[2024-01-24 12:42:09,836] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:42:09,840] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:42:09,840] [INFO] DQC Reference Directory: /var/lib/cwl/stgdb11fadd-f911-4b42-a058-62bdaa604544/dqc_reference
[2024-01-24 12:42:11,117] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:42:11,119] [INFO] Task started: Prodigal
[2024-01-24 12:42:11,120] [INFO] Running command: gunzip -c /var/lib/cwl/stg38f4505c-0697-44d9-bd8c-9d7f6e22e2c6/GCF_019693445.1_ASM1969344v1_genomic.fna.gz | prodigal -d GCF_019693445.1_ASM1969344v1_genomic.fna/cds.fna -a GCF_019693445.1_ASM1969344v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:42:23,306] [INFO] Task succeeded: Prodigal
[2024-01-24 12:42:23,307] [INFO] Task started: HMMsearch
[2024-01-24 12:42:23,307] [INFO] Running command: hmmsearch --tblout GCF_019693445.1_ASM1969344v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdb11fadd-f911-4b42-a058-62bdaa604544/dqc_reference/reference_markers.hmm GCF_019693445.1_ASM1969344v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:42:23,569] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:42:23,570] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg38f4505c-0697-44d9-bd8c-9d7f6e22e2c6/GCF_019693445.1_ASM1969344v1_genomic.fna.gz]
[2024-01-24 12:42:23,613] [INFO] Query marker FASTA was written to GCF_019693445.1_ASM1969344v1_genomic.fna/markers.fasta
[2024-01-24 12:42:23,613] [INFO] Task started: Blastn
[2024-01-24 12:42:23,613] [INFO] Running command: blastn -query GCF_019693445.1_ASM1969344v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb11fadd-f911-4b42-a058-62bdaa604544/dqc_reference/reference_markers.fasta -out GCF_019693445.1_ASM1969344v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:42:24,246] [INFO] Task succeeded: Blastn
[2024-01-24 12:42:24,250] [INFO] Selected 11 target genomes.
[2024-01-24 12:42:24,250] [INFO] Target genome list was writen to GCF_019693445.1_ASM1969344v1_genomic.fna/target_genomes.txt
[2024-01-24 12:42:24,255] [INFO] Task started: fastANI
[2024-01-24 12:42:24,255] [INFO] Running command: fastANI --query /var/lib/cwl/stg38f4505c-0697-44d9-bd8c-9d7f6e22e2c6/GCF_019693445.1_ASM1969344v1_genomic.fna.gz --refList GCF_019693445.1_ASM1969344v1_genomic.fna/target_genomes.txt --output GCF_019693445.1_ASM1969344v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:42:35,536] [INFO] Task succeeded: fastANI
[2024-01-24 12:42:35,537] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdb11fadd-f911-4b42-a058-62bdaa604544/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:42:35,537] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdb11fadd-f911-4b42-a058-62bdaa604544/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:42:35,547] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:42:35,547] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:42:35,547] [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
Deinococcus aquaedulcis	strain=SYSU M42101	GCA_019693445.1	2840455	2840455	type	True	100.0	1346	1347	95	conclusive
Deinococcus multiflagellatus	strain=KACC 19287	GCA_020166415.1	1656887	1656887	type	True	93.3922	1109	1347	95	below_threshold
Deinococcus arcticus	strain=OD32	GCA_003028415.1	2136176	2136176	type	True	88.5109	1067	1347	95	below_threshold
Deinococcus kurensis	strain=KR-1	GCA_009687825.1	2662757	2662757	type	True	80.7045	772	1347	95	below_threshold
Deinococcus arenae	strain=JCM 31047	GCA_014647995.1	1452751	1452751	type	True	80.6275	761	1347	95	below_threshold
Deinococcus soli (ex Cha et al. 2016)	strain=N5	GCA_001007995.1	1309411	1309411	type	True	80.5444	699	1347	95	below_threshold
Deinococcus daejeonensis	strain=JCM 16918	GCA_014647175.1	1007098	1007098	type	True	80.5137	744	1347	95	below_threshold
Deinococcus radiotolerans	strain=JCM 19173	GCA_014647435.1	1309407	1309407	type	True	80.3061	745	1347	95	below_threshold
Deinococcus koreensis	strain=SJW1-2	GCA_002901445.1	2054903	2054903	type	True	80.1715	728	1347	95	below_threshold
Deinococcus metalli	strain=DSM 27521	GCA_014201805.1	1141878	1141878	type	True	79.6033	676	1347	95	below_threshold
