011044995.1_ASM1104499v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:37:27,548] [INFO] Task succeeded: Prodigal
[2024-01-25 17:37:27,548] [INFO] Task started: HMMsearch
[2024-01-25 17:37:27,548] [INFO] Running command: hmmsearch --tblout GCF_011044995.1_ASM1104499v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg40594fcd-89ac-4bf2-a1a0-6b08c724ffa4/dqc_reference/reference_markers.hmm GCF_011044995.1_ASM1104499v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:37:27,989] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:37:27,991] [INFO] Found 6/6 markers.
[2024-01-25 17:37:28,058] [INFO] Query marker FASTA was written to GCF_011044995.1_ASM1104499v1_genomic.fna/markers.fasta
[2024-01-25 17:37:28,058] [INFO] Task started: Blastn
[2024-01-25 17:37:28,058] [INFO] Running command: blastn -query GCF_011044995.1_ASM1104499v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg40594fcd-89ac-4bf2-a1a0-6b08c724ffa4/dqc_reference/reference_markers.fasta -out GCF_011044995.1_ASM1104499v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:37:29,346] [INFO] Task succeeded: Blastn
[2024-01-25 17:37:29,352] [INFO] Selected 21 target genomes.
[2024-01-25 17:37:29,353] [INFO] Target genome list was writen to GCF_011044995.1_ASM1104499v1_genomic.fna/target_genomes.txt
[2024-01-25 17:37:29,359] [INFO] Task started: fastANI
[2024-01-25 17:37:29,359] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf28d077-d065-4366-9973-5f70425faa87/GCF_011044995.1_ASM1104499v1_genomic.fna.gz --refList GCF_011044995.1_ASM1104499v1_genomic.fna/target_genomes.txt --output GCF_011044995.1_ASM1104499v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:38:13,935] [INFO] Task succeeded: fastANI
[2024-01-25 17:38:13,936] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg40594fcd-89ac-4bf2-a1a0-6b08c724ffa4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:38:13,937] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg40594fcd-89ac-4bf2-a1a0-6b08c724ffa4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:38:13,949] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:38:13,949] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:38:13,950] [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 mesophilus	strain=YC504	GCA_011044995.1	1775132	1775132	type	True	100.0	2724	2752	95	conclusive
Streptomyces polyasparticus	strain=TRM66268-LWL	GCA_014493765.1	2767826	2767826	type	True	90.0733	2198	2752	95	below_threshold
Streptomyces boluensis	strain=YC537	GCA_009908195.1	1775135	1775135	type	True	83.1518	1317	2752	95	below_threshold
Streptomyces silaceus	strain=NRRL B-24166	GCA_001419745.1	545123	545123	type	True	82.3354	1374	2752	95	below_threshold
Streptomyces aureoverticillatus	strain=JCM 4347	GCA_014649395.1	66871	66871	type	True	82.12	1487	2752	95	below_threshold
Streptomyces durmitorensis	strain=MS405	GCA_023498005.1	319947	319947	type	True	82.0799	1595	2752	95	below_threshold
Streptomyces apocyni	strain=TRM 66233	GCA_009739465.1	2654677	2654677	type	True	81.9654	1276	2752	95	below_threshold
Streptomyces xanthii	strain=CRXT-Y-14	GCA_014621695.1	2768069	2768069	type	True	81.9245	1447	2752	95	below_threshold
Streptomyces alfalfae	strain=XY25	GCA_004212445.1	1642299	1642299	type	True	81.8772	1365	2752	95	below_threshold
Streptomyces lasiicapitis	strain=CGMCC 4.7349	GCA_014646335.1	1923961	1923961	type	True	81.8664	1540	2752	95	below_threshold
Streptomyces spectabilis	strain=KCTC9218	GCA_022698305.1	68270	68270	type	True	81.7635	1478	2752	95	below_threshold
Streptomyces phaeochromogenes	strain=NRRL B-1248	GCA_001418655.1	1923	1923	type	True	81.7245	1409	2752	95	below_threshold
Streptomyces minutiscleroticus	strain=JCM 4790	GCA_014650875.1	68238	68238	type	True	81.6374	1324	2752	95	below_threshold
Streptomyces glaucescens	strain=NRRL B-2706	GCA_002154375.1	1907	1907	type	True	81.6152	1184	2752	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	81.5276	1486	2752	95	below_threshold
Streptomyces lateritius	strain=JCM 4389	GCA_014649715.1	67313	67313	type	True	81.4611	1267	2752	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	81.4466	1248	2752	95	below_threshold
Streptomyces triticiradicis	strain=NEAU-H2	GCA_008868685.1	2651189	2651189	type	True	81.4071	1373	2752	95	below_threshold
Streptomyces lanatus	strain=JCM 4588	GCA_014655715.1	66900	66900	type	True	81.3863	1467	2752	95	below_threshold
