[2024-01-24 14:12:35,669] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:12:35,672] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:12:35,672] [INFO] DQC Reference Directory: /var/lib/cwl/stgdc029b95-ec47-4634-a1d1-90bccffb049a/dqc_reference
[2024-01-24 14:12:37,013] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:12:37,014] [INFO] Task started: Prodigal
[2024-01-24 14:12:37,014] [INFO] Running command: gunzip -c /var/lib/cwl/stg9601b623-e1dc-43ad-87e5-f03c460e31b6/GCF_007991475.1_ASM799147v1_genomic.fna.gz | prodigal -d GCF_007991475.1_ASM799147v1_genomic.fna/cds.fna -a GCF_007991475.1_ASM799147v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:47,768] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:47,769] [INFO] Task started: HMMsearch
[2024-01-24 14:12:47,769] [INFO] Running command: hmmsearch --tblout GCF_007991475.1_ASM799147v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdc029b95-ec47-4634-a1d1-90bccffb049a/dqc_reference/reference_markers.hmm GCF_007991475.1_ASM799147v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:48,052] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:48,055] [INFO] Found 6/6 markers.
[2024-01-24 14:12:48,107] [INFO] Query marker FASTA was written to GCF_007991475.1_ASM799147v1_genomic.fna/markers.fasta
[2024-01-24 14:12:48,108] [INFO] Task started: Blastn
[2024-01-24 14:12:48,108] [INFO] Running command: blastn -query GCF_007991475.1_ASM799147v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc029b95-ec47-4634-a1d1-90bccffb049a/dqc_reference/reference_markers.fasta -out GCF_007991475.1_ASM799147v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:49,533] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:49,536] [INFO] Selected 26 target genomes.
[2024-01-24 14:12:49,536] [INFO] Target genome list was writen to GCF_007991475.1_ASM799147v1_genomic.fna/target_genomes.txt
[2024-01-24 14:12:49,542] [INFO] Task started: fastANI
[2024-01-24 14:12:49,543] [INFO] Running command: fastANI --query /var/lib/cwl/stg9601b623-e1dc-43ad-87e5-f03c460e31b6/GCF_007991475.1_ASM799147v1_genomic.fna.gz --refList GCF_007991475.1_ASM799147v1_genomic.fna/target_genomes.txt --output GCF_007991475.1_ASM799147v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:13:09,288] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:09,289] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdc029b95-ec47-4634-a1d1-90bccffb049a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:13:09,289] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdc029b95-ec47-4634-a1d1-90bccffb049a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:13:09,308] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:13:09,309] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:13:09,309] [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 carbonis	strain=T26	GCA_000767175.1	1386092	1386092	type	True	80.132	596	1235	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	80.0697	689	1235	95	below_threshold
Cellulomonas carbonis	strain=CGMCC 1.10786	GCA_014636275.1	1386092	1386092	type	True	80.0011	660	1235	95	below_threshold
Actinotalea subterranea	strain=HO-Ch2	GCA_008364845.1	2607497	2607497	type	True	79.9951	676	1235	95	below_threshold
Cellulomonas gelida	strain=NBRC 3748	GCA_006538725.1	1712	1712	type	True	79.2577	560	1235	95	below_threshold
Cellulomonas persica	strain=NBRC 101101	GCA_007989825.1	76861	76861	type	True	79.2421	554	1235	95	below_threshold
Cellulomonas gelida	strain=JCM 1490	GCA_014647015.1	1712	1712	type	True	79.24	567	1235	95	below_threshold
Cellulomonas hominis	strain=DSM 9581	GCA_014201095.1	156981	156981	suspected-type	True	79.079	587	1235	95	below_threshold
Cellulomonas massiliensis	strain=JC225	GCA_000312005.1	1465811	1465811	type	True	79.0691	543	1235	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	78.9661	594	1235	95	below_threshold
Cellulomonas telluris	strain=CPCC 204705	GCA_004886325.1	2306636	2306636	type	True	78.9491	587	1235	95	below_threshold
Cellulomonas hominis	strain=NBRC 16055	GCA_007989225.1	156981	156981	suspected-type	True	78.9391	567	1235	95	below_threshold
Cellulomonas iranensis	strain=NBRC 101100	GCA_001552375.1	76862	76862	type	True	78.8987	593	1235	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	78.8172	560	1235	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	78.7274	573	1235	95	below_threshold
Oerskovia turbata	strain=JCM3160	GCA_004121315.1	1713	1713	type	True	78.6331	465	1235	95	below_threshold
Sediminihabitans luteus	strain=NBRC 108568	GCA_016863455.1	1138585	1138585	type	True	78.5203	498	1235	95	below_threshold
Sediminihabitans luteus	strain=DSM 25478	GCA_002797595.1	1138585	1138585	type	True	78.4755	497	1235	95	below_threshold
Oerskovia enterophila	strain=DSM 43852	GCA_001692445.1	43678	43678	type	True	78.3418	489	1235	95	below_threshold
Oerskovia merdavium	strain=Sa2CUA9	GCA_014836755.1	2762227	2762227	type	True	78.2893	482	1235	95	below_threshold
Sanguibacter keddieii	strain=DSM 10542	GCA_000024925.1	60920	60920	type	True	78.1083	476	1235	95	below_threshold
Demequina rhizosphaerae	strain=NBRC 109397	GCA_000971255.1	1638985	1638985	type	True	77.8769	370	1235	95	below_threshold
Demequina maris	strain=NBRC 109392	GCA_000971155.1	1638982	1638982	type	True	77.8469	377	1235	95	below_threshold
Demequina phytophila	strain=NBRC 109391	GCA_000971135.1	1638981	1638981	type	True	77.7101	338	1235	95	below_threshold
Demequina pelophila	strain=NBRC 109393	GCA_000971175.1	1638984	1638984	type	True	77.651	329	1235	95	below_threshold
