[2024-01-24 12:21:44,650] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:44,652] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:44,652] [INFO] DQC Reference Directory: /var/lib/cwl/stg3fb5e9ac-cdc5-46a7-8aa0-fe822bc82f49/dqc_reference
[2024-01-24 12:21:45,915] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:45,916] [INFO] Task started: Prodigal
[2024-01-24 12:21:45,916] [INFO] Running command: gunzip -c /var/lib/cwl/stg601628cd-1610-4a4d-b4e1-21e02528b56c/GCF_003696205.1_ASM369620v1_genomic.fna.gz | prodigal -d GCF_003696205.1_ASM369620v1_genomic.fna/cds.fna -a GCF_003696205.1_ASM369620v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:21:56,681] [INFO] Task succeeded: Prodigal
[2024-01-24 12:21:56,681] [INFO] Task started: HMMsearch
[2024-01-24 12:21:56,681] [INFO] Running command: hmmsearch --tblout GCF_003696205.1_ASM369620v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3fb5e9ac-cdc5-46a7-8aa0-fe822bc82f49/dqc_reference/reference_markers.hmm GCF_003696205.1_ASM369620v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:21:57,017] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:21:57,024] [INFO] Found 6/6 markers.
[2024-01-24 12:21:57,067] [INFO] Query marker FASTA was written to GCF_003696205.1_ASM369620v1_genomic.fna/markers.fasta
[2024-01-24 12:21:57,067] [INFO] Task started: Blastn
[2024-01-24 12:21:57,067] [INFO] Running command: blastn -query GCF_003696205.1_ASM369620v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3fb5e9ac-cdc5-46a7-8aa0-fe822bc82f49/dqc_reference/reference_markers.fasta -out GCF_003696205.1_ASM369620v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:21:58,518] [INFO] Task succeeded: Blastn
[2024-01-24 12:21:58,523] [INFO] Selected 19 target genomes.
[2024-01-24 12:21:58,523] [INFO] Target genome list was writen to GCF_003696205.1_ASM369620v1_genomic.fna/target_genomes.txt
[2024-01-24 12:21:58,530] [INFO] Task started: fastANI
[2024-01-24 12:21:58,530] [INFO] Running command: fastANI --query /var/lib/cwl/stg601628cd-1610-4a4d-b4e1-21e02528b56c/GCF_003696205.1_ASM369620v1_genomic.fna.gz --refList GCF_003696205.1_ASM369620v1_genomic.fna/target_genomes.txt --output GCF_003696205.1_ASM369620v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:16,567] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:16,568] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3fb5e9ac-cdc5-46a7-8aa0-fe822bc82f49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:16,568] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3fb5e9ac-cdc5-46a7-8aa0-fe822bc82f49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:16,584] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:22:16,584] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:22:16,584] [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 hominis	strain=NBRC 16055	GCA_007989225.1	156981	156981	suspected-type	True	85.2439	843	1322	95	below_threshold
Cellulomonas hominis	strain=DSM 9581	GCA_014201095.1	156981	156981	suspected-type	True	85.2064	885	1322	95	below_threshold
Cellulomonas taurus	strain=P40-2	GCA_012931845.1	2729175	2729175	type	True	81.6828	710	1322	95	below_threshold
Cellulomonas biazotea	strain=NBRC12680	GCA_004306155.1	1709	1709	type	True	80.7174	622	1322	95	below_threshold
Cellulomonas cellasea	strain=DSM 20118	GCA_000767135.1	43670	43670	type	True	80.5288	573	1322	95	below_threshold
Cellulomonas fimi	strain=NCTC7547	GCA_900637695.1	1708	1708	type	True	80.4186	686	1322	95	below_threshold
Cellulomonas rhizosphaerae	strain=NEAU-TCZ24	GCA_003470205.1	2293719	2293719	type	True	80.4158	567	1322	95	below_threshold
Cellulomonas soli	strain=DSM 24484	GCA_013409305.1	931535	931535	type	True	80.4119	666	1322	95	below_threshold
Cellulomonas cellasea	strain=NBRC 3753	GCA_006538745.1	43670	43670	type	True	80.3249	694	1322	95	below_threshold
Cellulomonas fimi	strain=ATCC 484	GCA_000212695.1	1708	1708	type	True	80.3183	709	1322	95	below_threshold
Cellulomonas timonensis	strain=SN7	GCA_900046455.1	1689271	1689271	type	True	80.2699	621	1322	95	below_threshold
Cellulomonas massiliensis	strain=JC225	GCA_000312005.1	1465811	1465811	type	True	80.2666	626	1322	95	below_threshold
Cellulomonas terrae	strain=NBRC 100819	GCA_007990265.1	311234	311234	type	True	80.1912	632	1322	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	80.1734	638	1322	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	79.9809	637	1322	95	below_threshold
