[2024-01-24 11:05:27,892] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:27,895] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:27,896] [INFO] DQC Reference Directory: /var/lib/cwl/stgdd40f1e8-da5a-4f20-bbb3-cd7b26d4c967/dqc_reference
[2024-01-24 11:05:29,234] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:29,235] [INFO] Task started: Prodigal
[2024-01-24 11:05:29,235] [INFO] Running command: gunzip -c /var/lib/cwl/stgd8fb0b54-af37-4131-a071-bcdda123ae0d/GCF_015689475.1_ASM1568947v1_genomic.fna.gz | prodigal -d GCF_015689475.1_ASM1568947v1_genomic.fna/cds.fna -a GCF_015689475.1_ASM1568947v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:06:49,388] [INFO] Task succeeded: Prodigal
[2024-01-24 11:06:49,388] [INFO] Task started: HMMsearch
[2024-01-24 11:06:49,389] [INFO] Running command: hmmsearch --tblout GCF_015689475.1_ASM1568947v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdd40f1e8-da5a-4f20-bbb3-cd7b26d4c967/dqc_reference/reference_markers.hmm GCF_015689475.1_ASM1568947v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:06:49,823] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:06:49,825] [INFO] Found 6/6 markers.
[2024-01-24 11:06:49,912] [INFO] Query marker FASTA was written to GCF_015689475.1_ASM1568947v1_genomic.fna/markers.fasta
[2024-01-24 11:06:49,913] [INFO] Task started: Blastn
[2024-01-24 11:06:49,913] [INFO] Running command: blastn -query GCF_015689475.1_ASM1568947v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd40f1e8-da5a-4f20-bbb3-cd7b26d4c967/dqc_reference/reference_markers.fasta -out GCF_015689475.1_ASM1568947v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:51,205] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:51,209] [INFO] Selected 16 target genomes.
[2024-01-24 11:06:51,210] [INFO] Target genome list was writen to GCF_015689475.1_ASM1568947v1_genomic.fna/target_genomes.txt
[2024-01-24 11:06:51,221] [INFO] Task started: fastANI
[2024-01-24 11:06:51,222] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8fb0b54-af37-4131-a071-bcdda123ae0d/GCF_015689475.1_ASM1568947v1_genomic.fna.gz --refList GCF_015689475.1_ASM1568947v1_genomic.fna/target_genomes.txt --output GCF_015689475.1_ASM1568947v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:07:47,294] [INFO] Task succeeded: fastANI
[2024-01-24 11:07:47,295] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdd40f1e8-da5a-4f20-bbb3-cd7b26d4c967/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:07:47,296] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdd40f1e8-da5a-4f20-bbb3-cd7b26d4c967/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:07:47,313] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:07:47,313] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:07:47,313] [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 sabulosicollis	strain=PRKS01-29	GCA_016103465.1	2715963	2715963	type	True	92.1545	2210	3879	95	below_threshold
Streptomyces yatensis	strain=DSM 41771	GCA_018069625.1	155177	155177	type	True	92.0916	2742	3879	95	below_threshold
Streptomyces antimycoticus	strain=NBRC 12839	GCA_005405925.1	68175	68175	type	True	92.0056	2806	3879	95	below_threshold
Streptomyces iranensis	strain=DSM 41954	GCA_017874715.1	576784	576784	type	True	91.935	2740	3879	95	below_threshold
Streptomyces rapamycinicus	strain=DSM 41530	GCA_014205315.1	1226757	1226757	type	True	91.918	2912	3879	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_003675955.1	1226757	1226757	type	True	91.8857	2907	3879	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_024298965.1	1226757	1226757	type	True	91.8702	2879	3879	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_000418455.1	1226757	1226757	type	True	91.8334	2922	3879	95	below_threshold
Streptomyces javensis	strain=DSM 41764	GCA_016103505.1	114698	114698	type	True	91.8128	2100	3879	95	below_threshold
Streptomyces hygroscopicus subsp. hygroscopicus	strain=NBRC 13472	GCA_001553455.1	68042	1912	type	True	90.2818	2120	3879	95	below_threshold
Streptomyces milbemycinicus	strain=NRRL 5739	GCA_002154605.1	476552	476552	type	True	84.0683	1795	3879	95	below_threshold
Streptomyces pactum	strain=ATCC 27456	GCA_016031615.1	68249	68249	type	True	81.4755	1528	3879	95	below_threshold
Streptomyces albireticuli	strain=NRRL B1670	GCA_021228125.1	1940	1940	type	True	80.9424	1441	3879	95	below_threshold
