[2024-01-24 13:31:57,653] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:57,654] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:57,655] [INFO] DQC Reference Directory: /var/lib/cwl/stgb9f56b3e-00ea-4d08-af1a-c12d496b55c3/dqc_reference
[2024-01-24 13:31:58,972] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:58,973] [INFO] Task started: Prodigal
[2024-01-24 13:31:58,973] [INFO] Running command: gunzip -c /var/lib/cwl/stg419b3fe9-5785-4341-9e41-f8d9d8707bee/GCF_030811555.1_ASM3081155v1_genomic.fna.gz | prodigal -d GCF_030811555.1_ASM3081155v1_genomic.fna/cds.fna -a GCF_030811555.1_ASM3081155v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:30,448] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:30,448] [INFO] Task started: HMMsearch
[2024-01-24 13:32:30,449] [INFO] Running command: hmmsearch --tblout GCF_030811555.1_ASM3081155v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb9f56b3e-00ea-4d08-af1a-c12d496b55c3/dqc_reference/reference_markers.hmm GCF_030811555.1_ASM3081155v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:30,776] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:30,777] [INFO] Found 6/6 markers.
[2024-01-24 13:32:30,840] [INFO] Query marker FASTA was written to GCF_030811555.1_ASM3081155v1_genomic.fna/markers.fasta
[2024-01-24 13:32:30,840] [INFO] Task started: Blastn
[2024-01-24 13:32:30,840] [INFO] Running command: blastn -query GCF_030811555.1_ASM3081155v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9f56b3e-00ea-4d08-af1a-c12d496b55c3/dqc_reference/reference_markers.fasta -out GCF_030811555.1_ASM3081155v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:32,068] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:32,071] [INFO] Selected 18 target genomes.
[2024-01-24 13:32:32,072] [INFO] Target genome list was writen to GCF_030811555.1_ASM3081155v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:32,079] [INFO] Task started: fastANI
[2024-01-24 13:32:32,079] [INFO] Running command: fastANI --query /var/lib/cwl/stg419b3fe9-5785-4341-9e41-f8d9d8707bee/GCF_030811555.1_ASM3081155v1_genomic.fna.gz --refList GCF_030811555.1_ASM3081155v1_genomic.fna/target_genomes.txt --output GCF_030811555.1_ASM3081155v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:53,273] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:53,273] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb9f56b3e-00ea-4d08-af1a-c12d496b55c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:53,274] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb9f56b3e-00ea-4d08-af1a-c12d496b55c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:53,294] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:32:53,294] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:32:53,294] [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
Kineosporia mesophila	strain=JCM 16902	GCA_021129235.1	566012	566012	type	True	84.6474	1709	2688	95	below_threshold
Kineosporia corallincola	strain=J2-2	GCA_018499875.1	2835133	2835133	type	True	84.0709	1712	2688	95	below_threshold
Kineosporia rhizophila	strain=JCM 9960	GCA_021277265.1	84633	84633	type	True	83.6225	1610	2688	95	below_threshold
Pedococcus cremeus	strain=CGMCC 1.6963	GCA_900111375.1	587636	587636	type	True	77.4751	500	2688	95	below_threshold
Cellulomonas denverensis	strain=ATCC BAA-788	GCA_012396125.1	264297	264297	type	True	76.8662	476	2688	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	76.8644	438	2688	95	below_threshold
Georgenia soli	strain=DSM 21838	GCA_002563695.1	638953	638953	type	True	76.7632	402	2688	95	below_threshold
Pseudokineococcus marinus	strain=JCM 14547	GCA_013004605.1	351215	351215	type	True	76.7136	365	2688	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	76.6502	469	2688	95	below_threshold
Cellulomonas iranensis	strain=NBRC 101100	GCA_001552375.1	76862	76862	type	True	76.5061	471	2688	95	below_threshold
Nocardioides anomalus	strain=HKS04	GCA_011046535.1	2712223	2712223	type	True	76.5005	576	2688	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	76.5002	439	2688	95	below_threshold
Cellulomonas cellasea	strain=DSM 20118	GCA_000767135.1	43670	43670	type	True	76.4665	413	2688	95	below_threshold
Cellulomonas cellasea	strain=NBRC 3753	GCA_006538745.1	43670	43670	type	True	76.466	499	2688	95	below_threshold
Streptomyces spongiicola	strain=HNM0071	GCA_003122365.1	1690221	1690221	type	True	76.3929	505	2688	95	below_threshold
Streptomyces xanthii	strain=CRXT-Y-14	GCA_014621695.1	2768069	2768069	type	True	76.3611	592	2688	95	below_threshold
Thermomonospora curvata	strain=DSM 43183	GCA_000024385.1	2020	2020	type	True	76.3562	515	2688	95	below_threshold
Actinomadura oligospora	strain=ATCC 43269	GCA_000518265.1	111804	111804	type	True	76.2427	579	2688	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:53,296] [INFO] DFAST Taxonomy check result was written to GCF_030811555.1_ASM3081155v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:53,296] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:53,296] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:53,297] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb9f56b3e-00ea-4d08-af1a-c12d496b55c3/dqc_reference/checkm_data
[2024-01-24 13:32:53,298] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:53,373] [INFO] Task started: CheckM
