[2024-01-25 19:06:05,885] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:06:05,887] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:06:05,887] [INFO] DQC Reference Directory: /var/lib/cwl/stgdfdac9b2-cac2-42fc-8ff5-88da19427396/dqc_reference
[2024-01-25 19:06:07,024] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:06:07,024] [INFO] Task started: Prodigal
[2024-01-25 19:06:07,025] [INFO] Running command: gunzip -c /var/lib/cwl/stg0ba8c03d-cac7-4d0d-9d1d-aa1db0b1974b/GCF_017874715.1_ASM1787471v1_genomic.fna.gz | prodigal -d GCF_017874715.1_ASM1787471v1_genomic.fna/cds.fna -a GCF_017874715.1_ASM1787471v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:07:35,569] [INFO] Task succeeded: Prodigal
[2024-01-25 19:07:35,569] [INFO] Task started: HMMsearch
[2024-01-25 19:07:35,570] [INFO] Running command: hmmsearch --tblout GCF_017874715.1_ASM1787471v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdfdac9b2-cac2-42fc-8ff5-88da19427396/dqc_reference/reference_markers.hmm GCF_017874715.1_ASM1787471v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:07:36,035] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:07:36,037] [INFO] Found 6/6 markers.
[2024-01-25 19:07:36,124] [INFO] Query marker FASTA was written to GCF_017874715.1_ASM1787471v1_genomic.fna/markers.fasta
[2024-01-25 19:07:36,124] [INFO] Task started: Blastn
[2024-01-25 19:07:36,124] [INFO] Running command: blastn -query GCF_017874715.1_ASM1787471v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdfdac9b2-cac2-42fc-8ff5-88da19427396/dqc_reference/reference_markers.fasta -out GCF_017874715.1_ASM1787471v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:07:37,360] [INFO] Task succeeded: Blastn
[2024-01-25 19:07:37,363] [INFO] Selected 10 target genomes.
[2024-01-25 19:07:37,363] [INFO] Target genome list was writen to GCF_017874715.1_ASM1787471v1_genomic.fna/target_genomes.txt
[2024-01-25 19:07:37,371] [INFO] Task started: fastANI
[2024-01-25 19:07:37,371] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ba8c03d-cac7-4d0d-9d1d-aa1db0b1974b/GCF_017874715.1_ASM1787471v1_genomic.fna.gz --refList GCF_017874715.1_ASM1787471v1_genomic.fna/target_genomes.txt --output GCF_017874715.1_ASM1787471v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:08:15,985] [INFO] Task succeeded: fastANI
[2024-01-25 19:08:15,986] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdfdac9b2-cac2-42fc-8ff5-88da19427396/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:08:15,986] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdfdac9b2-cac2-42fc-8ff5-88da19427396/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:08:15,994] [INFO] Found 10 fastANI hits (5 hits with ANI > threshold)
[2024-01-25 19:08:15,994] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 19:08:15,995] [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 iranensis	strain=DSM 41954	GCA_017874715.1	576784	576784	type	True	100.0	3953	3955	95	inconclusive
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_003675955.1	1226757	1226757	type	True	95.6833	3236	3955	95	inconclusive
Streptomyces rapamycinicus	strain=DSM 41530	GCA_014205315.1	1226757	1226757	type	True	95.6584	3230	3955	95	inconclusive
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_024298965.1	1226757	1226757	type	True	95.6379	3230	3955	95	inconclusive
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_000418455.1	1226757	1226757	type	True	95.6357	3236	3955	95	inconclusive
Streptomyces javensis	strain=DSM 41764	GCA_016103505.1	114698	114698	type	True	94.4359	2230	3955	95	below_threshold
Streptomyces albireticuli	strain=NRRL B1670	GCA_021228125.1	1940	1940	type	True	81.1847	1399	3955	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=R7	GCA_022760195.1	132474	1927	type	True	80.9365	1574	3955	95	below_threshold
Streptomyces paromomycinus	strain=NBRC 15454	GCA_003865155.1	92743	92743	type	True	80.701	1590	3955	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	80.4152	1319	3955	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:08:15,996] [INFO] DFAST Taxonomy check result was written to GCF_017874715.1_ASM1787471v1_genomic.fna/tc_result.tsv
[2024-01-25 19:08:15,997] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:08:15,997] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:08:15,997] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdfdac9b2-cac2-42fc-8ff5-88da19427396/dqc_reference/checkm_data
[2024-01-25 19:08:15,998] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:08:16,107] [INFO] Task started: CheckM
[2024-01-25 19:08:16,107] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017874715.1_ASM1787471v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017874715.1_ASM1787471v1_genomic.fna/checkm_input GCF_017874715.1_ASM1787471v1_genomic.fna/checkm_result
[2024-01-25 19:13:36,538] [INFO] Task succeeded: CheckM
[2024-01-25 19:13:36,539] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:13:36,578] [INFO] ===== Completeness check finished =====
[2024-01-25 19:13:36,578] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:13:36,579] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017874715.1_ASM1787471v1_genomic.fna/markers.fasta)
[2024-01-25 19:13:36,579] [INFO] Task started: Blastn
[2024-01-25 19:13:36,580] [INFO] Running command: blastn -query GCF_017874715.1_ASM1787471v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdfdac9b2-cac2-42fc-8ff5-88da19427396/dqc_reference/reference_markers_gtdb.fasta -out GCF_017874715.1_ASM1787471v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:13:38,756] [INFO] Task succeeded: Blastn
[2024-01-25 19:13:38,763] [INFO] Selected 7 target genomes.
[2024-01-25 19:13:38,763] [INFO] Target genome list was writen to GCF_017874715.1_ASM1787471v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:13:38,780] [INFO] Task started: fastANI
[2024-01-25 19:13:38,780] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ba8c03d-cac7-4d0d-9d1d-aa1db0b1974b/GCF_017874715.1_ASM1787471v1_genomic.fna.gz --refList GCF_017874715.1_ASM1787471v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017874715.1_ASM1787471v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:14:11,883] [INFO] Task succeeded: fastANI
[2024-01-25 19:14:11,890] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:14:11,890] [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_017874715.1	s__Streptomyces iranensis	100.0	3953	3955	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.67	99.98	99.98	1.00	1.00	2	conclusive
GCF_003675955.1	s__Streptomyces rapamycinicus	95.653	3242	3955	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.67	99.95	99.91	0.99	0.99	3	-
GCF_016741935.1	s__Streptomyces sp016741935	94.9876	3087	3955	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0488	N/A	N/A	N/A	N/A	1	-
GCF_018138715.1	s__Streptomyces asiaticus	94.822	2954	3955	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.17	95.36	0.90	0.81	10	-
GCA_005405945.1	s__Streptomyces violaceusniger	94.1939	2850	3955	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.67	97.67	0.85	0.85	2	-
GCF_000968685.2	s__Streptomyces antioxidans	93.7175	2495	3955	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018069625.1	s__Streptomyces yatensis	92.0807	2814	3955	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.0185	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:14:11,891] [INFO] GTDB search result was written to GCF_017874715.1_ASM1787471v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:14:11,891] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:14:11,894] [INFO] DFAST_QC result json was written to GCF_017874715.1_ASM1787471v1_genomic.fna/dqc_result.json
[2024-01-25 19:14:11,894] [INFO] DFAST_QC completed!
[2024-01-25 19:14:11,894] [INFO] Total running time: 0h8m6s