[2024-01-24 12:15:19,123] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:15:19,124] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:15:19,125] [INFO] DQC Reference Directory: /var/lib/cwl/stg96bf9ce0-02a4-49ce-b9c2-3b851f5904ee/dqc_reference
[2024-01-24 12:15:20,481] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:15:20,482] [INFO] Task started: Prodigal
[2024-01-24 12:15:20,482] [INFO] Running command: gunzip -c /var/lib/cwl/stgd5801636-010f-475c-a772-d3805883c863/GCF_017353555.1_ASM1735355v1_genomic.fna.gz | prodigal -d GCF_017353555.1_ASM1735355v1_genomic.fna/cds.fna -a GCF_017353555.1_ASM1735355v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:33,595] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:33,595] [INFO] Task started: HMMsearch
[2024-01-24 12:15:33,595] [INFO] Running command: hmmsearch --tblout GCF_017353555.1_ASM1735355v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg96bf9ce0-02a4-49ce-b9c2-3b851f5904ee/dqc_reference/reference_markers.hmm GCF_017353555.1_ASM1735355v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:33,876] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:33,878] [INFO] Found 6/6 markers.
[2024-01-24 12:15:33,918] [INFO] Query marker FASTA was written to GCF_017353555.1_ASM1735355v1_genomic.fna/markers.fasta
[2024-01-24 12:15:33,919] [INFO] Task started: Blastn
[2024-01-24 12:15:33,919] [INFO] Running command: blastn -query GCF_017353555.1_ASM1735355v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg96bf9ce0-02a4-49ce-b9c2-3b851f5904ee/dqc_reference/reference_markers.fasta -out GCF_017353555.1_ASM1735355v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:35,288] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:35,293] [INFO] Selected 17 target genomes.
[2024-01-24 12:15:35,294] [INFO] Target genome list was writen to GCF_017353555.1_ASM1735355v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:35,299] [INFO] Task started: fastANI
[2024-01-24 12:15:35,300] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5801636-010f-475c-a772-d3805883c863/GCF_017353555.1_ASM1735355v1_genomic.fna.gz --refList GCF_017353555.1_ASM1735355v1_genomic.fna/target_genomes.txt --output GCF_017353555.1_ASM1735355v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:51,862] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:51,863] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg96bf9ce0-02a4-49ce-b9c2-3b851f5904ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:51,864] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg96bf9ce0-02a4-49ce-b9c2-3b851f5904ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:51,882] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:15:51,883] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:15:51,883] [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 avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	85.4402	1015	1475	95	below_threshold
Cellulomonas flavigena	strain=DSM 20109	GCA_000092865.1	1711	1711	type	True	84.4529	967	1475	95	below_threshold
Cellulomonas iranensis	strain=NBRC 101100	GCA_001552375.1	76862	76862	type	True	84.2665	893	1475	95	below_threshold
Cellulomonas telluris	strain=CPCC 204705	GCA_004886325.1	2306636	2306636	type	True	82.7205	865	1475	95	below_threshold
Cellulomonas shaoxiangyii	strain=Z28	GCA_004798685.1	2566013	2566013	type	True	82.7166	875	1475	95	below_threshold
Cellulomonas oligotrophica	strain=DSM 24482	GCA_013409875.1	931536	931536	type	True	82.0222	878	1475	95	below_threshold
Cellulomonas biazotea	strain=NBRC12680	GCA_004306155.1	1709	1709	type	True	81.1397	695	1475	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	81.0487	733	1475	95	below_threshold
Cellulomonas persica	strain=NBRC 101101	GCA_007989825.1	76861	76861	type	True	80.8596	691	1475	95	below_threshold
Cellulomonas fimi	strain=ATCC 484	GCA_000212695.1	1708	1708	type	True	80.8384	804	1475	95	below_threshold
Cellulomonas fimi	strain=NCTC7547	GCA_900637695.1	1708	1708	type	True	80.8196	796	1475	95	below_threshold
Cellulomonas rhizosphaerae	strain=NEAU-TCZ24	GCA_003470205.1	2293719	2293719	type	True	80.81	609	1475	95	below_threshold
Cellulomonas gilvus	strain=ATCC 13127	GCA_000218545.1	11	11	type	True	80.7247	688	1475	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	80.7103	708	1475	95	below_threshold
