[2024-01-24 11:05:03,929] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:03,943] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:03,943] [INFO] DQC Reference Directory: /var/lib/cwl/stg999d35f8-b38d-49b6-ab8e-601ce6b735c4/dqc_reference
[2024-01-24 11:05:05,814] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:05,816] [INFO] Task started: Prodigal
[2024-01-24 11:05:05,816] [INFO] Running command: gunzip -c /var/lib/cwl/stgd8626e43-b518-41da-9134-9a1c5ddda4de/GCF_900111925.1_IMG-taxon_2675903053_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900111925.1_IMG-taxon_2675903053_annotated_assembly_genomic.fna/cds.fna -a GCF_900111925.1_IMG-taxon_2675903053_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:15,281] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:15,281] [INFO] Task started: HMMsearch
[2024-01-24 11:05:15,281] [INFO] Running command: hmmsearch --tblout GCF_900111925.1_IMG-taxon_2675903053_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg999d35f8-b38d-49b6-ab8e-601ce6b735c4/dqc_reference/reference_markers.hmm GCF_900111925.1_IMG-taxon_2675903053_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:15,553] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:15,554] [INFO] Found 6/6 markers.
[2024-01-24 11:05:15,606] [INFO] Query marker FASTA was written to GCF_900111925.1_IMG-taxon_2675903053_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 11:05:15,607] [INFO] Task started: Blastn
[2024-01-24 11:05:15,607] [INFO] Running command: blastn -query GCF_900111925.1_IMG-taxon_2675903053_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg999d35f8-b38d-49b6-ab8e-601ce6b735c4/dqc_reference/reference_markers.fasta -out GCF_900111925.1_IMG-taxon_2675903053_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:16,937] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:16,940] [INFO] Selected 16 target genomes.
[2024-01-24 11:05:16,940] [INFO] Target genome list was writen to GCF_900111925.1_IMG-taxon_2675903053_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 11:05:16,945] [INFO] Task started: fastANI
[2024-01-24 11:05:16,945] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8626e43-b518-41da-9134-9a1c5ddda4de/GCF_900111925.1_IMG-taxon_2675903053_annotated_assembly_genomic.fna.gz --refList GCF_900111925.1_IMG-taxon_2675903053_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900111925.1_IMG-taxon_2675903053_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:32,499] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:32,499] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg999d35f8-b38d-49b6-ab8e-601ce6b735c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:32,499] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg999d35f8-b38d-49b6-ab8e-601ce6b735c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:32,509] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:05:32,509] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:05:32,510] [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 marina	strain=CGMCC 4.6945	GCA_900111925.1	988821	988821	type	True	100.0	1301	1304	95	conclusive
Cellulomonas endophytica	strain=SYSUP0004	GCA_004123805.1	2494735	2494735	type	True	82.7025	843	1304	95	below_threshold
Cellulomonas massiliensis	strain=JC225	GCA_000312005.1	1465811	1465811	type	True	80.0851	609	1304	95	below_threshold
Cellulomonas fimi	strain=NCTC7547	GCA_900637695.1	1708	1708	type	True	80.0354	697	1304	95	below_threshold
Cellulomonas fimi	strain=ATCC 484	GCA_000212695.1	1708	1708	type	True	80.0195	707	1304	95	below_threshold
Cellulomonas telluris	strain=CPCC 204705	GCA_004886325.1	2306636	2306636	type	True	79.9422	716	1304	95	below_threshold
Cellulomonas biazotea	strain=NBRC12680	GCA_004306155.1	1709	1709	type	True	79.9068	640	1304	95	below_threshold
Cellulomonas iranensis	strain=NBRC 101100	GCA_001552375.1	76862	76862	type	True	79.8154	662	1304	95	below_threshold
Cellulomonas soli	strain=DSM 24484	GCA_013409305.1	931535	931535	type	True	79.8033	615	1304	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	79.6975	638	1304	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	79.5767	638	1304	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	79.5009	653	1304	95	below_threshold
Cellulomonas terrae	strain=NBRC 100819	GCA_007990265.1	311234	311234	type	True	79.4891	630	1304	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	78.8467	660	1304	95	below_threshold
Actinotalea subterranea	strain=HO-Ch2	GCA_008364845.1	2607497	2607497	type	True	78.7634	566	1304	95	below_threshold
