[2024-01-24 13:32:18,337] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:18,341] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:18,341] [INFO] DQC Reference Directory: /var/lib/cwl/stg5e4e32f7-2cd5-459a-9ac3-ccad3a5fa123/dqc_reference
[2024-01-24 13:32:19,762] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:19,763] [INFO] Task started: Prodigal
[2024-01-24 13:32:19,763] [INFO] Running command: gunzip -c /var/lib/cwl/stg7435807b-a8c1-4c19-8483-5c93be80873f/GCF_006538745.1_ASM653874v1_genomic.fna.gz | prodigal -d GCF_006538745.1_ASM653874v1_genomic.fna/cds.fna -a GCF_006538745.1_ASM653874v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:32,085] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:32,086] [INFO] Task started: HMMsearch
[2024-01-24 13:32:32,086] [INFO] Running command: hmmsearch --tblout GCF_006538745.1_ASM653874v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5e4e32f7-2cd5-459a-9ac3-ccad3a5fa123/dqc_reference/reference_markers.hmm GCF_006538745.1_ASM653874v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:32,407] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:32,408] [INFO] Found 6/6 markers.
[2024-01-24 13:32:32,449] [INFO] Query marker FASTA was written to GCF_006538745.1_ASM653874v1_genomic.fna/markers.fasta
[2024-01-24 13:32:32,450] [INFO] Task started: Blastn
[2024-01-24 13:32:32,450] [INFO] Running command: blastn -query GCF_006538745.1_ASM653874v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e4e32f7-2cd5-459a-9ac3-ccad3a5fa123/dqc_reference/reference_markers.fasta -out GCF_006538745.1_ASM653874v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:33,849] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:33,852] [INFO] Selected 19 target genomes.
[2024-01-24 13:32:33,853] [INFO] Target genome list was writen to GCF_006538745.1_ASM653874v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:33,859] [INFO] Task started: fastANI
[2024-01-24 13:32:33,860] [INFO] Running command: fastANI --query /var/lib/cwl/stg7435807b-a8c1-4c19-8483-5c93be80873f/GCF_006538745.1_ASM653874v1_genomic.fna.gz --refList GCF_006538745.1_ASM653874v1_genomic.fna/target_genomes.txt --output GCF_006538745.1_ASM653874v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:55,217] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:55,218] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5e4e32f7-2cd5-459a-9ac3-ccad3a5fa123/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:55,218] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5e4e32f7-2cd5-459a-9ac3-ccad3a5fa123/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:55,235] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:32:55,235] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:55,235] [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 cellasea	strain=NBRC 3753	GCA_006538745.1	43670	43670	type	True	100.0	1552	1554	95	conclusive
Cellulomonas cellasea	strain=DSM 20118	GCA_000767135.1	43670	43670	type	True	99.8111	1187	1554	95	conclusive
Cellulomonas fimi	strain=NCTC7547	GCA_900637695.1	1708	1708	type	True	81.4759	859	1554	95	below_threshold
Cellulomonas fimi	strain=ATCC 484	GCA_000212695.1	1708	1708	type	True	81.455	873	1554	95	below_threshold
Cellulomonas biazotea	strain=NBRC12680	GCA_004306155.1	1709	1709	type	True	81.4528	771	1554	95	below_threshold
Cellulomonas timonensis	strain=SN7	GCA_900046455.1	1689271	1689271	type	True	81.1044	739	1554	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	80.9738	786	1554	95	below_threshold
Cellulomonas rhizosphaerae	strain=NEAU-TCZ24	GCA_003470205.1	2293719	2293719	type	True	80.9373	703	1554	95	below_threshold
Cellulomonas uda	strain=NBRC 3747	GCA_006538705.1	1714	1714	type	True	80.7715	719	1554	95	below_threshold
Cellulomonas xylanilytica	strain=NBRC 101102	GCA_007989805.1	233583	233583	type	True	80.5911	794	1554	95	below_threshold
Cellulomonas soli	strain=DSM 24484	GCA_013409305.1	931535	931535	type	True	80.5411	728	1554	95	below_threshold
Cellulomonas hominis	strain=NBRC 16055	GCA_007989225.1	156981	156981	suspected-type	True	80.4042	731	1554	95	below_threshold
Cellulomonas oligotrophica	strain=DSM 24482	GCA_013409875.1	931536	931536	type	True	80.371	795	1554	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	80.3668	767	1554	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	80.2977	778	1554	95	below_threshold
Cellulomonas hominis	strain=DSM 9581	GCA_014201095.1	156981	156981	suspected-type	True	80.2914	767	1554	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	80.1489	800	1554	95	below_threshold
Oerskovia rustica	strain=Sa4CUA1	GCA_014836555.1	2762237	2762237	type	True	79.449	663	1554	95	below_threshold
Oerskovia douganii	strain=Sa1BUA8	GCA_015142735.1	2762210	2762210	type	True	79.2507	671	1554	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:55,237] [INFO] DFAST Taxonomy check result was written to GCF_006538745.1_ASM653874v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:55,238] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:55,238] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:55,239] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5e4e32f7-2cd5-459a-9ac3-ccad3a5fa123/dqc_reference/checkm_data
