[2024-01-24 11:51:36,870] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:36,873] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:36,873] [INFO] DQC Reference Directory: /var/lib/cwl/stg713ca65e-ee81-42f4-a82d-1f791d0378b1/dqc_reference
[2024-01-24 11:51:38,105] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:38,105] [INFO] Task started: Prodigal
[2024-01-24 11:51:38,106] [INFO] Running command: gunzip -c /var/lib/cwl/stg661e352a-115d-403b-88dd-b94e613b55d2/GCF_014201875.1_ASM1420187v1_genomic.fna.gz | prodigal -d GCF_014201875.1_ASM1420187v1_genomic.fna/cds.fna -a GCF_014201875.1_ASM1420187v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:54,791] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:54,792] [INFO] Task started: HMMsearch
[2024-01-24 11:51:54,792] [INFO] Running command: hmmsearch --tblout GCF_014201875.1_ASM1420187v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg713ca65e-ee81-42f4-a82d-1f791d0378b1/dqc_reference/reference_markers.hmm GCF_014201875.1_ASM1420187v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:55,077] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:55,079] [INFO] Found 6/6 markers.
[2024-01-24 11:51:55,132] [INFO] Query marker FASTA was written to GCF_014201875.1_ASM1420187v1_genomic.fna/markers.fasta
[2024-01-24 11:51:55,132] [INFO] Task started: Blastn
[2024-01-24 11:51:55,132] [INFO] Running command: blastn -query GCF_014201875.1_ASM1420187v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg713ca65e-ee81-42f4-a82d-1f791d0378b1/dqc_reference/reference_markers.fasta -out GCF_014201875.1_ASM1420187v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:55,758] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:55,764] [INFO] Selected 10 target genomes.
[2024-01-24 11:51:55,765] [INFO] Target genome list was writen to GCF_014201875.1_ASM1420187v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:55,770] [INFO] Task started: fastANI
[2024-01-24 11:51:55,770] [INFO] Running command: fastANI --query /var/lib/cwl/stg661e352a-115d-403b-88dd-b94e613b55d2/GCF_014201875.1_ASM1420187v1_genomic.fna.gz --refList GCF_014201875.1_ASM1420187v1_genomic.fna/target_genomes.txt --output GCF_014201875.1_ASM1420187v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:06,659] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:06,660] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg713ca65e-ee81-42f4-a82d-1f791d0378b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:06,660] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg713ca65e-ee81-42f4-a82d-1f791d0378b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:06,670] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:52:06,670] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:52:06,670] [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 humi	strain=DSM 27939	GCA_014201875.1	662880	662880	type	True	100.0	1879	1881	95	conclusive
Deinococcus humi	strain=JCM 17915	GCA_014647275.1	662880	662880	type	True	99.9931	1867	1881	95	conclusive
Deinococcus radiopugnans	strain=DSM 12027	GCA_014201625.1	57497	57497	type	True	86.3122	1070	1881	95	below_threshold
Deinococcus radiopugnans	strain=ATCC 19172	GCA_006335125.1	57497	57497	type	True	86.2969	1065	1881	95	below_threshold
Deinococcus aerolatus	strain=JCM 15442	GCA_014647055.1	522487	522487	type	True	84.9451	998	1881	95	below_threshold
Deinococcus frigens	strain=DSM 12807	GCA_000701425.1	249403	249403	type	True	84.4222	921	1881	95	below_threshold
Deinococcus marmoris	strain=DSM 12784	GCA_000701405.1	249408	249408	type	True	84.2757	982	1881	95	below_threshold
Deinococcus aerophilus	strain=JCM 15443	GCA_014647075.1	522488	522488	type	True	81.5775	746	1881	95	below_threshold
Deinococcus budaensis	strain=DSM 101791	GCA_014201885.1	1665626	1665626	type	True	78.7092	573	1881	95	below_threshold
Deinococcus multiflagellatus	strain=KACC 19287	GCA_020166415.1	1656887	1656887	type	True	78.6472	610	1881	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:06,672] [INFO] DFAST Taxonomy check result was written to GCF_014201875.1_ASM1420187v1_genomic.fna/tc_result.tsv
[2024-01-24 11:52:06,672] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:06,673] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:06,673] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg713ca65e-ee81-42f4-a82d-1f791d0378b1/dqc_reference/checkm_data
[2024-01-24 11:52:06,675] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:06,730] [INFO] Task started: CheckM
[2024-01-24 11:52:06,731] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014201875.1_ASM1420187v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014201875.1_ASM1420187v1_genomic.fna/checkm_input GCF_014201875.1_ASM1420187v1_genomic.fna/checkm_result
[2024-01-24 11:52:55,496] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:55,498] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:55,525] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:55,525] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:55,526] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014201875.1_ASM1420187v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:55,526] [INFO] Task started: Blastn
[2024-01-24 11:52:55,526] [INFO] Running command: blastn -query GCF_014201875.1_ASM1420187v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg713ca65e-ee81-42f4-a82d-1f791d0378b1/dqc_reference/reference_markers_gtdb.fasta -out GCF_014201875.1_ASM1420187v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:56,412] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:56,420] [INFO] Selected 11 target genomes.
[2024-01-24 11:52:56,420] [INFO] Target genome list was writen to GCF_014201875.1_ASM1420187v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:56,429] [INFO] Task started: fastANI
[2024-01-24 11:52:56,429] [INFO] Running command: fastANI --query /var/lib/cwl/stg661e352a-115d-403b-88dd-b94e613b55d2/GCF_014201875.1_ASM1420187v1_genomic.fna.gz --refList GCF_014201875.1_ASM1420187v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014201875.1_ASM1420187v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:53:07,775] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:07,789] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:53:07,789] [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_014201875.1	s__Deinococcus humi	100.0	1879	1881	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_006335125.1	s__Deinococcus radiopugnans	86.3006	1065	1881	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	98.45	97.61	0.92	0.87	4	-
GCF_014647055.1	s__Deinococcus aerolatus	84.9332	999	1881	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001949125.1	s__Deinococcus marmoris_A	84.3935	1013	1881	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000701405.1	s__Deinococcus marmoris	84.2644	984	1881	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009017495.1	s__Deinococcus sp009017495	84.1586	972	1881	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647075.1	s__Deinococcus aerophilus	81.5823	745	1881	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	78.6872	575	1881	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647655.1	s__Deinococcus malanensis	78.4841	468	1881	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	78.4549	513	1881	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176165.1	s__Deinococcus hopiensis	77.9934	531	1881	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 11:53:07,791] [INFO] GTDB search result was written to GCF_014201875.1_ASM1420187v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:53:07,791] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:53:07,794] [INFO] DFAST_QC result json was written to GCF_014201875.1_ASM1420187v1_genomic.fna/dqc_result.json
[2024-01-24 11:53:07,794] [INFO] DFAST_QC completed!
[2024-01-24 11:53:07,794] [INFO] Total running time: 0h1m31s