[2024-01-24 12:57:50,100] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:57:50,102] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:57:50,102] [INFO] DQC Reference Directory: /var/lib/cwl/stg7c147124-b776-4e19-9baf-35ce0660f98e/dqc_reference
[2024-01-24 12:57:51,255] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:57:51,256] [INFO] Task started: Prodigal
[2024-01-24 12:57:51,256] [INFO] Running command: gunzip -c /var/lib/cwl/stg442ad71a-3a67-4cf7-a021-a4d0fcd820ae/GCF_009834985.1_ASM983498v1_genomic.fna.gz | prodigal -d GCF_009834985.1_ASM983498v1_genomic.fna/cds.fna -a GCF_009834985.1_ASM983498v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:58:01,850] [INFO] Task succeeded: Prodigal
[2024-01-24 12:58:01,850] [INFO] Task started: HMMsearch
[2024-01-24 12:58:01,850] [INFO] Running command: hmmsearch --tblout GCF_009834985.1_ASM983498v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7c147124-b776-4e19-9baf-35ce0660f98e/dqc_reference/reference_markers.hmm GCF_009834985.1_ASM983498v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:58:02,047] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:58:02,049] [INFO] Found 6/6 markers.
[2024-01-24 12:58:02,082] [INFO] Query marker FASTA was written to GCF_009834985.1_ASM983498v1_genomic.fna/markers.fasta
[2024-01-24 12:58:02,082] [INFO] Task started: Blastn
[2024-01-24 12:58:02,083] [INFO] Running command: blastn -query GCF_009834985.1_ASM983498v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c147124-b776-4e19-9baf-35ce0660f98e/dqc_reference/reference_markers.fasta -out GCF_009834985.1_ASM983498v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:58:02,703] [INFO] Task succeeded: Blastn
[2024-01-24 12:58:02,705] [INFO] Selected 10 target genomes.
[2024-01-24 12:58:02,706] [INFO] Target genome list was writen to GCF_009834985.1_ASM983498v1_genomic.fna/target_genomes.txt
[2024-01-24 12:58:02,713] [INFO] Task started: fastANI
[2024-01-24 12:58:02,713] [INFO] Running command: fastANI --query /var/lib/cwl/stg442ad71a-3a67-4cf7-a021-a4d0fcd820ae/GCF_009834985.1_ASM983498v1_genomic.fna.gz --refList GCF_009834985.1_ASM983498v1_genomic.fna/target_genomes.txt --output GCF_009834985.1_ASM983498v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:58:13,918] [INFO] Task succeeded: fastANI
[2024-01-24 12:58:13,919] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7c147124-b776-4e19-9baf-35ce0660f98e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:58:13,919] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7c147124-b776-4e19-9baf-35ce0660f98e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:58:13,928] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:58:13,928] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:58:13,928] [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 xianganensis	strain=Y35	GCA_009834985.1	1507289	1507289	type	True	100.0	1273	1294	95	inconclusive
Deinococcus grandis	strain=ATCC 43672	GCA_001485435.1	57498	57498	type	True	95.6476	1096	1294	95	inconclusive
Deinococcus daejeonensis	strain=JCM 16918	GCA_014647175.1	1007098	1007098	type	True	95.1361	1032	1294	95	inconclusive
Deinococcus soli (ex Cha et al. 2016)	strain=N5	GCA_001007995.1	1309411	1309411	type	True	94.2034	942	1294	95	below_threshold
Deinococcus saudiensis	strain=CGMCC 1.15089	GCA_014640655.1	1765963	1765963	type	True	93.9564	1109	1294	95	below_threshold
Deinococcus sedimenti	strain=JCM 31405	GCA_014648135.1	1867090	1867090	type	True	91.9363	1015	1294	95	below_threshold
Deinococcus radiotolerans	strain=JCM 19173	GCA_014647435.1	1309407	1309407	type	True	89.9673	998	1294	95	below_threshold
Deinococcus koreensis	strain=SJW1-2	GCA_002901445.1	2054903	2054903	type	True	80.3214	728	1294	95	below_threshold
Deinococcus metallilatus	strain=DSM 105434	GCA_014202095.1	1211322	1211322	type	True	79.5271	609	1294	95	below_threshold
Deinococcus budaensis	strain=DSM 101791	GCA_014201885.1	1665626	1665626	type	True	79.4978	588	1294	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:58:13,930] [INFO] DFAST Taxonomy check result was written to GCF_009834985.1_ASM983498v1_genomic.fna/tc_result.tsv
[2024-01-24 12:58:13,930] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:58:13,930] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:58:13,931] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7c147124-b776-4e19-9baf-35ce0660f98e/dqc_reference/checkm_data
[2024-01-24 12:58:13,931] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:58:13,970] [INFO] Task started: CheckM
[2024-01-24 12:58:13,971] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009834985.1_ASM983498v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009834985.1_ASM983498v1_genomic.fna/checkm_input GCF_009834985.1_ASM983498v1_genomic.fna/checkm_result
[2024-01-24 12:58:49,084] [INFO] Task succeeded: CheckM
[2024-01-24 12:58:49,085] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:58:49,105] [INFO] ===== Completeness check finished =====
[2024-01-24 12:58:49,105] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:58:49,106] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009834985.1_ASM983498v1_genomic.fna/markers.fasta)
[2024-01-24 12:58:49,106] [INFO] Task started: Blastn
[2024-01-24 12:58:49,106] [INFO] Running command: blastn -query GCF_009834985.1_ASM983498v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c147124-b776-4e19-9baf-35ce0660f98e/dqc_reference/reference_markers_gtdb.fasta -out GCF_009834985.1_ASM983498v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:58:49,992] [INFO] Task succeeded: Blastn
[2024-01-24 12:58:49,995] [INFO] Selected 9 target genomes.
[2024-01-24 12:58:49,995] [INFO] Target genome list was writen to GCF_009834985.1_ASM983498v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:58:50,003] [INFO] Task started: fastANI
[2024-01-24 12:58:50,003] [INFO] Running command: fastANI --query /var/lib/cwl/stg442ad71a-3a67-4cf7-a021-a4d0fcd820ae/GCF_009834985.1_ASM983498v1_genomic.fna.gz --refList GCF_009834985.1_ASM983498v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009834985.1_ASM983498v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:59:00,577] [INFO] Task succeeded: fastANI
[2024-01-24 12:59:00,586] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:59:00,586] [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_001485435.1	s__Deinococcus grandis	95.6669	1095	1294	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	96.65	95.40	0.88	0.83	5	conclusive
GCF_001007995.1	s__Deinococcus soli	94.1931	943	1294	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	93.5454	1085	1294	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	92.1179	897	1294	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	96.26	96.21	0.94	0.94	4	-
GCF_014648135.1	s__Deinococcus sedimenti	91.8934	1017	1294	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	89.9808	997	1294	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002017875.1	s__Deinococcus sp002017875	86.7465	932	1294	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	96.85	96.85	0.84	0.84	2	-
GCF_002901445.1	s__Deinococcus koreensis	80.3072	730	1294	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201885.1	s__Deinococcus budaensis	79.5127	584	1294	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 12:59:00,587] [INFO] GTDB search result was written to GCF_009834985.1_ASM983498v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:59:00,588] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:59:00,590] [INFO] DFAST_QC result json was written to GCF_009834985.1_ASM983498v1_genomic.fna/dqc_result.json
[2024-01-24 12:59:00,590] [INFO] DFAST_QC completed!
[2024-01-24 12:59:00,591] [INFO] Total running time: 0h1m10s