[2024-01-25 18:25:35,492] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:25:35,494] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:25:35,494] [INFO] DQC Reference Directory: /var/lib/cwl/stgc56017a2-87ab-4fbe-a62b-8ccd05e117cb/dqc_reference
[2024-01-25 18:25:36,590] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:25:36,592] [INFO] Task started: Prodigal
[2024-01-25 18:25:36,592] [INFO] Running command: gunzip -c /var/lib/cwl/stg3d0e900e-23cf-458d-b47d-6ee125975527/GCF_021590045.1_ASM2159004v1_genomic.fna.gz | prodigal -d GCF_021590045.1_ASM2159004v1_genomic.fna/cds.fna -a GCF_021590045.1_ASM2159004v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:25:46,026] [INFO] Task succeeded: Prodigal
[2024-01-25 18:25:46,026] [INFO] Task started: HMMsearch
[2024-01-25 18:25:46,027] [INFO] Running command: hmmsearch --tblout GCF_021590045.1_ASM2159004v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc56017a2-87ab-4fbe-a62b-8ccd05e117cb/dqc_reference/reference_markers.hmm GCF_021590045.1_ASM2159004v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:25:46,233] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:25:46,234] [INFO] Found 6/6 markers.
[2024-01-25 18:25:46,265] [INFO] Query marker FASTA was written to GCF_021590045.1_ASM2159004v1_genomic.fna/markers.fasta
[2024-01-25 18:25:46,266] [INFO] Task started: Blastn
[2024-01-25 18:25:46,266] [INFO] Running command: blastn -query GCF_021590045.1_ASM2159004v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc56017a2-87ab-4fbe-a62b-8ccd05e117cb/dqc_reference/reference_markers.fasta -out GCF_021590045.1_ASM2159004v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:25:47,639] [INFO] Task succeeded: Blastn
[2024-01-25 18:25:47,643] [INFO] Selected 12 target genomes.
[2024-01-25 18:25:47,643] [INFO] Target genome list was writen to GCF_021590045.1_ASM2159004v1_genomic.fna/target_genomes.txt
[2024-01-25 18:25:47,659] [INFO] Task started: fastANI
[2024-01-25 18:25:47,660] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d0e900e-23cf-458d-b47d-6ee125975527/GCF_021590045.1_ASM2159004v1_genomic.fna.gz --refList GCF_021590045.1_ASM2159004v1_genomic.fna/target_genomes.txt --output GCF_021590045.1_ASM2159004v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:26:01,270] [INFO] Task succeeded: fastANI
[2024-01-25 18:26:01,271] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc56017a2-87ab-4fbe-a62b-8ccd05e117cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:26:01,271] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc56017a2-87ab-4fbe-a62b-8ccd05e117cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:26:01,279] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:26:01,279] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:26:01,280] [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 palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	100.0	1277	1278	95	conclusive
Cellulomonas uda	strain=NBRC 3747	GCA_006538705.1	1714	1714	type	True	90.4142	1004	1278	95	below_threshold
Cellulomonas persica	strain=NBRC 101101	GCA_007989825.1	76861	76861	type	True	86.1238	976	1278	95	below_threshold
Cellulomonas gelida	strain=NBRC 3748	GCA_006538725.1	1712	1712	type	True	85.8542	951	1278	95	below_threshold
Cellulomonas gelida	strain=JCM 1490	GCA_014647015.1	1712	1712	type	True	85.7046	987	1278	95	below_threshold
Cellulomonas gilvus	strain=ATCC 13127	GCA_000218545.1	11	11	type	True	84.2849	848	1278	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	83.971	886	1278	95	below_threshold
Cellulomonas biazotea	strain=NBRC12680	GCA_004306155.1	1709	1709	type	True	82.5615	716	1278	95	below_threshold
Cellulomonas flavigena	strain=DSM 20109	GCA_000092865.1	1711	1711	type	True	81.5191	747	1278	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	81.1747	757	1278	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	79.6518	685	1278	95	below_threshold
Actinotalea subterranea	strain=HO-Ch2	GCA_008364845.1	2607497	2607497	type	True	79.3561	606	1278	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:26:01,281] [INFO] DFAST Taxonomy check result was written to GCF_021590045.1_ASM2159004v1_genomic.fna/tc_result.tsv
[2024-01-25 18:26:01,282] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:26:01,282] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:26:01,282] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc56017a2-87ab-4fbe-a62b-8ccd05e117cb/dqc_reference/checkm_data
[2024-01-25 18:26:01,283] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:26:01,321] [INFO] Task started: CheckM
[2024-01-25 18:26:01,321] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021590045.1_ASM2159004v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021590045.1_ASM2159004v1_genomic.fna/checkm_input GCF_021590045.1_ASM2159004v1_genomic.fna/checkm_result
[2024-01-25 18:27:35,821] [INFO] Task succeeded: CheckM
[2024-01-25 18:27:35,822] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:27:35,857] [INFO] ===== Completeness check finished =====
[2024-01-25 18:27:35,857] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:27:35,858] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021590045.1_ASM2159004v1_genomic.fna/markers.fasta)
[2024-01-25 18:27:35,858] [INFO] Task started: Blastn
[2024-01-25 18:27:35,859] [INFO] Running command: blastn -query GCF_021590045.1_ASM2159004v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc56017a2-87ab-4fbe-a62b-8ccd05e117cb/dqc_reference/reference_markers_gtdb.fasta -out GCF_021590045.1_ASM2159004v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:27:38,422] [INFO] Task succeeded: Blastn
[2024-01-25 18:27:38,425] [INFO] Selected 9 target genomes.
[2024-01-25 18:27:38,425] [INFO] Target genome list was writen to GCF_021590045.1_ASM2159004v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:27:38,448] [INFO] Task started: fastANI
[2024-01-25 18:27:38,448] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d0e900e-23cf-458d-b47d-6ee125975527/GCF_021590045.1_ASM2159004v1_genomic.fna.gz --refList GCF_021590045.1_ASM2159004v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021590045.1_ASM2159004v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:27:48,071] [INFO] Task succeeded: fastANI
[2024-01-25 18:27:48,078] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:27:48,078] [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_006538705.1	s__Cellulomonas uda	90.4299	1003	1278	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	98.69	98.01	0.94	0.90	4	-
GCF_007989825.1	s__Cellulomonas persica	86.119	977	1278	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006538725.1	s__Cellulomonas gelida	85.8507	951	1278	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.61	99.23	0.96	0.91	3	-
GCF_000218545.1	s__Cellulomonas gilvus	84.2868	851	1278	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	83.9783	885	1278	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007990245.1	s__Cellulomonas composti	83.2121	805	1278	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004306155.1	s__Cellulomonas biazotea	82.5919	715	1278	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000212695.1	s__Cellulomonas fimi	82.4816	827	1278	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	99.99	1.00	1.00	3	-
GCF_003755175.1	s__Cellulomonas sp003755175	81.9958	738	1278	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:27:48,079] [INFO] GTDB search result was written to GCF_021590045.1_ASM2159004v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:27:48,080] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:27:48,083] [INFO] DFAST_QC result json was written to GCF_021590045.1_ASM2159004v1_genomic.fna/dqc_result.json
[2024-01-25 18:27:48,083] [INFO] DFAST_QC completed!
[2024-01-25 18:27:48,083] [INFO] Total running time: 0h2m13s