Demequina salsinemoris	strain=NBRC 105323	GCA_000974805.1	577470	577470	type	True	77.6235	336	1235	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:13:09,311] [INFO] DFAST Taxonomy check result was written to GCF_007991475.1_ASM799147v1_genomic.fna/tc_result.tsv
[2024-01-24 14:13:09,311] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:13:09,311] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:13:09,311] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdc029b95-ec47-4634-a1d1-90bccffb049a/dqc_reference/checkm_data
[2024-01-24 14:13:09,312] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:13:09,350] [INFO] Task started: CheckM
[2024-01-24 14:13:09,350] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007991475.1_ASM799147v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007991475.1_ASM799147v1_genomic.fna/checkm_input GCF_007991475.1_ASM799147v1_genomic.fna/checkm_result
[2024-01-24 14:14:05,666] [INFO] Task succeeded: CheckM
[2024-01-24 14:14:05,667] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:14:05,688] [INFO] ===== Completeness check finished =====
[2024-01-24 14:14:05,688] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:14:05,689] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007991475.1_ASM799147v1_genomic.fna/markers.fasta)
[2024-01-24 14:14:05,689] [INFO] Task started: Blastn
[2024-01-24 14:14:05,690] [INFO] Running command: blastn -query GCF_007991475.1_ASM799147v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc029b95-ec47-4634-a1d1-90bccffb049a/dqc_reference/reference_markers_gtdb.fasta -out GCF_007991475.1_ASM799147v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:07,721] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:07,726] [INFO] Selected 19 target genomes.
[2024-01-24 14:14:07,726] [INFO] Target genome list was writen to GCF_007991475.1_ASM799147v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:14:07,753] [INFO] Task started: fastANI
[2024-01-24 14:14:07,754] [INFO] Running command: fastANI --query /var/lib/cwl/stg9601b623-e1dc-43ad-87e5-f03c460e31b6/GCF_007991475.1_ASM799147v1_genomic.fna.gz --refList GCF_007991475.1_ASM799147v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007991475.1_ASM799147v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:14:22,335] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:22,353] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:14:22,354] [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
GCA_000767215.1	s__Actinotalea fermentans	99.6229	852	1235	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Actinotalea	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_012514545.1	s__Actinotalea sp012514545	82.909	564	1235	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Actinotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014042015.1	s__Actinotalea sp014042015	80.181	616	1235	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Actinotalea	95.0	99.62	99.62	0.98	0.98	2	-
GCF_016464425.1	s__Actinotalea solisilvae	80.0921	688	1235	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Actinotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014636275.1	s__Actinotalea carbonis	80.0233	657	1235	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Actinotalea	95.0	100.00	100.00	0.97	0.97	2	-
GCF_008364845.1	s__Actinotalea sp008364845	79.9781	678	1235	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Actinotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009996735.1	s__Actinotalea sp009996735	79.933	620	1235	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Actinotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000603945.1	s__Actinotalea ferrariae	79.6811	527	1235	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Actinotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014360395.1	s__Actinotalea sp014360395	79.6139	394	1235	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Actinotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006538725.1	s__Cellulomonas gelida	79.2551	561	1235	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.61	99.23	0.96	0.91	3	-
GCF_017565425.1	s__Actinotalea sp017565425	79.1652	544	1235	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Actinotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000312005.1	s__Cellulomonas massiliensis	79.037	547	1235	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_007991755.1	s__Cellulomonas aerilata	78.7572	540	1235	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	78.5874	537	1235	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017882855.1	s__JADGOR01 sp017882855	78.4968	296	1235	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__JADGOR01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907365.1	s__Oerskovia paurometabola	78.3787	511	1235	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia	95.0	99.20	99.20	0.97	0.97	2	-
GCF_014836755.1	s__Oerskovia sp014836755	78.2892	482	1235	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000971255.1	s__Demequina rhizosphaerae	77.8876	372	1235	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	97.98	97.96	0.93	0.92	3	-
GCF_002090075.1	s__Demequina sp002090075	77.7872	283	1235	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:14:22,356] [INFO] GTDB search result was written to GCF_007991475.1_ASM799147v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:14:22,356] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:14:22,361] [INFO] DFAST_QC result json was written to GCF_007991475.1_ASM799147v1_genomic.fna/dqc_result.json
[2024-01-24 14:14:22,361] [INFO] DFAST_QC completed!
[2024-01-24 14:14:22,361] [INFO] Total running time: 0h1m47s