[2024-01-24 15:14:51,078] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:14:51,084] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:14:51,084] [INFO] DQC Reference Directory: /var/lib/cwl/stg65d4c3dd-92c4-42da-9b9b-294ea98f3a67/dqc_reference
[2024-01-24 15:14:52,347] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:14:52,348] [INFO] Task started: Prodigal
[2024-01-24 15:14:52,349] [INFO] Running command: gunzip -c /var/lib/cwl/stg96522bbf-4036-44a8-b6c3-dc3a96e21757/GCF_014647435.1_ASM1464743v1_genomic.fna.gz | prodigal -d GCF_014647435.1_ASM1464743v1_genomic.fna/cds.fna -a GCF_014647435.1_ASM1464743v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:15:05,386] [INFO] Task succeeded: Prodigal
[2024-01-24 15:15:05,386] [INFO] Task started: HMMsearch
[2024-01-24 15:15:05,387] [INFO] Running command: hmmsearch --tblout GCF_014647435.1_ASM1464743v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg65d4c3dd-92c4-42da-9b9b-294ea98f3a67/dqc_reference/reference_markers.hmm GCF_014647435.1_ASM1464743v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:15:05,681] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:15:05,683] [INFO] Found 6/6 markers.
[2024-01-24 15:15:05,724] [INFO] Query marker FASTA was written to GCF_014647435.1_ASM1464743v1_genomic.fna/markers.fasta
[2024-01-24 15:15:05,724] [INFO] Task started: Blastn
[2024-01-24 15:15:05,725] [INFO] Running command: blastn -query GCF_014647435.1_ASM1464743v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg65d4c3dd-92c4-42da-9b9b-294ea98f3a67/dqc_reference/reference_markers.fasta -out GCF_014647435.1_ASM1464743v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:15:06,424] [INFO] Task succeeded: Blastn
[2024-01-24 15:15:06,428] [INFO] Selected 10 target genomes.
[2024-01-24 15:15:06,428] [INFO] Target genome list was writen to GCF_014647435.1_ASM1464743v1_genomic.fna/target_genomes.txt
[2024-01-24 15:15:06,433] [INFO] Task started: fastANI
[2024-01-24 15:15:06,433] [INFO] Running command: fastANI --query /var/lib/cwl/stg96522bbf-4036-44a8-b6c3-dc3a96e21757/GCF_014647435.1_ASM1464743v1_genomic.fna.gz --refList GCF_014647435.1_ASM1464743v1_genomic.fna/target_genomes.txt --output GCF_014647435.1_ASM1464743v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:15:17,155] [INFO] Task succeeded: fastANI
[2024-01-24 15:15:17,156] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg65d4c3dd-92c4-42da-9b9b-294ea98f3a67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:15:17,156] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg65d4c3dd-92c4-42da-9b9b-294ea98f3a67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:15:17,171] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:15:17,172] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:15:17,172] [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 radiotolerans	strain=JCM 19173	GCA_014647435.1	1309407	1309407	type	True	100.0	1500	1504	95	conclusive
Deinococcus actinosclerus	strain=BM2	GCA_001507665.1	1768108	1768108	type	True	91.0046	973	1504	95	below_threshold
Deinococcus soli (ex Cha et al. 2016)	strain=N5	GCA_001007995.1	1309411	1309411	type	True	90.5349	942	1504	95	below_threshold
Deinococcus arenae	strain=JCM 31047	GCA_014647995.1	1452751	1452751	type	True	90.4038	1100	1504	95	below_threshold
Deinococcus kurensis	strain=KR-1	GCA_009687825.1	2662757	2662757	type	True	90.3153	1088	1504	95	below_threshold
Deinococcus grandis	strain=ATCC 43672	GCA_001485435.1	57498	57498	type	True	90.2357	1055	1504	95	below_threshold
Deinococcus xianganensis	strain=Y35	GCA_009834985.1	1507289	1507289	type	True	90.2282	966	1504	95	below_threshold
Deinococcus daejeonensis	strain=JCM 16918	GCA_014647175.1	1007098	1007098	type	True	90.2124	1043	1504	95	below_threshold
Deinococcus saudiensis	strain=CGMCC 1.15089	GCA_014640655.1	1765963	1765963	type	True	90.1224	1062	1504	95	below_threshold
Deinococcus sedimenti	strain=JCM 31405	GCA_014648135.1	1867090	1867090	type	True	89.4999	1059	1504	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:15:17,174] [INFO] DFAST Taxonomy check result was written to GCF_014647435.1_ASM1464743v1_genomic.fna/tc_result.tsv
[2024-01-24 15:15:17,174] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:15:17,174] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:15:17,174] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg65d4c3dd-92c4-42da-9b9b-294ea98f3a67/dqc_reference/checkm_data
[2024-01-24 15:15:17,175] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:15:17,219] [INFO] Task started: CheckM
[2024-01-24 15:15:17,219] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014647435.1_ASM1464743v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014647435.1_ASM1464743v1_genomic.fna/checkm_input GCF_014647435.1_ASM1464743v1_genomic.fna/checkm_result
[2024-01-24 15:16:18,028] [INFO] Task succeeded: CheckM
[2024-01-24 15:16:18,029] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:16:18,049] [INFO] ===== Completeness check finished =====
[2024-01-24 15:16:18,050] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:16:18,050] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014647435.1_ASM1464743v1_genomic.fna/markers.fasta)
[2024-01-24 15:16:18,051] [INFO] Task started: Blastn
[2024-01-24 15:16:18,051] [INFO] Running command: blastn -query GCF_014647435.1_ASM1464743v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg65d4c3dd-92c4-42da-9b9b-294ea98f3a67/dqc_reference/reference_markers_gtdb.fasta -out GCF_014647435.1_ASM1464743v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:16:19,093] [INFO] Task succeeded: Blastn
[2024-01-24 15:16:19,098] [INFO] Selected 7 target genomes.
[2024-01-24 15:16:19,098] [INFO] Target genome list was writen to GCF_014647435.1_ASM1464743v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:16:19,106] [INFO] Task started: fastANI
[2024-01-24 15:16:19,106] [INFO] Running command: fastANI --query /var/lib/cwl/stg96522bbf-4036-44a8-b6c3-dc3a96e21757/GCF_014647435.1_ASM1464743v1_genomic.fna.gz --refList GCF_014647435.1_ASM1464743v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014647435.1_ASM1464743v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:16:26,788] [INFO] Task succeeded: fastANI
[2024-01-24 15:16:26,799] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:16:26,799] [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_014647435.1	s__Deinococcus radiotolerans	100.0	1500	1504	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001507665.1	s__Deinococcus actinosclerus	90.998	973	1504	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	96.26	96.21	0.94	0.94	4	-
GCF_001007995.1	s__Deinococcus soli	90.5069	943	1504	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	98.09	98.03	0.94	0.93	3	-
GCF_001485435.1	s__Deinococcus grandis	90.1935	1058	1504	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	96.65	95.40	0.88	0.83	5	-
GCF_013337115.1	s__Deinococcus sp013337115	89.6626	1037	1504	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	89.5281	1057	1504	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	85.4268	901	1504	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	99.28	99.28	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:16:26,802] [INFO] GTDB search result was written to GCF_014647435.1_ASM1464743v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:16:26,803] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:16:26,806] [INFO] DFAST_QC result json was written to GCF_014647435.1_ASM1464743v1_genomic.fna/dqc_result.json
[2024-01-24 15:16:26,806] [INFO] DFAST_QC completed!
[2024-01-24 15:16:26,806] [INFO] Total running time: 0h1m36s