[2024-01-24 12:31:34,059] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:34,061] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:34,062] [INFO] DQC Reference Directory: /var/lib/cwl/stg26e510e4-fca8-4383-a661-c9821529840f/dqc_reference
[2024-01-24 12:31:35,365] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:35,366] [INFO] Task started: Prodigal
[2024-01-24 12:31:35,367] [INFO] Running command: gunzip -c /var/lib/cwl/stg731cf964-e812-43b4-a5c6-66964446ada8/GCF_020229735.1_ASM2022973v1_genomic.fna.gz | prodigal -d GCF_020229735.1_ASM2022973v1_genomic.fna/cds.fna -a GCF_020229735.1_ASM2022973v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:48,940] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:48,940] [INFO] Task started: HMMsearch
[2024-01-24 12:31:48,940] [INFO] Running command: hmmsearch --tblout GCF_020229735.1_ASM2022973v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg26e510e4-fca8-4383-a661-c9821529840f/dqc_reference/reference_markers.hmm GCF_020229735.1_ASM2022973v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:49,277] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:49,278] [INFO] Found 6/6 markers.
[2024-01-24 12:31:49,327] [INFO] Query marker FASTA was written to GCF_020229735.1_ASM2022973v1_genomic.fna/markers.fasta
[2024-01-24 12:31:49,328] [INFO] Task started: Blastn
[2024-01-24 12:31:49,328] [INFO] Running command: blastn -query GCF_020229735.1_ASM2022973v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg26e510e4-fca8-4383-a661-c9821529840f/dqc_reference/reference_markers.fasta -out GCF_020229735.1_ASM2022973v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:50,044] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:50,047] [INFO] Selected 12 target genomes.
[2024-01-24 12:31:50,048] [INFO] Target genome list was writen to GCF_020229735.1_ASM2022973v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:50,054] [INFO] Task started: fastANI
[2024-01-24 12:31:50,054] [INFO] Running command: fastANI --query /var/lib/cwl/stg731cf964-e812-43b4-a5c6-66964446ada8/GCF_020229735.1_ASM2022973v1_genomic.fna.gz --refList GCF_020229735.1_ASM2022973v1_genomic.fna/target_genomes.txt --output GCF_020229735.1_ASM2022973v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:00,911] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:00,912] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg26e510e4-fca8-4383-a661-c9821529840f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:00,912] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg26e510e4-fca8-4383-a661-c9821529840f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:00,927] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:32:00,927] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:32:00,927] [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 actinosclerus	strain=BM2	GCA_001507665.1	1768108	1768108	type	True	83.7033	816	1536	95	below_threshold
Deinococcus soli (ex Cha et al. 2016)	strain=N5	GCA_001007995.1	1309411	1309411	type	True	83.6524	795	1536	95	below_threshold
Deinococcus grandis	strain=ATCC 43672	GCA_001485435.1	57498	57498	type	True	83.6086	875	1536	95	below_threshold
Deinococcus xianganensis	strain=Y35	GCA_009834985.1	1507289	1507289	type	True	83.5619	828	1536	95	below_threshold
Deinococcus kurensis	strain=KR-1	GCA_009687825.1	2662757	2662757	type	True	83.4125	905	1536	95	below_threshold
Deinococcus arenae	strain=JCM 31047	GCA_014647995.1	1452751	1452751	type	True	83.3985	882	1536	95	below_threshold
Deinococcus daejeonensis	strain=JCM 16918	GCA_014647175.1	1007098	1007098	type	True	83.3102	897	1536	95	below_threshold
Deinococcus sedimenti	strain=JCM 31405	GCA_014648135.1	1867090	1867090	type	True	83.2775	903	1536	95	below_threshold
Deinococcus saudiensis	strain=CGMCC 1.15089	GCA_014640655.1	1765963	1765963	type	True	83.2153	882	1536	95	below_threshold
Deinococcus radiotolerans	strain=JCM 19173	GCA_014647435.1	1309407	1309407	type	True	83.1195	916	1536	95	below_threshold
Deinococcus knuensis	strain=JCM 31406	GCA_014648155.1	1837380	1837380	type	True	82.5575	856	1536	95	below_threshold
Deinococcus seoulensis	strain=JCM 31404	GCA_014648115.1	1837379	1837379	type	True	82.4601	846	1536	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:00,929] [INFO] DFAST Taxonomy check result was written to GCF_020229735.1_ASM2022973v1_genomic.fna/tc_result.tsv
[2024-01-24 12:32:00,929] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:00,930] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:00,930] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg26e510e4-fca8-4383-a661-c9821529840f/dqc_reference/checkm_data
[2024-01-24 12:32:00,931] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:00,975] [INFO] Task started: CheckM
[2024-01-24 12:32:00,975] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020229735.1_ASM2022973v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020229735.1_ASM2022973v1_genomic.fna/checkm_input GCF_020229735.1_ASM2022973v1_genomic.fna/checkm_result
[2024-01-24 12:32:49,353] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:49,354] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:49,379] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:49,379] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:49,380] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020229735.1_ASM2022973v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:49,380] [INFO] Task started: Blastn
[2024-01-24 12:32:49,381] [INFO] Running command: blastn -query GCF_020229735.1_ASM2022973v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg26e510e4-fca8-4383-a661-c9821529840f/dqc_reference/reference_markers_gtdb.fasta -out GCF_020229735.1_ASM2022973v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:50,548] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:50,553] [INFO] Selected 10 target genomes.
[2024-01-24 12:32:50,553] [INFO] Target genome list was writen to GCF_020229735.1_ASM2022973v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:50,570] [INFO] Task started: fastANI
[2024-01-24 12:32:50,570] [INFO] Running command: fastANI --query /var/lib/cwl/stg731cf964-e812-43b4-a5c6-66964446ada8/GCF_020229735.1_ASM2022973v1_genomic.fna.gz --refList GCF_020229735.1_ASM2022973v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020229735.1_ASM2022973v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:59,692] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:59,705] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:32:59,706] [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_001507665.1	s__Deinococcus actinosclerus	83.7373	814	1536	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	96.26	96.21	0.94	0.94	4	-
GCF_001485435.1	s__Deinococcus grandis	83.6009	874	1536	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	83.5841	796	1536	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	98.09	98.03	0.94	0.93	3	-
GCF_013337115.1	s__Deinococcus sp013337115	83.2966	873	1536	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648135.1	s__Deinococcus sedimenti	83.2867	902	1536	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	83.126	914	1536	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002198095.1	s__Deinococcus indicus	82.5918	847	1536	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	99.28	99.28	0.90	0.90	2	-
GCF_002017875.1	s__Deinococcus sp002017875	82.5451	858	1536	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	96.85	96.85	0.84	0.84	2	-
GCF_014648115.1	s__Deinococcus seoulensis	82.4506	847	1536	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	97.69	97.69	0.87	0.87	2	-
GCA_018260555.1	s__Deinococcus sp018260555	81.6326	683	1536	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 12:32:59,708] [INFO] GTDB search result was written to GCF_020229735.1_ASM2022973v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:59,708] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:59,713] [INFO] DFAST_QC result json was written to GCF_020229735.1_ASM2022973v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:59,713] [INFO] DFAST_QC completed!
[2024-01-24 12:32:59,713] [INFO] Total running time: 0h1m26s