Streptomyces paromomycinus	strain=NBRC 15454	GCA_003865155.1	92743	92743	type	True	80.7133	1520	3879	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	80.5511	1397	3879	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	80.2095	1325	3879	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:07:47,315] [INFO] DFAST Taxonomy check result was written to GCF_015689475.1_ASM1568947v1_genomic.fna/tc_result.tsv
[2024-01-24 11:07:47,316] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:07:47,316] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:07:47,316] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdd40f1e8-da5a-4f20-bbb3-cd7b26d4c967/dqc_reference/checkm_data
[2024-01-24 11:07:47,317] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:07:47,417] [INFO] Task started: CheckM
[2024-01-24 11:07:47,417] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015689475.1_ASM1568947v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015689475.1_ASM1568947v1_genomic.fna/checkm_input GCF_015689475.1_ASM1568947v1_genomic.fna/checkm_result
[2024-01-24 11:12:43,382] [INFO] Task succeeded: CheckM
[2024-01-24 11:12:43,383] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:12:43,417] [INFO] ===== Completeness check finished =====
[2024-01-24 11:12:43,417] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:12:43,418] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015689475.1_ASM1568947v1_genomic.fna/markers.fasta)
[2024-01-24 11:12:43,419] [INFO] Task started: Blastn
[2024-01-24 11:12:43,419] [INFO] Running command: blastn -query GCF_015689475.1_ASM1568947v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd40f1e8-da5a-4f20-bbb3-cd7b26d4c967/dqc_reference/reference_markers_gtdb.fasta -out GCF_015689475.1_ASM1568947v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:45,567] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:45,573] [INFO] Selected 10 target genomes.
[2024-01-24 11:12:45,573] [INFO] Target genome list was writen to GCF_015689475.1_ASM1568947v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:12:45,944] [INFO] Task started: fastANI
[2024-01-24 11:12:45,945] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8fb0b54-af37-4131-a071-bcdda123ae0d/GCF_015689475.1_ASM1568947v1_genomic.fna.gz --refList GCF_015689475.1_ASM1568947v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015689475.1_ASM1568947v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:13:31,945] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:31,967] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:13:31,967] [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_015689475.1	s__Streptomyces solisilvae	100.0	3879	3879	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.71	97.94	0.94	0.86	10	conclusive
GCF_016741935.1	s__Streptomyces sp016741935	92.178	2941	3879	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0488	N/A	N/A	N/A	N/A	1	-
GCF_018069625.1	s__Streptomyces yatensis	92.1085	2740	3879	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.0185	N/A	N/A	N/A	N/A	1	-
GCF_018138715.1	s__Streptomyces asiaticus	92.019	2795	3879	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.17	95.36	0.90	0.81	10	-
GCF_005405925.1	s__Streptomyces antimycoticus	91.9864	2806	3879	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.0185	97.28	96.80	0.85	0.81	7	-
GCA_005405945.1	s__Streptomyces violaceusniger	91.9495	2764	3879	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.67	97.67	0.85	0.85	2	-
GCF_003675955.1	s__Streptomyces rapamycinicus	91.8863	2908	3879	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.67	99.95	99.91	0.99	0.99	3	-
GCF_017874715.1	s__Streptomyces iranensis	91.8853	2747	3879	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.67	99.98	99.98	1.00	1.00	2	-
GCF_000147815.2	s__Streptomyces violaceusniger_A	91.8168	2693	3879	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3301	95.69	95.54	0.80	0.80	4	-
GCF_001553455.1	s__Streptomyces hygroscopicus	90.2786	2120	3879	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.24	98.00	0.92	0.90	7	-
--------------------------------------------------------------------------------
[2024-01-24 11:13:31,970] [INFO] GTDB search result was written to GCF_015689475.1_ASM1568947v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:13:31,971] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:13:31,976] [INFO] DFAST_QC result json was written to GCF_015689475.1_ASM1568947v1_genomic.fna/dqc_result.json
[2024-01-24 11:13:31,976] [INFO] DFAST_QC completed!
[2024-01-24 11:13:31,976] [INFO] Total running time: 0h8m4s