Streptomyces monashensis	strain=MUSC 1	GCA_001866665.1	1678012	1678012	type	True	81.1857	1322	2752	95	below_threshold
Streptomyces caniscabiei	strain=NE06-02D	GCA_014930365.1	2746961	2746961	type	True	81.1533	1399	2752	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:38:13,953] [INFO] DFAST Taxonomy check result was written to GCF_011044995.1_ASM1104499v1_genomic.fna/tc_result.tsv
[2024-01-25 17:38:13,954] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:38:13,954] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:38:13,954] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg40594fcd-89ac-4bf2-a1a0-6b08c724ffa4/dqc_reference/checkm_data
[2024-01-25 17:38:13,955] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:38:14,038] [INFO] Task started: CheckM
[2024-01-25 17:38:14,038] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011044995.1_ASM1104499v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011044995.1_ASM1104499v1_genomic.fna/checkm_input GCF_011044995.1_ASM1104499v1_genomic.fna/checkm_result
[2024-01-25 17:39:44,641] [INFO] Task succeeded: CheckM
[2024-01-25 17:39:44,642] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 57.14%
--------------------------------------------------------------------------------
[2024-01-25 17:39:44,664] [INFO] ===== Completeness check finished =====
[2024-01-25 17:39:44,664] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:39:44,664] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011044995.1_ASM1104499v1_genomic.fna/markers.fasta)
[2024-01-25 17:39:44,665] [INFO] Task started: Blastn
[2024-01-25 17:39:44,665] [INFO] Running command: blastn -query GCF_011044995.1_ASM1104499v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg40594fcd-89ac-4bf2-a1a0-6b08c724ffa4/dqc_reference/reference_markers_gtdb.fasta -out GCF_011044995.1_ASM1104499v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:39:46,857] [INFO] Task succeeded: Blastn
[2024-01-25 17:39:46,859] [INFO] Selected 12 target genomes.
[2024-01-25 17:39:46,860] [INFO] Target genome list was writen to GCF_011044995.1_ASM1104499v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:39:46,875] [INFO] Task started: fastANI
[2024-01-25 17:39:46,875] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf28d077-d065-4366-9973-5f70425faa87/GCF_011044995.1_ASM1104499v1_genomic.fna.gz --refList GCF_011044995.1_ASM1104499v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011044995.1_ASM1104499v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:40:13,777] [INFO] Task succeeded: fastANI
[2024-01-25 17:40:13,786] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:40:13,786] [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_011044995.1	s__Streptomyces mesophilus	100.0	2724	2752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.19	95.19	0.86	0.86	2	conclusive
GCF_014493765.1	s__Streptomyces polyasparticus	90.0813	2197	2752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000721375.1	s__Streptomyces sp000721375	88.4556	2102	2752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100315.1	s__Streptomyces indicus	88.1169	2016	2752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009908195.1	s__Streptomyces boluensis	83.1731	1315	2752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004684775.1	s__Streptomyces sp004684775	82.3981	1411	2752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649395.1	s__Streptomyces aureoverticillatus	82.0986	1491	2752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009769735.1	s__Streptomyces sp009769735	82.0646	1542	2752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259365.1	s__Streptomyces sp003259365	81.9737	1485	2752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000414115.1	s__Streptomyces aurantiacus_A	81.8928	1386	2752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008905045.1	s__Streptomyces albicerus	81.6848	1552	2752	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	81.3346	1323	2752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:40:13,788] [INFO] GTDB search result was written to GCF_011044995.1_ASM1104499v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:40:13,788] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:40:13,792] [INFO] DFAST_QC result json was written to GCF_011044995.1_ASM1104499v1_genomic.fna/dqc_result.json
[2024-01-25 17:40:13,792] [INFO] DFAST_QC completed!
[2024-01-25 17:40:13,792] [INFO] Total running time: 0h3m8s