[2024-01-24 12:21:56,938] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:56,941] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:56,941] [INFO] DQC Reference Directory: /var/lib/cwl/stg6985d784-5070-4b0b-bc72-b42fb4f6e0e1/dqc_reference
[2024-01-24 12:21:58,332] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:58,333] [INFO] Task started: Prodigal
[2024-01-24 12:21:58,333] [INFO] Running command: gunzip -c /var/lib/cwl/stgaf975bfd-ea39-447c-ae67-5ddf0acdd0f5/GCF_020532645.1_ASM2053264v1_genomic.fna.gz | prodigal -d GCF_020532645.1_ASM2053264v1_genomic.fna/cds.fna -a GCF_020532645.1_ASM2053264v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:19,836] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:19,837] [INFO] Task started: HMMsearch
[2024-01-24 12:22:19,837] [INFO] Running command: hmmsearch --tblout GCF_020532645.1_ASM2053264v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6985d784-5070-4b0b-bc72-b42fb4f6e0e1/dqc_reference/reference_markers.hmm GCF_020532645.1_ASM2053264v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:20,253] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:20,254] [INFO] Found 6/6 markers.
[2024-01-24 12:22:20,330] [INFO] Query marker FASTA was written to GCF_020532645.1_ASM2053264v1_genomic.fna/markers.fasta
[2024-01-24 12:22:20,331] [INFO] Task started: Blastn
[2024-01-24 12:22:20,331] [INFO] Running command: blastn -query GCF_020532645.1_ASM2053264v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6985d784-5070-4b0b-bc72-b42fb4f6e0e1/dqc_reference/reference_markers.fasta -out GCF_020532645.1_ASM2053264v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:21,745] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:21,749] [INFO] Selected 23 target genomes.
[2024-01-24 12:22:21,749] [INFO] Target genome list was writen to GCF_020532645.1_ASM2053264v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:21,760] [INFO] Task started: fastANI
[2024-01-24 12:22:21,760] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf975bfd-ea39-447c-ae67-5ddf0acdd0f5/GCF_020532645.1_ASM2053264v1_genomic.fna.gz --refList GCF_020532645.1_ASM2053264v1_genomic.fna/target_genomes.txt --output GCF_020532645.1_ASM2053264v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:06,403] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:06,403] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6985d784-5070-4b0b-bc72-b42fb4f6e0e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:06,404] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6985d784-5070-4b0b-bc72-b42fb4f6e0e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:06,422] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:23:06,422] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:06,422] [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 bambusae	strain=T110	GCA_020532645.1	1550616	1550616	type	True	100.0	2686	2693	95	conclusive
Streptomyces katrae	strain=NRRL ISP-5550	GCA_000966975.1	68223	68223	type	True	84.537	1287	2693	95	below_threshold
Streptomyces subrutilus	strain=ATCC 27467	GCA_008704535.1	36818	36818	type	True	84.5073	1504	2693	95	below_threshold
Streptomyces subrutilus	strain=JCM 4834	GCA_014650935.1	36818	36818	type	True	84.4274	1493	2693	95	below_threshold
Streptomyces vinaceus	strain=ATCC 27476	GCA_008704935.1	1960	1960	type	True	84.3888	1568	2693	95	below_threshold
Streptomyces virginiae	strain=NRRL ISP-5094	GCA_000720455.1	1961	1961	suspected-type	True	84.382	1591	2693	95	below_threshold
Streptomyces goshikiensis	strain=JCM 4640	GCA_014650555.1	1942	1942	type	True	84.3051	1592	2693	95	below_threshold
Streptomyces vinaceus	strain=JCM 4849	GCA_014656155.1	1960	1960	type	True	84.2401	1610	2693	95	below_threshold
Streptomyces spororaveus	strain=NBRC 15456	GCA_016755875.1	284039	284039	type	True	84.2227	1622	2693	95	below_threshold
Streptomyces nojiriensis	strain=JCM 3382	GCA_014648615.1	66374	66374	type	True	84.2179	1628	2693	95	below_threshold
Streptomyces nojiriensis	strain=NBRC 13794	GCA_016755855.1	66374	66374	type	True	84.2092	1624	2693	95	below_threshold
Streptomyces amritsarensis	strain=MTCC 11845	GCA_001953875.1	681158	681158	type	True	84.1623	1575	2693	95	below_threshold
Streptomyces nojiriensis	strain=JCM 3382	GCA_017639205.1	66374	66374	type	True	84.162	1630	2693	95	below_threshold
Streptomyces toxytricini	strain=JCM 4421	GCA_014649915.1	67369	67369	type	True	83.9905	1544	2693	95	below_threshold
Streptomyces cirratus	strain=JCM 4738	GCA_014650775.1	68187	68187	type	True	83.7973	1504	2693	95	below_threshold
Streptomyces termitum	strain=JCM 4518	GCA_014650175.1	67368	67368	type	True	82.5993	1386	2693	95	below_threshold
Streptomyces omiyaensis	strain=JCM 4806	GCA_014650895.1	68247	68247	type	True	82.427	1491	2693	95	below_threshold
Streptomyces roseolus	strain=JCM 4411	GCA_014649855.1	67358	67358	type	True	82.3845	1426	2693	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	81.7269	1320	2693	95	below_threshold
Streptomyces genisteinicus	strain=CRPJ-33	GCA_014489615.1	2768068	2768068	type	True	81.7111	1370	2693	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	81.5293	1239	2693	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	81.5077	1149	2693	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	81.2019	1295	2693	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:06,425] [INFO] DFAST Taxonomy check result was written to GCF_020532645.1_ASM2053264v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:06,426] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:06,426] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:06,427] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6985d784-5070-4b0b-bc72-b42fb4f6e0e1/dqc_reference/checkm_data
