[2024-01-24 15:10:37,294] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:37,297] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:37,297] [INFO] DQC Reference Directory: /var/lib/cwl/stg3813245a-120c-4a98-8d14-51614e681f54/dqc_reference
[2024-01-24 15:10:40,100] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:40,101] [INFO] Task started: Prodigal
[2024-01-24 15:10:40,102] [INFO] Running command: gunzip -c /var/lib/cwl/stgf8ba608a-d0d6-4e82-a4e3-1ae23c74b957/GCF_003751805.1_ASM375180v1_genomic.fna.gz | prodigal -d GCF_003751805.1_ASM375180v1_genomic.fna/cds.fna -a GCF_003751805.1_ASM375180v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:50,163] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:50,163] [INFO] Task started: HMMsearch
[2024-01-24 15:10:50,163] [INFO] Running command: hmmsearch --tblout GCF_003751805.1_ASM375180v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3813245a-120c-4a98-8d14-51614e681f54/dqc_reference/reference_markers.hmm GCF_003751805.1_ASM375180v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:50,461] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:50,462] [INFO] Found 6/6 markers.
[2024-01-24 15:10:50,505] [INFO] Query marker FASTA was written to GCF_003751805.1_ASM375180v1_genomic.fna/markers.fasta
[2024-01-24 15:10:50,505] [INFO] Task started: Blastn
[2024-01-24 15:10:50,506] [INFO] Running command: blastn -query GCF_003751805.1_ASM375180v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3813245a-120c-4a98-8d14-51614e681f54/dqc_reference/reference_markers.fasta -out GCF_003751805.1_ASM375180v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:51,839] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:51,842] [INFO] Selected 28 target genomes.
[2024-01-24 15:10:51,842] [INFO] Target genome list was writen to GCF_003751805.1_ASM375180v1_genomic.fna/target_genomes.txt
[2024-01-24 15:10:51,852] [INFO] Task started: fastANI
[2024-01-24 15:10:51,852] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8ba608a-d0d6-4e82-a4e3-1ae23c74b957/GCF_003751805.1_ASM375180v1_genomic.fna.gz --refList GCF_003751805.1_ASM375180v1_genomic.fna/target_genomes.txt --output GCF_003751805.1_ASM375180v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:17,461] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:17,462] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3813245a-120c-4a98-8d14-51614e681f54/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:17,462] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3813245a-120c-4a98-8d14-51614e681f54/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:17,483] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:11:17,483] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:11:17,483] [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
Cellulomonas biazotea	strain=NBRC12680	GCA_004306155.1	1709	1709	type	True	78.0853	478	1297	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	78.0802	504	1297	95	below_threshold
Cellulomonas hominis	strain=DSM 9581	GCA_014201095.1	156981	156981	suspected-type	True	78.0718	510	1297	95	below_threshold
Beutenbergia cavernae	strain=DSM 12333	GCA_000023105.1	84757	84757	type	True	78.0672	550	1297	95	below_threshold
Georgenia faecalis	strain=ZLJ0423	GCA_003710105.1	2483799	2483799	type	True	77.9799	429	1297	95	below_threshold
Cellulomonas iranensis	strain=NBRC 101100	GCA_001552375.1	76862	76862	type	True	77.9709	522	1297	95	below_threshold
Cellulosimicrobium marinum	strain=NBRC 110994	GCA_020551945.1	1638992	1638992	type	True	77.9325	469	1297	95	below_threshold
Cellulomonas hominis	strain=NBRC 16055	GCA_007989225.1	156981	156981	suspected-type	True	77.9077	504	1297	95	below_threshold
Cellulosimicrobium funkei	strain=JCM 14302	GCA_004519295.1	264251	264251	suspected-type	True	77.8652	538	1297	95	below_threshold
Sediminihabitans luteus	strain=NBRC 108568	GCA_016863455.1	1138585	1138585	type	True	77.8519	460	1297	95	below_threshold
Cellulomonas carbonis	strain=T26	GCA_000767175.1	1386092	1386092	type	True	77.8284	446	1297	95	below_threshold
Cellulosimicrobium funkei	strain=NBRC 104118	GCA_001570825.1	264251	264251	suspected-type	True	77.8251	533	1297	95	below_threshold
Oerskovia rustica	strain=Sa4CUA1	GCA_014836555.1	2762237	2762237	type	True	77.8111	444	1297	95	below_threshold
Oerskovia merdavium	strain=Sa2CUA9	GCA_014836755.1	2762227	2762227	type	True	77.7893	421	1297	95	below_threshold
Cellulomonas carbonis	strain=CGMCC 1.10786	GCA_014636275.1	1386092	1386092	type	True	77.6966	481	1297	95	below_threshold
Sanguibacter keddieii	strain=DSM 10542	GCA_000024925.1	60920	60920	type	True	77.6744	411	1297	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	77.6683	538	1297	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	77.6415	500	1297	95	below_threshold
Oerskovia douganii	strain=Sa1BUA8	GCA_015142735.1	2762210	2762210	type	True	77.5907	429	1297	95	below_threshold
Actinotalea subterranea	strain=HO-Ch2	GCA_008364845.1	2607497	2607497	type	True	77.586	444	1297	95	below_threshold
Promicromonospora citrea	strain=ATCC 15908	GCA_013004695.1	43677	43677	type	True	77.5859	457	1297	95	below_threshold
Demequina silvatica	strain=NBRC 109395	GCA_000971215.1	1638988	1638988	type	True	77.5313	300	1297	95	below_threshold
Cellulomonas humilata	strain=ATCC 25174	GCA_013359775.1	144055	144055	type	True	77.5209	445	1297	95	below_threshold
