[2024-01-24 11:19:55,155] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:19:55,158] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:19:55,159] [INFO] DQC Reference Directory: /var/lib/cwl/stgbcfc068e-dd23-47fb-af03-641c39da3f16/dqc_reference
[2024-01-24 11:19:56,534] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:19:56,535] [INFO] Task started: Prodigal
[2024-01-24 11:19:56,535] [INFO] Running command: gunzip -c /var/lib/cwl/stgd421182c-0329-4096-bd38-ecfcbd2a0ae3/GCF_010119385.1_ASM1011938v1_genomic.fna.gz | prodigal -d GCF_010119385.1_ASM1011938v1_genomic.fna/cds.fna -a GCF_010119385.1_ASM1011938v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:07,163] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:07,164] [INFO] Task started: HMMsearch
[2024-01-24 11:20:07,164] [INFO] Running command: hmmsearch --tblout GCF_010119385.1_ASM1011938v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbcfc068e-dd23-47fb-af03-641c39da3f16/dqc_reference/reference_markers.hmm GCF_010119385.1_ASM1011938v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:07,426] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:07,427] [INFO] Found 6/6 markers.
[2024-01-24 11:20:07,464] [INFO] Query marker FASTA was written to GCF_010119385.1_ASM1011938v1_genomic.fna/markers.fasta
[2024-01-24 11:20:07,464] [INFO] Task started: Blastn
[2024-01-24 11:20:07,464] [INFO] Running command: blastn -query GCF_010119385.1_ASM1011938v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbcfc068e-dd23-47fb-af03-641c39da3f16/dqc_reference/reference_markers.fasta -out GCF_010119385.1_ASM1011938v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:08,326] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:08,329] [INFO] Selected 17 target genomes.
[2024-01-24 11:20:08,330] [INFO] Target genome list was writen to GCF_010119385.1_ASM1011938v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:08,337] [INFO] Task started: fastANI
[2024-01-24 11:20:08,337] [INFO] Running command: fastANI --query /var/lib/cwl/stgd421182c-0329-4096-bd38-ecfcbd2a0ae3/GCF_010119385.1_ASM1011938v1_genomic.fna.gz --refList GCF_010119385.1_ASM1011938v1_genomic.fna/target_genomes.txt --output GCF_010119385.1_ASM1011938v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:19,702] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:19,702] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbcfc068e-dd23-47fb-af03-641c39da3f16/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:19,703] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbcfc068e-dd23-47fb-af03-641c39da3f16/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:19,716] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:20:19,716] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:20:19,716] [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 haasae	strain=Hz 6-5	GCA_010119385.1	2587813	2587813	type	True	100.0	1124	1126	95	conclusive
Nesterenkonia salmonea	strain=GY074	GCA_005771525.1	1804987	1804987	type	True	83.7559	708	1126	95	below_threshold
Nesterenkonia natronophila	strain=M8	GCA_003595215.1	2174932	2174932	type	True	79.894	464	1126	95	below_threshold
Nesterenkonia sphaerica	strain=GY239	GCA_005771565.1	1804988	1804988	type	True	79.4161	438	1126	95	below_threshold
Nesterenkonia alkaliphila	strain=CGMCC 1.12781	GCA_014639295.1	1463631	1463631	type	True	78.4495	306	1126	95	below_threshold
Nesterenkonia ebinurensis	strain=MD2	GCA_008711175.1	2608252	2608252	type	True	78.2341	325	1126	95	below_threshold
Nesterenkonia muleiensis	strain=RB2	GCA_003600155.1	2282648	2282648	type	True	78.2252	336	1126	95	below_threshold
Garicola koreensis	strain=DSM 28238	GCA_014195445.1	1262554	1262554	type	True	77.5528	191	1126	95	below_threshold
Nesterenkonia halotolerans	strain=DSM 15474	GCA_014874065.1	225325	225325	type	True	77.289	178	1126	95	below_threshold
Micrococcus flavus	strain=DSM 19079	GCA_022348285.1	384602	384602	type	True	76.6654	65	1126	95	below_threshold
Paeniglutamicibacter cryotolerans	strain=DSM 22826	GCA_014190875.1	670079	670079	type	True	76.5799	65	1126	95	below_threshold