Cellulosimicrobium marinum	strain=NBRC 110994	GCA_020551945.1	1638992	1638992	type	True	78.634	564	1304	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:32,511] [INFO] DFAST Taxonomy check result was written to GCF_900111925.1_IMG-taxon_2675903053_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 11:05:32,511] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:32,512] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:32,512] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg999d35f8-b38d-49b6-ab8e-601ce6b735c4/dqc_reference/checkm_data
[2024-01-24 11:05:32,512] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:32,551] [INFO] Task started: CheckM
[2024-01-24 11:05:32,552] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900111925.1_IMG-taxon_2675903053_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900111925.1_IMG-taxon_2675903053_annotated_assembly_genomic.fna/checkm_input GCF_900111925.1_IMG-taxon_2675903053_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 11:06:24,064] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:24,065] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:24,083] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:24,083] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:24,083] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900111925.1_IMG-taxon_2675903053_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 11:06:24,083] [INFO] Task started: Blastn
[2024-01-24 11:06:24,083] [INFO] Running command: blastn -query GCF_900111925.1_IMG-taxon_2675903053_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg999d35f8-b38d-49b6-ab8e-601ce6b735c4/dqc_reference/reference_markers_gtdb.fasta -out GCF_900111925.1_IMG-taxon_2675903053_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:26,349] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:26,352] [INFO] Selected 17 target genomes.
[2024-01-24 11:06:26,352] [INFO] Target genome list was writen to GCF_900111925.1_IMG-taxon_2675903053_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:26,361] [INFO] Task started: fastANI
[2024-01-24 11:06:26,361] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8626e43-b518-41da-9134-9a1c5ddda4de/GCF_900111925.1_IMG-taxon_2675903053_annotated_assembly_genomic.fna.gz --refList GCF_900111925.1_IMG-taxon_2675903053_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900111925.1_IMG-taxon_2675903053_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:42,510] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:42,520] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:06:42,521] [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_900111925.1	s__Cellulomonas marina	100.0	1301	1304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_004123805.1	s__Cellulomonas endophytica	82.6836	845	1304	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	80.1618	615	1304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	97.47	95.68	0.95	0.94	3	-
GCF_000312005.1	s__Cellulomonas massiliensis	80.0364	615	1304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000212695.1	s__Cellulomonas fimi	79.9954	710	1304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	99.99	1.00	1.00	3	-
GCF_009720485.1	s__Cellulomonas sp009720485	79.9274	707	1304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001462455.1	s__Cellulomonas sp001462455	79.91	628	1304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004886325.1	s__Cellulomonas telluris	79.868	727	1304	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	79.8469	658	1304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	98.21	97.89	0.91	0.88	6	-
GCF_013409305.1	s__Cellulomonas soli	79.7977	616	1304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018623035.1	s__Cellulomonas sp018623035	79.7333	628	1304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.51	99.03	0.98	0.95	3	-
GCF_014837175.1	s__Cellulomonas sp014837175	79.5554	595	1304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018531375.1	s__Cellulomonas sp018531375	79.5419	642	1304	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	79.5222	609	1304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.65	99.29	0.98	0.97	3	-
GCF_007990265.1	s__Cellulomonas terrae	79.4983	629	1304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011603975.1	s__Cellulomonas sp011603975	79.4826	614	1304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001019615.1	s__Cellulosimicrobium cellulans_E	78.3348	617	1304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	98.64	98.58	0.94	0.93	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:06:42,522] [INFO] GTDB search result was written to GCF_900111925.1_IMG-taxon_2675903053_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:42,522] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:42,525] [INFO] DFAST_QC result json was written to GCF_900111925.1_IMG-taxon_2675903053_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 11:06:42,526] [INFO] DFAST_QC completed!
[2024-01-24 11:06:42,526] [INFO] Total running time: 0h1m39s