Cellulomonas xylanilytica	strain=NBRC 101102	GCA_007989805.1	233583	233583	type	True	79.9262	650	1322	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	79.8007	637	1322	95	below_threshold
Oerskovia merdavium	strain=Sa2CUA9	GCA_014836755.1	2762227	2762227	type	True	78.8719	527	1322	95	below_threshold
Oerskovia rustica	strain=Sa4CUA1	GCA_014836555.1	2762237	2762237	type	True	78.8571	539	1322	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:16,587] [INFO] DFAST Taxonomy check result was written to GCF_003696205.1_ASM369620v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:16,587] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:16,588] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:16,588] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3fb5e9ac-cdc5-46a7-8aa0-fe822bc82f49/dqc_reference/checkm_data
[2024-01-24 12:22:16,590] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:16,647] [INFO] Task started: CheckM
[2024-01-24 12:22:16,647] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003696205.1_ASM369620v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003696205.1_ASM369620v1_genomic.fna/checkm_input GCF_003696205.1_ASM369620v1_genomic.fna/checkm_result
[2024-01-24 12:23:17,260] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:17,261] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:17,287] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:17,287] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:17,288] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003696205.1_ASM369620v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:17,288] [INFO] Task started: Blastn
[2024-01-24 12:23:17,288] [INFO] Running command: blastn -query GCF_003696205.1_ASM369620v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3fb5e9ac-cdc5-46a7-8aa0-fe822bc82f49/dqc_reference/reference_markers_gtdb.fasta -out GCF_003696205.1_ASM369620v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:19,623] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:19,628] [INFO] Selected 12 target genomes.
[2024-01-24 12:23:19,629] [INFO] Target genome list was writen to GCF_003696205.1_ASM369620v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:19,638] [INFO] Task started: fastANI
[2024-01-24 12:23:19,639] [INFO] Running command: fastANI --query /var/lib/cwl/stg601628cd-1610-4a4d-b4e1-21e02528b56c/GCF_003696205.1_ASM369620v1_genomic.fna.gz --refList GCF_003696205.1_ASM369620v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003696205.1_ASM369620v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:32,945] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:32,957] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:32,958] [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_003696205.1	s__Cellulomonas sp003696205	100.0	1317	1322	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_011603975.1	s__Cellulomonas sp011603975	86.1047	842	1322	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005239125.1	s__Cellulomonas hominis_A	86.0962	838	1322	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008033115.1	s__Cellulomonas sp008033115	85.8651	969	1322	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	96.34	96.34	0.91	0.91	2	-
GCF_007679345.1	s__Cellulomonas cellulans_A	85.7193	949	1322	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862755.1	s__Cellulomonas pakistanensis	85.6547	917	1322	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201095.1	s__Cellulomonas hominis	85.2275	883	1322	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.15	98.63	0.95	0.92	4	-
GCF_013409475.1	s__Cellulomonas hominis_B	85.1107	862	1322	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	85.1093	862	1322	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006538745.1	s__Cellulomonas cellasea	80.3213	696	1322	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	97.79	95.59	0.95	0.91	3	-
GCF_000312005.1	s__Cellulomonas massiliensis	80.2922	623	1322	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_006715865.1	s__Cellulomonas sp006715865	80.0524	703	1322	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 12:23:32,960] [INFO] GTDB search result was written to GCF_003696205.1_ASM369620v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:32,960] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:32,965] [INFO] DFAST_QC result json was written to GCF_003696205.1_ASM369620v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:32,965] [INFO] DFAST_QC completed!
[2024-01-24 12:23:32,965] [INFO] Total running time: 0h1m48s