[2024-01-24 13:32:53,374] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030811555.1_ASM3081155v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030811555.1_ASM3081155v1_genomic.fna/checkm_input GCF_030811555.1_ASM3081155v1_genomic.fna/checkm_result
[2024-01-24 13:35:26,318] [INFO] Task succeeded: CheckM
[2024-01-24 13:35:26,319] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:35:26,341] [INFO] ===== Completeness check finished =====
[2024-01-24 13:35:26,341] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:35:26,341] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030811555.1_ASM3081155v1_genomic.fna/markers.fasta)
[2024-01-24 13:35:26,342] [INFO] Task started: Blastn
[2024-01-24 13:35:26,342] [INFO] Running command: blastn -query GCF_030811555.1_ASM3081155v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9f56b3e-00ea-4d08-af1a-c12d496b55c3/dqc_reference/reference_markers_gtdb.fasta -out GCF_030811555.1_ASM3081155v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:35:28,291] [INFO] Task succeeded: Blastn
[2024-01-24 13:35:28,294] [INFO] Selected 20 target genomes.
[2024-01-24 13:35:28,294] [INFO] Target genome list was writen to GCF_030811555.1_ASM3081155v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:35:28,422] [INFO] Task started: fastANI
[2024-01-24 13:35:28,422] [INFO] Running command: fastANI --query /var/lib/cwl/stg419b3fe9-5785-4341-9e41-f8d9d8707bee/GCF_030811555.1_ASM3081155v1_genomic.fna.gz --refList GCF_030811555.1_ASM3081155v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030811555.1_ASM3081155v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:35:50,220] [INFO] Task succeeded: fastANI
[2024-01-24 13:35:50,236] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:35:50,236] [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_018499875.1	s__Kineosporia sp018499875	84.0756	1711	2688	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineosporiaceae;g__Kineosporia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000719025.1	s__Kineosporia aurantiaca	82.6418	1610	2688	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineosporiaceae;g__Kineosporia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713225.1	s__JADJPO01 sp016713225	77.5811	509	2688	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineosporiaceae;g__JADJPO01	95.0	99.38	99.28	0.94	0.94	3	-
GCA_016794595.1	s__JADJPO01 sp016794595	77.451	503	2688	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineosporiaceae;g__JADJPO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111375.1	s__Pedococcus cremeus	77.4336	510	2688	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	95.41	95.41	0.91	0.91	2	-
GCF_006716885.1	s__Ornithinimicrobium humiphilum	77.2553	407	2688	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002198655.1	s__R-H-3 sp002198655	77.1982	753	2688	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineosporiaceae;g__R-H-3	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002198675.1	s__R-H-3 sp002198675	77.1882	748	2688	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineosporiaceae;g__R-H-3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016213575.1	s__R-H-3 sp016213575	77.0022	619	2688	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineosporiaceae;g__R-H-3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000955875.1	s__Terrabacter sp000955875	76.9285	487	2688	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013004605.1	s__Pseudokineococcus marinus	76.7215	364	2688	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Quadrisphaeraceae;g__Pseudokineococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002563695.1	s__Georgenia soli	76.696	409	2688	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012719445.1	s__JAAYAH01 sp012719445	76.6296	481	2688	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineosporiaceae;g__JAAYAH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007991755.1	s__Cellulomonas aerilata	76.5784	441	2688	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014635665.1	s__Isoptericola cucumis	76.5348	478	2688	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167525.1	s__Isoptericola flava	76.5344	493	2688	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024385.1	s__Thermomonospora curvata	76.3638	507	2688	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermomonospora	95.0	99.63	99.63	0.99	0.99	2	-
GCF_000518265.1	s__Spirillospora oligospora	76.2353	582	2688	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003594875.1	s__Bailinhaonella thermotolerans	75.8196	664	2688	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Bailinhaonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002893095.1	s__Stenotrophomonas sp002893095	74.8805	135	2688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.47	97.41	0.90	0.90	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:35:50,238] [INFO] GTDB search result was written to GCF_030811555.1_ASM3081155v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:35:50,239] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:35:50,243] [INFO] DFAST_QC result json was written to GCF_030811555.1_ASM3081155v1_genomic.fna/dqc_result.json
[2024-01-24 13:35:50,244] [INFO] DFAST_QC completed!
[2024-01-24 13:35:50,244] [INFO] Total running time: 0h3m53s