[2024-01-24 13:32:55,240] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:55,302] [INFO] Task started: CheckM
[2024-01-24 13:32:55,302] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006538745.1_ASM653874v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006538745.1_ASM653874v1_genomic.fna/checkm_input GCF_006538745.1_ASM653874v1_genomic.fna/checkm_result
[2024-01-24 13:34:03,773] [INFO] Task succeeded: CheckM
[2024-01-24 13:34:03,775] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:34:03,797] [INFO] ===== Completeness check finished =====
[2024-01-24 13:34:03,797] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:34:03,798] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006538745.1_ASM653874v1_genomic.fna/markers.fasta)
[2024-01-24 13:34:03,798] [INFO] Task started: Blastn
[2024-01-24 13:34:03,798] [INFO] Running command: blastn -query GCF_006538745.1_ASM653874v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e4e32f7-2cd5-459a-9ac3-ccad3a5fa123/dqc_reference/reference_markers_gtdb.fasta -out GCF_006538745.1_ASM653874v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:05,851] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:05,856] [INFO] Selected 21 target genomes.
[2024-01-24 13:34:05,856] [INFO] Target genome list was writen to GCF_006538745.1_ASM653874v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:34:05,918] [INFO] Task started: fastANI
[2024-01-24 13:34:05,918] [INFO] Running command: fastANI --query /var/lib/cwl/stg7435807b-a8c1-4c19-8483-5c93be80873f/GCF_006538745.1_ASM653874v1_genomic.fna.gz --refList GCF_006538745.1_ASM653874v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006538745.1_ASM653874v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:28,306] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:28,327] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:28,328] [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_006538745.1	s__Cellulomonas cellasea	100.0	1552	1554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	97.79	95.59	0.95	0.91	3	conclusive
GCF_012396155.1	s__Cellulomonas septica	82.1152	552	1554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003851725.1	s__Cellulomonas algicola	81.7425	785	1554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	97.47	95.68	0.95	0.94	3	-
GCF_003115775.1	s__Cellulomonas sp003115775	81.7053	737	1554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000212695.1	s__Cellulomonas fimi	81.4522	872	1554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	99.99	1.00	1.00	3	-
GCF_900046455.1	s__Cellulomonas timonensis	81.0889	741	1554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	100.00	0.99	0.99	2	-
GCA_017744555.1	s__Cellulomonas sp017744555	80.8992	818	1554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862675.1	s__Cellulomonas chitinilytica	80.7345	860	1554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409305.1	s__Cellulomonas soli	80.576	724	1554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007989805.1	s__Cellulomonas xylanilytica	80.5559	798	1554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013359775.1	s__Cellulomonas humilata	80.4685	786	1554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009720485.1	s__Cellulomonas sp009720485	80.4417	809	1554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_901521055.1	s__Cellulomonas hominis_C	80.3631	748	1554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018388465.1	s__Cellulomonas sp018388465	80.3513	773	1554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.65	99.29	0.98	0.97	3	-
GCF_014201095.1	s__Cellulomonas hominis	80.3172	764	1554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.15	98.63	0.95	0.92	4	-
GCF_016464425.1	s__Actinotalea solisilvae	80.1818	795	1554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Actinotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763765.1	s__Cellulomonas sp014763765	80.1711	672	1554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018388445.1	s__Cellulomonas sp018388445	80.136	766	1554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.55	99.30	0.98	0.97	4	-
GCF_013409475.1	s__Cellulomonas hominis_B	80.1244	749	1554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007991755.1	s__Cellulomonas aerilata	79.9424	698	1554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539945.1	s__Cellulosimicrobium cellulans	79.4005	739	1554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:28,329] [INFO] GTDB search result was written to GCF_006538745.1_ASM653874v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:28,330] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:28,334] [INFO] DFAST_QC result json was written to GCF_006538745.1_ASM653874v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:28,334] [INFO] DFAST_QC completed!
[2024-01-24 13:34:28,334] [INFO] Total running time: 0h2m10s