[2024-01-24 12:14:33,649] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:33,650] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:33,651] [INFO] DQC Reference Directory: /var/lib/cwl/stg12acc641-739d-471a-a699-cebed2980e8d/dqc_reference
[2024-01-24 12:14:35,032] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:35,033] [INFO] Task started: Prodigal
[2024-01-24 12:14:35,033] [INFO] Running command: gunzip -c /var/lib/cwl/stg7b5c61e8-d780-4b3d-a50f-722d567d492b/GCF_018388465.1_ASM1838846v1_genomic.fna.gz | prodigal -d GCF_018388465.1_ASM1838846v1_genomic.fna/cds.fna -a GCF_018388465.1_ASM1838846v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:46,433] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:46,433] [INFO] Task started: HMMsearch
[2024-01-24 12:14:46,434] [INFO] Running command: hmmsearch --tblout GCF_018388465.1_ASM1838846v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg12acc641-739d-471a-a699-cebed2980e8d/dqc_reference/reference_markers.hmm GCF_018388465.1_ASM1838846v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:46,740] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:46,741] [INFO] Found 6/6 markers.
[2024-01-24 12:14:46,780] [INFO] Query marker FASTA was written to GCF_018388465.1_ASM1838846v1_genomic.fna/markers.fasta
[2024-01-24 12:14:46,781] [INFO] Task started: Blastn
[2024-01-24 12:14:46,781] [INFO] Running command: blastn -query GCF_018388465.1_ASM1838846v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg12acc641-739d-471a-a699-cebed2980e8d/dqc_reference/reference_markers.fasta -out GCF_018388465.1_ASM1838846v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:48,204] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:48,208] [INFO] Selected 16 target genomes.
[2024-01-24 12:14:48,208] [INFO] Target genome list was writen to GCF_018388465.1_ASM1838846v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:48,218] [INFO] Task started: fastANI
[2024-01-24 12:14:48,218] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b5c61e8-d780-4b3d-a50f-722d567d492b/GCF_018388465.1_ASM1838846v1_genomic.fna.gz --refList GCF_018388465.1_ASM1838846v1_genomic.fna/target_genomes.txt --output GCF_018388465.1_ASM1838846v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:03,753] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:03,754] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg12acc641-739d-471a-a699-cebed2980e8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:03,754] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg12acc641-739d-471a-a699-cebed2980e8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:03,768] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:15:03,768] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:15:03,768] [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	85.6924	967	1329	95	below_threshold
Cellulomonas terrae	strain=NBRC 100819	GCA_007990265.1	311234	311234	type	True	85.5223	974	1329	95	below_threshold
Cellulomonas xylanilytica	strain=NBRC 101102	GCA_007989805.1	233583	233583	type	True	85.485	1005	1329	95	below_threshold
Cellulomonas rhizosphaerae	strain=NEAU-TCZ24	GCA_003470205.1	2293719	2293719	type	True	81.881	658	1329	95	below_threshold
Cellulomonas fimi	strain=NCTC7547	GCA_900637695.1	1708	1708	type	True	81.6655	835	1329	95	below_threshold
Cellulomonas fimi	strain=ATCC 484	GCA_000212695.1	1708	1708	type	True	81.6619	842	1329	95	below_threshold
Cellulomonas soli	strain=DSM 24484	GCA_013409305.1	931535	931535	type	True	80.9141	714	1329	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	80.8592	712	1329	95	below_threshold
Cellulomonas massiliensis	strain=JC225	GCA_000312005.1	1465811	1465811	type	True	80.8571	704	1329	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	80.7402	716	1329	95	below_threshold
Cellulomonas persica	strain=NBRC 101101	GCA_007989825.1	76861	76861	type	True	80.7376	674	1329	95	below_threshold
Cellulomonas uda	strain=NBRC 3747	GCA_006538705.1	1714	1714	type	True	80.667	670	1329	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	80.4347	726	1329	95	below_threshold
Cellulomonas hominis	strain=DSM 9581	GCA_014201095.1	156981	156981	suspected-type	True	80.241	676	1329	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	79.3716	626	1329	95	below_threshold
Oerskovia rustica	strain=Sa4CUA1	GCA_014836555.1	2762237	2762237	type	True	79.0453	536	1329	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:03,770] [INFO] DFAST Taxonomy check result was written to GCF_018388465.1_ASM1838846v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:03,775] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:03,775] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:03,775] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg12acc641-739d-471a-a699-cebed2980e8d/dqc_reference/checkm_data
[2024-01-24 12:15:03,776] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:03,839] [INFO] Task started: CheckM
[2024-01-24 12:15:03,840] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018388465.1_ASM1838846v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018388465.1_ASM1838846v1_genomic.fna/checkm_input GCF_018388465.1_ASM1838846v1_genomic.fna/checkm_result
[2024-01-24 12:16:18,111] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:18,113] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:18,138] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:18,139] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:18,139] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018388465.1_ASM1838846v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:18,140] [INFO] Task started: Blastn
[2024-01-24 12:16:18,140] [INFO] Running command: blastn -query GCF_018388465.1_ASM1838846v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg12acc641-739d-471a-a699-cebed2980e8d/dqc_reference/reference_markers_gtdb.fasta -out GCF_018388465.1_ASM1838846v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:20,290] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:20,294] [INFO] Selected 12 target genomes.
[2024-01-24 12:16:20,295] [INFO] Target genome list was writen to GCF_018388465.1_ASM1838846v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:20,336] [INFO] Task started: fastANI
[2024-01-24 12:16:20,336] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b5c61e8-d780-4b3d-a50f-722d567d492b/GCF_018388465.1_ASM1838846v1_genomic.fna.gz --refList GCF_018388465.1_ASM1838846v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018388465.1_ASM1838846v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:32,345] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:32,367] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:32,367] [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_018388465.1	s__Cellulomonas sp018388465	100.0	1329	1329	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.65	99.29	0.98	0.97	3	conclusive
GCA_001429255.1	s__Cellulomonas sp001429255	85.9045	985	1329	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	85.7146	988	1329	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013359775.1	s__Cellulomonas humilata	85.6662	970	1329	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	85.6105	1008	1329	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	85.5298	951	1329	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	85.5109	975	1329	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	85.4851	1005	1329	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003470205.1	s__Cellulomonas rhizosphaerae	81.8937	657	1329	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	81.7158	839	1329	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	99.99	1.00	1.00	3	-
GCF_013409305.1	s__Cellulomonas soli	80.8985	714	1329	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000312005.1	s__Cellulomonas massiliensis	80.8438	704	1329	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:32,369] [INFO] GTDB search result was written to GCF_018388465.1_ASM1838846v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:32,370] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:32,373] [INFO] DFAST_QC result json was written to GCF_018388465.1_ASM1838846v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:32,373] [INFO] DFAST_QC completed!
[2024-01-24 12:16:32,373] [INFO] Total running time: 0h1m59s