Paenarthrobacter nicotinovorans	strain=ATCC 49919	GCA_021919345.1	29320	29320	suspected-type	True	76.4878	60	1126	95	below_threshold
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	76.3829	70	1126	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:19,718] [INFO] DFAST Taxonomy check result was written to GCF_010119385.1_ASM1011938v1_genomic.fna/tc_result.tsv
[2024-01-24 11:20:19,719] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:19,719] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:19,719] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbcfc068e-dd23-47fb-af03-641c39da3f16/dqc_reference/checkm_data
[2024-01-24 11:20:19,721] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:19,762] [INFO] Task started: CheckM
[2024-01-24 11:20:19,762] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010119385.1_ASM1011938v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010119385.1_ASM1011938v1_genomic.fna/checkm_input GCF_010119385.1_ASM1011938v1_genomic.fna/checkm_result
[2024-01-24 11:20:55,096] [INFO] Task succeeded: CheckM
[2024-01-24 11:20:55,098] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:20:55,119] [INFO] ===== Completeness check finished =====
[2024-01-24 11:20:55,119] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:20:55,120] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010119385.1_ASM1011938v1_genomic.fna/markers.fasta)
[2024-01-24 11:20:55,120] [INFO] Task started: Blastn
[2024-01-24 11:20:55,120] [INFO] Running command: blastn -query GCF_010119385.1_ASM1011938v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbcfc068e-dd23-47fb-af03-641c39da3f16/dqc_reference/reference_markers_gtdb.fasta -out GCF_010119385.1_ASM1011938v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:56,306] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:56,311] [INFO] Selected 13 target genomes.
[2024-01-24 11:20:56,311] [INFO] Target genome list was writen to GCF_010119385.1_ASM1011938v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:20:56,323] [INFO] Task started: fastANI
[2024-01-24 11:20:56,323] [INFO] Running command: fastANI --query /var/lib/cwl/stgd421182c-0329-4096-bd38-ecfcbd2a0ae3/GCF_010119385.1_ASM1011938v1_genomic.fna.gz --refList GCF_010119385.1_ASM1011938v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010119385.1_ASM1011938v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:21:05,329] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:05,342] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:21:05,342] [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_010119385.1	s__Nesterenkonia haasae	100.0	1124	1126	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	98.27	98.27	0.87	0.87	2	conclusive
GCF_005771525.1	s__Nesterenkonia salmonea	83.7558	709	1126	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	79.9035	464	1126	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	79.4052	439	1126	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	78.3601	311	1126	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_008711175.1	s__Nesterenkonia sp008711175	78.2569	323	1126	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003600155.1	s__Nesterenkonia muleiensis	78.2103	338	1126	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	77.5505	192	1126	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001302565.1	s__Glutamicibacter halophytocola	76.5467	54	1126	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter	95.0	98.28	98.01	0.91	0.89	4	-
GCF_006094275.1	s__Glutamicibacter creatinolyticus	76.3723	75	1126	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter	95.0	98.17	97.78	0.92	0.89	4	-
GCF_001484605.1	s__Pseudarthrobacter sulfonivorans_A	76.0708	75	1126	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:21:05,344] [INFO] GTDB search result was written to GCF_010119385.1_ASM1011938v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:21:05,344] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:21:05,348] [INFO] DFAST_QC result json was written to GCF_010119385.1_ASM1011938v1_genomic.fna/dqc_result.json
[2024-01-24 11:21:05,348] [INFO] DFAST_QC completed!
[2024-01-24 11:21:05,348] [INFO] Total running time: 0h1m10s