[2024-01-24 11:12:52,599] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:52,601] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:52,601] [INFO] DQC Reference Directory: /var/lib/cwl/stgc4376887-d146-4c0f-879c-cc196a520f15/dqc_reference
[2024-01-24 11:12:53,887] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:53,889] [INFO] Task started: Prodigal
[2024-01-24 11:12:53,889] [INFO] Running command: gunzip -c /var/lib/cwl/stgcc1469bc-1552-45f8-9b9d-9a5ae4cf7f77/GCF_013359775.1_ASM1335977v1_genomic.fna.gz | prodigal -d GCF_013359775.1_ASM1335977v1_genomic.fna/cds.fna -a GCF_013359775.1_ASM1335977v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:07,679] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:07,679] [INFO] Task started: HMMsearch
[2024-01-24 11:13:07,679] [INFO] Running command: hmmsearch --tblout GCF_013359775.1_ASM1335977v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc4376887-d146-4c0f-879c-cc196a520f15/dqc_reference/reference_markers.hmm GCF_013359775.1_ASM1335977v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:08,046] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:08,048] [INFO] Found 6/6 markers.
[2024-01-24 11:13:08,087] [INFO] Query marker FASTA was written to GCF_013359775.1_ASM1335977v1_genomic.fna/markers.fasta
[2024-01-24 11:13:08,088] [INFO] Task started: Blastn
[2024-01-24 11:13:08,088] [INFO] Running command: blastn -query GCF_013359775.1_ASM1335977v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc4376887-d146-4c0f-879c-cc196a520f15/dqc_reference/reference_markers.fasta -out GCF_013359775.1_ASM1335977v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:09,529] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:09,533] [INFO] Selected 15 target genomes.
[2024-01-24 11:13:09,533] [INFO] Target genome list was writen to GCF_013359775.1_ASM1335977v1_genomic.fna/target_genomes.txt
[2024-01-24 11:13:09,539] [INFO] Task started: fastANI
[2024-01-24 11:13:09,539] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc1469bc-1552-45f8-9b9d-9a5ae4cf7f77/GCF_013359775.1_ASM1335977v1_genomic.fna.gz --refList GCF_013359775.1_ASM1335977v1_genomic.fna/target_genomes.txt --output GCF_013359775.1_ASM1335977v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:24,550] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:24,551] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc4376887-d146-4c0f-879c-cc196a520f15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:24,551] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc4376887-d146-4c0f-879c-cc196a520f15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:24,565] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:13:24,565] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:24,565] [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 humilata	strain=ATCC 25174	GCA_013359775.1	144055	144055	type	True	100.0	1526	1527	95	conclusive
Cellulomonas terrae	strain=NBRC 100819	GCA_007990265.1	311234	311234	type	True	86.7325	1098	1527	95	below_threshold
Cellulomonas xylanilytica	strain=NBRC 101102	GCA_007989805.1	233583	233583	type	True	86.3479	1097	1527	95	below_threshold
Cellulomonas rhizosphaerae	strain=NEAU-TCZ24	GCA_003470205.1	2293719	2293719	type	True	82.1968	716	1527	95	below_threshold
Cellulomonas biazotea	strain=NBRC12680	GCA_004306155.1	1709	1709	type	True	82.0082	792	1527	95	below_threshold
Cellulomonas fimi	strain=NCTC7547	GCA_900637695.1	1708	1708	type	True	81.7976	849	1527	95	below_threshold
Cellulomonas fimi	strain=ATCC 484	GCA_000212695.1	1708	1708	type	True	81.6914	874	1527	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	81.0875	727	1527	95	below_threshold
Cellulomonas soli	strain=DSM 24484	GCA_013409305.1	931535	931535	type	True	80.9579	740	1527	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	80.6389	752	1527	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	80.3799	688	1527	95	below_threshold
Cellulomonas telluris	strain=CPCC 204705	GCA_004886325.1	2306636	2306636	type	True	80.361	750	1527	95	below_threshold
Cellulomonas hominis	strain=DSM 9581	GCA_014201095.1	156981	156981	suspected-type	True	80.1233	714	1527	95	below_threshold
Actinotalea subterranea	strain=HO-Ch2	GCA_008364845.1	2607497	2607497	type	True	79.0803	597	1527	95	below_threshold
Oerskovia rustica	strain=Sa4CUA1	GCA_014836555.1	2762237	2762237	type	True	78.878	556	1527	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:24,575] [INFO] DFAST Taxonomy check result was written to GCF_013359775.1_ASM1335977v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:24,576] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:24,576] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:24,576] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc4376887-d146-4c0f-879c-cc196a520f15/dqc_reference/checkm_data
[2024-01-24 11:13:24,578] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:24,629] [INFO] Task started: CheckM
[2024-01-24 11:13:24,629] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013359775.1_ASM1335977v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013359775.1_ASM1335977v1_genomic.fna/checkm_input GCF_013359775.1_ASM1335977v1_genomic.fna/checkm_result
[2024-01-24 11:14:33,592] [INFO] Task succeeded: CheckM
[2024-01-24 11:14:33,593] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:14:33,611] [INFO] ===== Completeness check finished =====
[2024-01-24 11:14:33,612] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:14:33,612] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013359775.1_ASM1335977v1_genomic.fna/markers.fasta)
[2024-01-24 11:14:33,612] [INFO] Task started: Blastn
[2024-01-24 11:14:33,613] [INFO] Running command: blastn -query GCF_013359775.1_ASM1335977v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc4376887-d146-4c0f-879c-cc196a520f15/dqc_reference/reference_markers_gtdb.fasta -out GCF_013359775.1_ASM1335977v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:14:35,677] [INFO] Task succeeded: Blastn
[2024-01-24 11:14:35,682] [INFO] Selected 9 target genomes.
[2024-01-24 11:14:35,682] [INFO] Target genome list was writen to GCF_013359775.1_ASM1335977v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:14:35,688] [INFO] Task started: fastANI
[2024-01-24 11:14:35,688] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc1469bc-1552-45f8-9b9d-9a5ae4cf7f77/GCF_013359775.1_ASM1335977v1_genomic.fna.gz --refList GCF_013359775.1_ASM1335977v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013359775.1_ASM1335977v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:45,993] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:46,004] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:14:46,004] [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_013359775.1	s__Cellulomonas humilata	100.0	1526	1527	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001429255.1	s__Cellulomonas sp001429255	91.4678	1210	1527	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	98.79	98.79	0.94	0.94	2	-
GCF_001426705.1	s__Cellulomonas sp001426705	86.8488	1150	1527	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007990265.1	s__Cellulomonas terrae	86.7163	1100	1527	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424195.1	s__Cellulomonas sp001424195	86.7004	1130	1527	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	86.544	1055	1527	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	86.3481	1097	1527	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	85.6367	992	1527	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.65	99.29	0.98	0.97	3	-
GCF_004886325.1	s__Cellulomonas telluris	80.4135	744	1527	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 11:14:46,006] [INFO] GTDB search result was written to GCF_013359775.1_ASM1335977v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:46,006] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:46,009] [INFO] DFAST_QC result json was written to GCF_013359775.1_ASM1335977v1_genomic.fna/dqc_result.json
[2024-01-24 11:14:46,010] [INFO] DFAST_QC completed!
[2024-01-24 11:14:46,010] [INFO] Total running time: 0h1m53s