[2024-01-24 13:19:11,567] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:19:11,569] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:19:11,569] [INFO] DQC Reference Directory: /var/lib/cwl/stg15c5be27-ae75-4820-81cd-b4f02c6aaf48/dqc_reference
[2024-01-24 13:19:12,852] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:19:12,853] [INFO] Task started: Prodigal
[2024-01-24 13:19:12,854] [INFO] Running command: gunzip -c /var/lib/cwl/stg2e3a4bdc-72fd-43cb-80a0-e7ed52a929fc/GCF_020686765.1_ASM2068676v1_genomic.fna.gz | prodigal -d GCF_020686765.1_ASM2068676v1_genomic.fna/cds.fna -a GCF_020686765.1_ASM2068676v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:24,583] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:24,584] [INFO] Task started: HMMsearch
[2024-01-24 13:19:24,584] [INFO] Running command: hmmsearch --tblout GCF_020686765.1_ASM2068676v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg15c5be27-ae75-4820-81cd-b4f02c6aaf48/dqc_reference/reference_markers.hmm GCF_020686765.1_ASM2068676v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:24,936] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:24,937] [INFO] Found 6/6 markers.
[2024-01-24 13:19:24,986] [INFO] Query marker FASTA was written to GCF_020686765.1_ASM2068676v1_genomic.fna/markers.fasta
[2024-01-24 13:19:24,987] [INFO] Task started: Blastn
[2024-01-24 13:19:24,987] [INFO] Running command: blastn -query GCF_020686765.1_ASM2068676v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg15c5be27-ae75-4820-81cd-b4f02c6aaf48/dqc_reference/reference_markers.fasta -out GCF_020686765.1_ASM2068676v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:26,610] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:26,613] [INFO] Selected 15 target genomes.
[2024-01-24 13:19:26,614] [INFO] Target genome list was writen to GCF_020686765.1_ASM2068676v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:26,616] [INFO] Task started: fastANI
[2024-01-24 13:19:26,616] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e3a4bdc-72fd-43cb-80a0-e7ed52a929fc/GCF_020686765.1_ASM2068676v1_genomic.fna.gz --refList GCF_020686765.1_ASM2068676v1_genomic.fna/target_genomes.txt --output GCF_020686765.1_ASM2068676v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:42,961] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:42,961] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg15c5be27-ae75-4820-81cd-b4f02c6aaf48/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:42,962] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg15c5be27-ae75-4820-81cd-b4f02c6aaf48/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:42,974] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:19:42,974] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:19:42,975] [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 avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	85.8491	1018	1355	95	below_threshold
Cellulomonas flavigena	strain=DSM 20109	GCA_000092865.1	1711	1711	type	True	84.6024	971	1355	95	below_threshold
Cellulomonas iranensis	strain=NBRC 101100	GCA_001552375.1	76862	76862	type	True	84.4745	866	1355	95	below_threshold
Cellulomonas shaoxiangyii	strain=Z28	GCA_004798685.1	2566013	2566013	type	True	82.8953	856	1355	95	below_threshold
Cellulomonas telluris	strain=CPCC 204705	GCA_004886325.1	2306636	2306636	type	True	82.5431	870	1355	95	below_threshold
Cellulomonas oligotrophica	strain=DSM 24482	GCA_013409875.1	931536	931536	type	True	82.2155	851	1355	95	below_threshold
Cellulomonas biazotea	strain=NBRC12680	GCA_004306155.1	1709	1709	type	True	81.2367	709	1355	95	below_threshold
Cellulomonas fimi	strain=NCTC7547	GCA_900637695.1	1708	1708	type	True	81.1613	790	1355	95	below_threshold
Cellulomonas fimi	strain=ATCC 484	GCA_000212695.1	1708	1708	type	True	81.1429	801	1355	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	81.115	752	1355	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	80.8016	718	1355	95	below_threshold
Cellulomonas massiliensis	strain=JC225	GCA_000312005.1	1465811	1465811	type	True	80.5802	694	1355	95	below_threshold
Cellulomonas composti	strain=NBRC 100758	GCA_007990245.1	266130	266130	type	True	80.5719	659	1355	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	79.1723	674	1355	95	below_threshold
Oerskovia merdavium	strain=Sa2CUA9	GCA_014836755.1	2762227	2762227	type	True	78.7396	557	1355	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:42,976] [INFO] DFAST Taxonomy check result was written to GCF_020686765.1_ASM2068676v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:42,977] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:42,977] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:42,977] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg15c5be27-ae75-4820-81cd-b4f02c6aaf48/dqc_reference/checkm_data
[2024-01-24 13:19:42,978] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:43,039] [INFO] Task started: CheckM
[2024-01-24 13:19:43,039] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020686765.1_ASM2068676v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020686765.1_ASM2068676v1_genomic.fna/checkm_input GCF_020686765.1_ASM2068676v1_genomic.fna/checkm_result
[2024-01-24 13:20:51,766] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:51,767] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:51,785] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:51,786] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:51,786] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020686765.1_ASM2068676v1_genomic.fna/markers.fasta)
[2024-01-24 13:20:51,786] [INFO] Task started: Blastn
[2024-01-24 13:20:51,786] [INFO] Running command: blastn -query GCF_020686765.1_ASM2068676v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg15c5be27-ae75-4820-81cd-b4f02c6aaf48/dqc_reference/reference_markers_gtdb.fasta -out GCF_020686765.1_ASM2068676v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:54,341] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:54,350] [INFO] Selected 12 target genomes.
[2024-01-24 13:20:54,351] [INFO] Target genome list was writen to GCF_020686765.1_ASM2068676v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:54,367] [INFO] Task started: fastANI
[2024-01-24 13:20:54,368] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e3a4bdc-72fd-43cb-80a0-e7ed52a929fc/GCF_020686765.1_ASM2068676v1_genomic.fna.gz --refList GCF_020686765.1_ASM2068676v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020686765.1_ASM2068676v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:21:07,935] [INFO] Task succeeded: fastANI
[2024-01-24 13:21:07,948] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:21:07,949] [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_018388445.1	s__Cellulomonas sp018388445	86.8482	1090	1355	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.55	99.30	0.98	0.97	4	-
GCF_900114185.1	s__Cellulomonas sp900114185	86.317	1038	1355	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014836445.1	s__Cellulomonas sp014836445	85.8828	1014	1355	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018623035.1	s__Cellulomonas sp018623035	85.709	1014	1355	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.51	99.03	0.98	0.95	3	-
GCA_015234515.1	s__Cellulomonas sp015234515	85.5381	1017	1355	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862775.1	s__Cellulomonas phragmiteti	85.0434	940	1355	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000092865.1	s__Cellulomonas flavigena	84.5629	975	1355	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	84.4855	865	1355	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	98.21	97.89	0.91	0.88	6	-
GCF_001462455.1	s__Cellulomonas sp001462455	84.3689	869	1355	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004798685.1	s__Cellulomonas shaoxiangyii	82.84	862	1355	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_004886325.1	s__Cellulomonas telluris	82.5791	867	1355	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009720485.1	s__Cellulomonas sp009720485	82.5122	866	1355	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 13:21:07,950] [INFO] GTDB search result was written to GCF_020686765.1_ASM2068676v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:21:07,951] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:21:07,954] [INFO] DFAST_QC result json was written to GCF_020686765.1_ASM2068676v1_genomic.fna/dqc_result.json
[2024-01-24 13:21:07,955] [INFO] DFAST_QC completed!
[2024-01-24 13:21:07,955] [INFO] Total running time: 0h1m56s