Promicromonospora citrea	strain=JCM 3051	GCA_014647735.1	43677	43677	type	True	77.4675	482	1297	95	below_threshold
Ruania albidiflava	strain=DSM 18029	GCA_000421225.1	366586	366586	type	True	77.2395	290	1297	95	below_threshold
Jiangella alba	strain=DSM 45237	GCA_900106035.1	561176	561176	type	True	76.3635	511	1297	95	below_threshold
Sphaerisporangium rubeum	strain=DSM 44936	GCA_014207705.1	321317	321317	type	True	76.053	325	1297	95	below_threshold
Actinomadura meyerae	strain=DSM 44715	GCA_900188445.1	240840	240840	type	True	75.7962	452	1297	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:17,485] [INFO] DFAST Taxonomy check result was written to GCF_003751805.1_ASM375180v1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:17,485] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:17,485] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:17,486] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3813245a-120c-4a98-8d14-51614e681f54/dqc_reference/checkm_data
[2024-01-24 15:11:17,487] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:17,529] [INFO] Task started: CheckM
[2024-01-24 15:11:17,530] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003751805.1_ASM375180v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003751805.1_ASM375180v1_genomic.fna/checkm_input GCF_003751805.1_ASM375180v1_genomic.fna/checkm_result
[2024-01-24 15:12:07,246] [INFO] Task succeeded: CheckM
[2024-01-24 15:12:07,248] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:12:07,267] [INFO] ===== Completeness check finished =====
[2024-01-24 15:12:07,267] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:12:07,267] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003751805.1_ASM375180v1_genomic.fna/markers.fasta)
[2024-01-24 15:12:07,267] [INFO] Task started: Blastn
[2024-01-24 15:12:07,267] [INFO] Running command: blastn -query GCF_003751805.1_ASM375180v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3813245a-120c-4a98-8d14-51614e681f54/dqc_reference/reference_markers_gtdb.fasta -out GCF_003751805.1_ASM375180v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:12:09,258] [INFO] Task succeeded: Blastn
[2024-01-24 15:12:09,262] [INFO] Selected 14 target genomes.
[2024-01-24 15:12:09,263] [INFO] Target genome list was writen to GCF_003751805.1_ASM375180v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:12:09,275] [INFO] Task started: fastANI
[2024-01-24 15:12:09,276] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8ba608a-d0d6-4e82-a4e3-1ae23c74b957/GCF_003751805.1_ASM375180v1_genomic.fna.gz --refList GCF_003751805.1_ASM375180v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003751805.1_ASM375180v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:12:21,715] [INFO] Task succeeded: fastANI
[2024-01-24 15:12:21,731] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:12:21,731] [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_003751805.1	s__Salana multivorans	100.0	1293	1297	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Salana	95.0	99.05	99.05	0.93	0.93	2	conclusive
GCF_006351005.1	s__Miniimonas arenae	80.615	625	1297	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Miniimonas	95.0	98.18	97.40	0.91	0.83	3	-
GCF_003121705.1	s__Serinibacter_A sp003121705	80.1164	623	1297	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Serinibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004786095.1	s__Serinibacter_A arcticus	79.8704	568	1297	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Serinibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002563925.1	s__Serinibacter salmoneus	78.4903	400	1297	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Serinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001750215.1	s__Xylanimonas variabilis_A	78.1885	379	1297	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Xylanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000023105.1	s__Beutenbergia cavernae	78.0074	554	1297	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Beutenbergia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011603975.1	s__Cellulomonas sp011603975	77.9674	485	1297	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001942335.1	s__Cellulosimicrobium sp001942335	77.8652	465	1297	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001462455.1	s__Cellulomonas sp001462455	77.8257	515	1297	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907755.1	s__Cellulosimicrobium cellulans_D	77.825	548	1297	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	99.18	99.18	0.97	0.97	2	-
GCF_009846865.1	s__Xylanimonas puerhi	77.6492	480	1297	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Xylanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008364845.1	s__Actinotalea sp008364845	77.6425	435	1297	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Actinotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188445.1	s__Spirillospora meyerae	75.7818	456	1297	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:12:21,733] [INFO] GTDB search result was written to GCF_003751805.1_ASM375180v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:12:21,733] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:12:21,737] [INFO] DFAST_QC result json was written to GCF_003751805.1_ASM375180v1_genomic.fna/dqc_result.json
[2024-01-24 15:12:21,738] [INFO] DFAST_QC completed!
[2024-01-24 15:12:21,738] [INFO] Total running time: 0h1m44s