[2024-01-24 12:23:06,428] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:06,503] [INFO] Task started: CheckM
[2024-01-24 12:23:06,504] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020532645.1_ASM2053264v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020532645.1_ASM2053264v1_genomic.fna/checkm_input GCF_020532645.1_ASM2053264v1_genomic.fna/checkm_result
[2024-01-24 12:24:55,598] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:55,599] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:55,620] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:55,620] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:55,620] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020532645.1_ASM2053264v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:55,620] [INFO] Task started: Blastn
[2024-01-24 12:24:55,621] [INFO] Running command: blastn -query GCF_020532645.1_ASM2053264v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6985d784-5070-4b0b-bc72-b42fb4f6e0e1/dqc_reference/reference_markers_gtdb.fasta -out GCF_020532645.1_ASM2053264v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:57,707] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:57,711] [INFO] Selected 23 target genomes.
[2024-01-24 12:24:57,711] [INFO] Target genome list was writen to GCF_020532645.1_ASM2053264v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:57,748] [INFO] Task started: fastANI
[2024-01-24 12:24:57,748] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf975bfd-ea39-447c-ae67-5ddf0acdd0f5/GCF_020532645.1_ASM2053264v1_genomic.fna.gz --refList GCF_020532645.1_ASM2053264v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020532645.1_ASM2053264v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:25:41,670] [INFO] Task succeeded: fastANI
[2024-01-24 12:25:41,688] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:25:41,688] [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_000717915.1	s__Streptomyces sp000717915	84.6813	1501	2693	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.92	95.47	0.90	0.89	4	-
GCF_003949795.1	s__Streptomyces sp003949795	84.6125	1434	2693	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001746425.1	s__Streptomyces subrutilus_A	84.5664	1555	2693	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000719335.1	s__Streptomyces sp000719335	84.5325	1653	2693	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008642295.1	s__Streptomyces venezuelae_C	84.4569	1577	2693	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008642275.1	s__Streptomyces venezuelae_E	84.4417	1558	2693	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720145.1	s__Streptomyces sp000720145	84.4335	1615	2693	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008704935.1	s__Streptomyces vinaceus	84.4015	1566	2693	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.65	97.63	0.95	0.92	5	-
GCF_003950035.1	s__Streptomyces sp000158895	84.3951	1644	2693	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.52	95.50	0.87	0.87	3	-
GCA_001298555.1	s__Streptomyces sp001298555	84.3848	1545	2693	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001941845.1	s__Streptomyces sp001941845	84.309	1523	2693	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.45	99.45	0.96	0.96	2	-
GCF_016755875.1	s__Streptomyces spororaveus	84.2431	1618	2693	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002803845.1	s__Streptomyces lavendulae_C	84.2397	1609	2693	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.97	0.99	0.99	3	-
GCF_017639205.1	s__Streptomyces nojiriensis	84.2295	1617	2693	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	3	-
GCF_001953875.1	s__Streptomyces amritsarensis	84.2156	1568	2693	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.17	98.97	0.95	0.93	4	-
GCF_013401435.1	s__Streptomyces sp013401435	84.1424	1390	2693	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000719345.1	s__Streptomyces sp000719345	84.1347	1506	2693	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000716685.1	s__Streptomyces virginiae_A	84.1326	1619	2693	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.46	95.91	0.89	0.84	3	-
GCF_003325375.1	s__Streptomyces globosus	84.1045	1533	2693	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.29	95.29	0.89	0.89	2	-
GCF_014649915.1	s__Streptomyces toxytricini	83.9756	1547	2693	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.98	99.98	0.99	0.99	2	-
GCF_000719555.1	s__Streptomyces sp000719555	82.7653	1429	2693	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000721275.1	s__Streptomyces sp000721275	82.6672	1425	2693	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649855.1	s__Streptomyces roseolus	82.4253	1418	2693	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:25:41,690] [INFO] GTDB search result was written to GCF_020532645.1_ASM2053264v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:25:41,690] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:25:41,694] [INFO] DFAST_QC result json was written to GCF_020532645.1_ASM2053264v1_genomic.fna/dqc_result.json
[2024-01-24 12:25:41,695] [INFO] DFAST_QC completed!
[2024-01-24 12:25:41,695] [INFO] Total running time: 0h3m45s