[2024-01-24 13:49:29,938] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:29,940] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:29,941] [INFO] DQC Reference Directory: /var/lib/cwl/stg74989908-11b5-4e6b-9a7a-03042545af68/dqc_reference
[2024-01-24 13:49:31,189] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:31,190] [INFO] Task started: Prodigal
[2024-01-24 13:49:31,191] [INFO] Running command: gunzip -c /var/lib/cwl/stg7868c5d2-c00d-49e7-8bf5-e66cb3fe1eef/GCF_003600155.1_ASM360015v1_genomic.fna.gz | prodigal -d GCF_003600155.1_ASM360015v1_genomic.fna/cds.fna -a GCF_003600155.1_ASM360015v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:42,604] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:42,604] [INFO] Task started: HMMsearch
[2024-01-24 13:49:42,604] [INFO] Running command: hmmsearch --tblout GCF_003600155.1_ASM360015v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg74989908-11b5-4e6b-9a7a-03042545af68/dqc_reference/reference_markers.hmm GCF_003600155.1_ASM360015v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:42,894] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:42,895] [INFO] Found 6/6 markers.
[2024-01-24 13:49:42,928] [INFO] Query marker FASTA was written to GCF_003600155.1_ASM360015v1_genomic.fna/markers.fasta
[2024-01-24 13:49:42,929] [INFO] Task started: Blastn
[2024-01-24 13:49:42,929] [INFO] Running command: blastn -query GCF_003600155.1_ASM360015v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg74989908-11b5-4e6b-9a7a-03042545af68/dqc_reference/reference_markers.fasta -out GCF_003600155.1_ASM360015v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:43,998] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:44,001] [INFO] Selected 14 target genomes.
[2024-01-24 13:49:44,001] [INFO] Target genome list was writen to GCF_003600155.1_ASM360015v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:44,020] [INFO] Task started: fastANI
[2024-01-24 13:49:44,020] [INFO] Running command: fastANI --query /var/lib/cwl/stg7868c5d2-c00d-49e7-8bf5-e66cb3fe1eef/GCF_003600155.1_ASM360015v1_genomic.fna.gz --refList GCF_003600155.1_ASM360015v1_genomic.fna/target_genomes.txt --output GCF_003600155.1_ASM360015v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:52,602] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:52,603] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg74989908-11b5-4e6b-9a7a-03042545af68/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:52,603] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg74989908-11b5-4e6b-9a7a-03042545af68/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:52,615] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:52,615] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:52,615] [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
Nesterenkonia muleiensis	strain=RB2	GCA_003600155.1	2282648	2282648	type	True	100.0	1195	1197	95	conclusive
Nesterenkonia ebinurensis	strain=MD2	GCA_008711175.1	2608252	2608252	type	True	81.8738	553	1197	95	below_threshold
Nesterenkonia alkaliphila	strain=F10	GCA_009758175.1	1463631	1463631	type	True	80.6695	523	1197	95	below_threshold
Nesterenkonia alkaliphila	strain=CGMCC 1.12781	GCA_014639295.1	1463631	1463631	type	True	80.6583	533	1197	95	below_threshold
Nesterenkonia sedimenti	strain=MY13	GCA_012641515.1	1463632	1463632	type	True	79.8325	428	1197	95	below_threshold
Nesterenkonia sphaerica	strain=GY239	GCA_005771565.1	1804988	1804988	type	True	79.1622	406	1197	95	below_threshold
Nesterenkonia lacusekhoensis	strain=DSM 12544	GCA_017876395.1	150832	150832	type	True	79.1544	351	1197	95	below_threshold
Garicola koreensis	strain=DSM 28238	GCA_014195445.1	1262554	1262554	type	True	79.137	331	1197	95	below_threshold
Nesterenkonia halophila	strain=DSM 16378	GCA_009467795.1	302044	302044	type	True	78.6207	263	1197	95	below_threshold
Nesterenkonia natronophila	strain=M8	GCA_003595215.1	2174932	2174932	type	True	78.6186	329	1197	95	below_threshold
Nesterenkonia alba	strain=DSM 19423	GCA_000421745.1	515814	515814	type	True	78.454	288	1197	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	77.0006	153	1197	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_017898065.1	2817475	2817475	type	True	76.9748	154	1197	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	76.5739	81	1197	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:52,623] [INFO] DFAST Taxonomy check result was written to GCF_003600155.1_ASM360015v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:52,632] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:52,633] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:52,633] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg74989908-11b5-4e6b-9a7a-03042545af68/dqc_reference/checkm_data
[2024-01-24 13:49:52,634] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:52,673] [INFO] Task started: CheckM
[2024-01-24 13:49:52,673] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003600155.1_ASM360015v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003600155.1_ASM360015v1_genomic.fna/checkm_input GCF_003600155.1_ASM360015v1_genomic.fna/checkm_result
[2024-01-24 13:50:30,174] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:30,175] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:30,194] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:30,195] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:30,195] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003600155.1_ASM360015v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:30,196] [INFO] Task started: Blastn
[2024-01-24 13:50:30,196] [INFO] Running command: blastn -query GCF_003600155.1_ASM360015v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg74989908-11b5-4e6b-9a7a-03042545af68/dqc_reference/reference_markers_gtdb.fasta -out GCF_003600155.1_ASM360015v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:31,796] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:31,799] [INFO] Selected 13 target genomes.
[2024-01-24 13:50:31,800] [INFO] Target genome list was writen to GCF_003600155.1_ASM360015v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:31,808] [INFO] Task started: fastANI
[2024-01-24 13:50:31,809] [INFO] Running command: fastANI --query /var/lib/cwl/stg7868c5d2-c00d-49e7-8bf5-e66cb3fe1eef/GCF_003600155.1_ASM360015v1_genomic.fna.gz --refList GCF_003600155.1_ASM360015v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003600155.1_ASM360015v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:40,349] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:40,367] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:40,368] [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_003600155.1	s__Nesterenkonia muleiensis	100.0	1195	1197	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_008711175.1	s__Nesterenkonia sp008711175	81.8533	555	1197	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009758175.1	s__Nesterenkonia alkaliphila	80.6654	523	1197	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_012641515.1	s__Nesterenkonia sp012641515	79.8463	426	1197	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014642675.1	s__Nesterenkonia cremea	79.221	387	1197	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005771565.1	s__Nesterenkonia sphaerica	79.1675	405	1197	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876395.1	s__Nesterenkonia lacusekhoensis	79.1674	350	1197	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014195445.1	s__Nesterenkonia koreensis	79.1507	330	1197	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410215.1	s__Nesterenkonia sandarakina	78.8043	356	1197	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	97.10	97.05	0.88	0.86	3	-
GCF_009467795.1	s__Nesterenkonia halophila	78.6361	262	1197	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003595215.1	s__Nesterenkonia natronophila	78.6183	329	1197	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000421745.1	s__Nesterenkonia alba	78.454	288	1197	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005771525.1	s__Nesterenkonia salmonea	78.2598	354	1197	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:40,369] [INFO] GTDB search result was written to GCF_003600155.1_ASM360015v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:40,370] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:40,374] [INFO] DFAST_QC result json was written to GCF_003600155.1_ASM360015v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:40,374] [INFO] DFAST_QC completed!
[2024-01-24 13:50:40,374] [INFO] Total running time: 0h1m10s