Deinococcus phoenicis	strain=1P10ME	GCA_000599865.1	1476583	1476583	type	True	79.4815	593	1347	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:42:35,549] [INFO] DFAST Taxonomy check result was written to GCF_019693445.1_ASM1969344v1_genomic.fna/tc_result.tsv
[2024-01-24 12:42:35,549] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:42:35,550] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:42:35,550] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdb11fadd-f911-4b42-a058-62bdaa604544/dqc_reference/checkm_data
[2024-01-24 12:42:35,551] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:42:35,592] [INFO] Task started: CheckM
[2024-01-24 12:42:35,593] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019693445.1_ASM1969344v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019693445.1_ASM1969344v1_genomic.fna/checkm_input GCF_019693445.1_ASM1969344v1_genomic.fna/checkm_result
[2024-01-24 12:43:13,648] [INFO] Task succeeded: CheckM
[2024-01-24 12:43:13,649] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:43:13,671] [INFO] ===== Completeness check finished =====
[2024-01-24 12:43:13,672] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:43:13,672] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019693445.1_ASM1969344v1_genomic.fna/markers.fasta)
[2024-01-24 12:43:13,673] [INFO] Task started: Blastn
[2024-01-24 12:43:13,673] [INFO] Running command: blastn -query GCF_019693445.1_ASM1969344v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb11fadd-f911-4b42-a058-62bdaa604544/dqc_reference/reference_markers_gtdb.fasta -out GCF_019693445.1_ASM1969344v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:43:14,550] [INFO] Task succeeded: Blastn
[2024-01-24 12:43:14,554] [INFO] Selected 11 target genomes.
[2024-01-24 12:43:14,554] [INFO] Target genome list was writen to GCF_019693445.1_ASM1969344v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:43:14,562] [INFO] Task started: fastANI
[2024-01-24 12:43:14,562] [INFO] Running command: fastANI --query /var/lib/cwl/stg38f4505c-0697-44d9-bd8c-9d7f6e22e2c6/GCF_019693445.1_ASM1969344v1_genomic.fna.gz --refList GCF_019693445.1_ASM1969344v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019693445.1_ASM1969344v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:43:24,719] [INFO] Task succeeded: fastANI
[2024-01-24 12:43:24,732] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:43:24,733] [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_003028415.1	s__Deinococcus sp003028415	88.5238	1066	1347	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009755355.1	s__Deinococcus sp009755355	82.8801	907	1347	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507665.1	s__Deinococcus actinosclerus	80.8827	712	1347	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	96.26	96.21	0.94	0.94	4	-
GCF_002017875.1	s__Deinococcus sp002017875	80.7408	738	1347	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	96.85	96.85	0.84	0.84	2	-
GCF_001485435.1	s__Deinococcus grandis	80.6341	762	1347	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	96.65	95.40	0.88	0.83	5	-
GCF_001007995.1	s__Deinococcus soli	80.5609	697	1347	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	98.09	98.03	0.94	0.93	3	-
GCF_014648135.1	s__Deinococcus sedimenti	80.467	743	1347	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647435.1	s__Deinococcus radiotolerans	80.2506	752	1347	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013337115.1	s__Deinococcus sp013337115	80.1629	744	1347	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201805.1	s__Deinococcus metalli	79.6226	673	1347	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000599865.1	s__Deinococcus phoenicis	79.4939	591	1347	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:43:24,734] [INFO] GTDB search result was written to GCF_019693445.1_ASM1969344v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:43:24,736] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:43:24,740] [INFO] DFAST_QC result json was written to GCF_019693445.1_ASM1969344v1_genomic.fna/dqc_result.json
[2024-01-24 12:43:24,740] [INFO] DFAST_QC completed!
[2024-01-24 12:43:24,740] [INFO] Total running time: 0h1m15s