[2024-01-24 13:57:16,325] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:16,327] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:16,327] [INFO] DQC Reference Directory: /var/lib/cwl/stg1afbc579-bda9-4b96-b0bd-3eb7afdcbb35/dqc_reference
[2024-01-24 13:57:17,728] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:17,729] [INFO] Task started: Prodigal
[2024-01-24 13:57:17,729] [INFO] Running command: gunzip -c /var/lib/cwl/stg4d832c45-4af7-4e1e-8096-d03b3aed87de/GCF_007990265.1_ASM799026v1_genomic.fna.gz | prodigal -d GCF_007990265.1_ASM799026v1_genomic.fna/cds.fna -a GCF_007990265.1_ASM799026v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:29,408] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:29,408] [INFO] Task started: HMMsearch
[2024-01-24 13:57:29,409] [INFO] Running command: hmmsearch --tblout GCF_007990265.1_ASM799026v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1afbc579-bda9-4b96-b0bd-3eb7afdcbb35/dqc_reference/reference_markers.hmm GCF_007990265.1_ASM799026v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:29,722] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:29,724] [INFO] Found 6/6 markers.
[2024-01-24 13:57:29,770] [INFO] Query marker FASTA was written to GCF_007990265.1_ASM799026v1_genomic.fna/markers.fasta
[2024-01-24 13:57:29,771] [INFO] Task started: Blastn
[2024-01-24 13:57:29,771] [INFO] Running command: blastn -query GCF_007990265.1_ASM799026v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1afbc579-bda9-4b96-b0bd-3eb7afdcbb35/dqc_reference/reference_markers.fasta -out GCF_007990265.1_ASM799026v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:31,142] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:31,145] [INFO] Selected 15 target genomes.
[2024-01-24 13:57:31,146] [INFO] Target genome list was writen to GCF_007990265.1_ASM799026v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:31,150] [INFO] Task started: fastANI
[2024-01-24 13:57:31,150] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d832c45-4af7-4e1e-8096-d03b3aed87de/GCF_007990265.1_ASM799026v1_genomic.fna.gz --refList GCF_007990265.1_ASM799026v1_genomic.fna/target_genomes.txt --output GCF_007990265.1_ASM799026v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:46,525] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:46,525] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1afbc579-bda9-4b96-b0bd-3eb7afdcbb35/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:46,526] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1afbc579-bda9-4b96-b0bd-3eb7afdcbb35/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:46,539] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:57:46,539] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:46,539] [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 terrae	strain=NBRC 100819	GCA_007990265.1	311234	311234	type	True	100.0	1411	1415	95	conclusive
Cellulomonas xylanilytica	strain=NBRC 101102	GCA_007989805.1	233583	233583	type	True	89.0833	1186	1415	95	below_threshold
Cellulomonas humilata	strain=ATCC 25174	GCA_013359775.1	144055	144055	type	True	86.697	1099	1415	95	below_threshold
Cellulomonas biazotea	strain=NBRC12680	GCA_004306155.1	1709	1709	type	True	82.2178	787	1415	95	below_threshold
Cellulomonas fimi	strain=ATCC 484	GCA_000212695.1	1708	1708	type	True	82.029	876	1415	95	below_threshold
Cellulomonas rhizosphaerae	strain=NEAU-TCZ24	GCA_003470205.1	2293719	2293719	type	True	81.967	715	1415	95	below_threshold
Cellulomonas fimi	strain=NCTC7547	GCA_900637695.1	1708	1708	type	True	81.9599	876	1415	95	below_threshold
Cellulomonas soli	strain=DSM 24484	GCA_013409305.1	931535	931535	type	True	81.147	696	1415	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	81.0698	734	1415	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	80.9609	738	1415	95	below_threshold
Cellulomonas telluris	strain=CPCC 204705	GCA_004886325.1	2306636	2306636	type	True	80.6325	751	1415	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	80.4151	722	1415	95	below_threshold
Cellulomonas hominis	strain=DSM 9581	GCA_014201095.1	156981	156981	suspected-type	True	80.2421	677	1415	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	79.3966	686	1415	95	below_threshold
Actinotalea subterranea	strain=HO-Ch2	GCA_008364845.1	2607497	2607497	type	True	79.2468	565	1415	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:46,541] [INFO] DFAST Taxonomy check result was written to GCF_007990265.1_ASM799026v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:46,542] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:46,542] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:46,542] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1afbc579-bda9-4b96-b0bd-3eb7afdcbb35/dqc_reference/checkm_data
[2024-01-24 13:57:46,543] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:46,586] [INFO] Task started: CheckM
[2024-01-24 13:57:46,586] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007990265.1_ASM799026v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007990265.1_ASM799026v1_genomic.fna/checkm_input GCF_007990265.1_ASM799026v1_genomic.fna/checkm_result
[2024-01-24 13:58:47,494] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:47,495] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:47,516] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:47,516] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:47,517] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007990265.1_ASM799026v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:47,517] [INFO] Task started: Blastn
[2024-01-24 13:58:47,517] [INFO] Running command: blastn -query GCF_007990265.1_ASM799026v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1afbc579-bda9-4b96-b0bd-3eb7afdcbb35/dqc_reference/reference_markers_gtdb.fasta -out GCF_007990265.1_ASM799026v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:49,766] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:49,770] [INFO] Selected 9 target genomes.
[2024-01-24 13:58:49,771] [INFO] Target genome list was writen to GCF_007990265.1_ASM799026v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:49,781] [INFO] Task started: fastANI
[2024-01-24 13:58:49,782] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d832c45-4af7-4e1e-8096-d03b3aed87de/GCF_007990265.1_ASM799026v1_genomic.fna.gz --refList GCF_007990265.1_ASM799026v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007990265.1_ASM799026v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:59,866] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:59,875] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:59,875] [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_007990265.1	s__Cellulomonas terrae	100.0	1411	1415	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001424195.1	s__Cellulomonas sp001424195	91.6237	1225	1415	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001426705.1	s__Cellulomonas sp001426705	89.9989	1227	1415	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007989805.1	s__Cellulomonas xylanilytica	89.0833	1186	1415	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424125.1	s__Cellulomonas sp001424125	88.981	1072	1415	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001429255.1	s__Cellulomonas sp001429255	86.9065	1072	1415	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	98.79	98.79	0.94	0.94	2	-
GCF_013359775.1	s__Cellulomonas humilata	86.7374	1095	1415	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	85.5651	967	1415	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.65	99.29	0.98	0.97	3	-
GCF_000212695.1	s__Cellulomonas fimi	82.0019	879	1415	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	99.99	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:59,877] [INFO] GTDB search result was written to GCF_007990265.1_ASM799026v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:59,877] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:59,882] [INFO] DFAST_QC result json was written to GCF_007990265.1_ASM799026v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:59,882] [INFO] DFAST_QC completed!
[2024-01-24 13:58:59,883] [INFO] Total running time: 0h1m44s