[2024-01-24 13:17:41,515] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:41,517] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:41,517] [INFO] DQC Reference Directory: /var/lib/cwl/stgd05fa5d2-4415-4976-9f7d-82dbea6ca660/dqc_reference
[2024-01-24 13:17:42,708] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:42,709] [INFO] Task started: Prodigal
[2024-01-24 13:17:42,709] [INFO] Running command: gunzip -c /var/lib/cwl/stg64fa88ba-30ca-40ae-bdce-cd5b11c65074/GCF_025244745.1_ASM2524474v1_genomic.fna.gz | prodigal -d GCF_025244745.1_ASM2524474v1_genomic.fna/cds.fna -a GCF_025244745.1_ASM2524474v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:51,505] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:51,506] [INFO] Task started: HMMsearch
[2024-01-24 13:17:51,506] [INFO] Running command: hmmsearch --tblout GCF_025244745.1_ASM2524474v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd05fa5d2-4415-4976-9f7d-82dbea6ca660/dqc_reference/reference_markers.hmm GCF_025244745.1_ASM2524474v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:51,766] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:51,768] [INFO] Found 6/6 markers.
[2024-01-24 13:17:51,797] [INFO] Query marker FASTA was written to GCF_025244745.1_ASM2524474v1_genomic.fna/markers.fasta
[2024-01-24 13:17:51,797] [INFO] Task started: Blastn
[2024-01-24 13:17:51,797] [INFO] Running command: blastn -query GCF_025244745.1_ASM2524474v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd05fa5d2-4415-4976-9f7d-82dbea6ca660/dqc_reference/reference_markers.fasta -out GCF_025244745.1_ASM2524474v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:52,488] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:52,491] [INFO] Selected 8 target genomes.
[2024-01-24 13:17:52,492] [INFO] Target genome list was writen to GCF_025244745.1_ASM2524474v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:52,548] [INFO] Task started: fastANI
[2024-01-24 13:17:52,549] [INFO] Running command: fastANI --query /var/lib/cwl/stg64fa88ba-30ca-40ae-bdce-cd5b11c65074/GCF_025244745.1_ASM2524474v1_genomic.fna.gz --refList GCF_025244745.1_ASM2524474v1_genomic.fna/target_genomes.txt --output GCF_025244745.1_ASM2524474v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:59,117] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:59,118] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd05fa5d2-4415-4976-9f7d-82dbea6ca660/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:59,118] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd05fa5d2-4415-4976-9f7d-82dbea6ca660/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:59,133] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:17:59,134] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:59,134] [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 rubellus	strain=Ant6	GCA_025244745.1	1889240	1889240	type	True	100.0	1012	1013	95	conclusive
Deinococcus alpinitundrae	strain=LMG 24283	GCA_009982895.1	468913	468913	type	True	87.8137	834	1013	95	below_threshold
Deinococcus irradiatisoli	strain=17bor-2	GCA_003173015.1	2202254	2202254	type	True	83.6237	711	1013	95	below_threshold
Deinococcus psychrotolerans	strain=S14-83	GCA_003860465.1	2489213	2489213	type	True	82.0588	694	1013	95	below_threshold
Deinococcus detaillensis	strain=H1	GCA_007280555.1	2592048	2592048	type	True	81.888	702	1013	95	below_threshold
Deinococcus gobiensis	strain=I-0	GCA_000252445.1	502394	502394	type	True	78.6611	428	1013	95	below_threshold
Deinococcus wulumuqiensis	strain=R12	GCA_014875975.1	980427	980427	type	True	78.2206	375	1013	95	below_threshold
Deinococcus wulumuqiensis	strain=R12	GCA_014875835.1	980427	980427	type	True	78.0882	367	1013	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:59,136] [INFO] DFAST Taxonomy check result was written to GCF_025244745.1_ASM2524474v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:59,137] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:59,137] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:59,137] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd05fa5d2-4415-4976-9f7d-82dbea6ca660/dqc_reference/checkm_data
[2024-01-24 13:17:59,139] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:59,170] [INFO] Task started: CheckM
[2024-01-24 13:17:59,170] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025244745.1_ASM2524474v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025244745.1_ASM2524474v1_genomic.fna/checkm_input GCF_025244745.1_ASM2524474v1_genomic.fna/checkm_result
[2024-01-24 13:18:29,889] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:29,890] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:29,909] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:29,909] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:29,910] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025244745.1_ASM2524474v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:29,910] [INFO] Task started: Blastn
[2024-01-24 13:18:29,910] [INFO] Running command: blastn -query GCF_025244745.1_ASM2524474v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd05fa5d2-4415-4976-9f7d-82dbea6ca660/dqc_reference/reference_markers_gtdb.fasta -out GCF_025244745.1_ASM2524474v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:30,890] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:30,894] [INFO] Selected 12 target genomes.
[2024-01-24 13:18:30,894] [INFO] Target genome list was writen to GCF_025244745.1_ASM2524474v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:31,020] [INFO] Task started: fastANI
[2024-01-24 13:18:31,020] [INFO] Running command: fastANI --query /var/lib/cwl/stg64fa88ba-30ca-40ae-bdce-cd5b11c65074/GCF_025244745.1_ASM2524474v1_genomic.fna.gz --refList GCF_025244745.1_ASM2524474v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025244745.1_ASM2524474v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:39,624] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:39,643] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:18:39,643] [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_009982895.1	s__Deinococcus alpinitundrae	87.8159	833	1013	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003173015.1	s__Deinococcus irradiatisoli	83.6576	710	1013	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003860465.1	s__Deinococcus sp003860465	82.0827	691	1013	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007280555.1	s__Deinococcus detaillensis	81.8949	701	1013	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000252445.1	s__Deinococcus gobiensis	78.674	426	1013	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000008565.1	s__Deinococcus radiodurans	78.4394	354	1013	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	99.94	99.91	0.99	0.99	8	-
GCF_011067105.1	s__Deinococcus wulumuqiensis	78.2815	389	1013	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	99.82	97.50	0.97	0.83	19	-
GCF_014648095.1	s__Deinococcus ruber	78.1709	425	1013	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	77.8397	336	1013	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	96.26	96.21	0.94	0.94	4	-
GCA_018260275.1	s__Deinococcus sp018260275	77.6702	212	1013	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000190555.1	s__Deinococcus proteolyticus	77.3993	241	1013	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000186385.1	s__Deinococcus_B maricopensis	77.3668	224	1013	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:39,644] [INFO] GTDB search result was written to GCF_025244745.1_ASM2524474v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:39,645] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:39,648] [INFO] DFAST_QC result json was written to GCF_025244745.1_ASM2524474v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:39,648] [INFO] DFAST_QC completed!
[2024-01-24 13:18:39,648] [INFO] Total running time: 0h0m58s