Cellulomonas massiliensis	strain=JC225	GCA_000312005.1	1465811	1465811	type	True	80.476	704	1475	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	79.1742	641	1475	95	below_threshold
Oerskovia douganii	strain=Sa1BUA8	GCA_015142735.1	2762210	2762210	type	True	78.9	542	1475	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:51,886] [INFO] DFAST Taxonomy check result was written to GCF_017353555.1_ASM1735355v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:51,886] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:51,887] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:51,887] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg96bf9ce0-02a4-49ce-b9c2-3b851f5904ee/dqc_reference/checkm_data
[2024-01-24 12:15:51,888] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:51,933] [INFO] Task started: CheckM
[2024-01-24 12:15:51,933] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017353555.1_ASM1735355v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017353555.1_ASM1735355v1_genomic.fna/checkm_input GCF_017353555.1_ASM1735355v1_genomic.fna/checkm_result
[2024-01-24 12:17:13,510] [INFO] Task succeeded: CheckM
[2024-01-24 12:17:13,512] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:17:13,542] [INFO] ===== Completeness check finished =====
[2024-01-24 12:17:13,543] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:17:13,543] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017353555.1_ASM1735355v1_genomic.fna/markers.fasta)
[2024-01-24 12:17:13,544] [INFO] Task started: Blastn
[2024-01-24 12:17:13,544] [INFO] Running command: blastn -query GCF_017353555.1_ASM1735355v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg96bf9ce0-02a4-49ce-b9c2-3b851f5904ee/dqc_reference/reference_markers_gtdb.fasta -out GCF_017353555.1_ASM1735355v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:17:15,629] [INFO] Task succeeded: Blastn
[2024-01-24 12:17:15,633] [INFO] Selected 10 target genomes.
[2024-01-24 12:17:15,633] [INFO] Target genome list was writen to GCF_017353555.1_ASM1735355v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:17:15,639] [INFO] Task started: fastANI
[2024-01-24 12:17:15,640] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5801636-010f-475c-a772-d3805883c863/GCF_017353555.1_ASM1735355v1_genomic.fna.gz --refList GCF_017353555.1_ASM1735355v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017353555.1_ASM1735355v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:17:26,963] [INFO] Task succeeded: fastANI
[2024-01-24 12:17:26,976] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:17:26,976] [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_018388445.1	s__Cellulomonas sp018388445	99.9987	1351	1475	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.55	99.30	0.98	0.97	4	conclusive
GCF_900114185.1	s__Cellulomonas sp900114185	93.2947	1182	1475	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014836445.1	s__Cellulomonas sp014836445	85.445	1015	1475	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018623035.1	s__Cellulomonas sp018623035	85.3388	1009	1475	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.51	99.03	0.98	0.95	3	-
GCA_015234515.1	s__Cellulomonas sp015234515	85.1136	1025	1475	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862775.1	s__Cellulomonas phragmiteti	84.8138	969	1475	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000092865.1	s__Cellulomonas flavigena	84.4811	964	1475	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552375.1	s__Cellulomonas iranensis	84.2554	894	1475	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	98.21	97.89	0.91	0.88	6	-
GCF_001462455.1	s__Cellulomonas sp001462455	84.1757	852	1475	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715865.1	s__Cellulomonas sp006715865	81.9916	894	1475	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:17:26,978] [INFO] GTDB search result was written to GCF_017353555.1_ASM1735355v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:17:26,979] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:17:26,982] [INFO] DFAST_QC result json was written to GCF_017353555.1_ASM1735355v1_genomic.fna/dqc_result.json
[2024-01-24 12:17:26,982] [INFO] DFAST_QC completed!
[2024-01-24 12:17:26,982] [INFO] Total running time: 0h2m8s