[2023-06-28 16:48:20,866] [INFO] DFAST_QC pipeline started.
[2023-06-28 16:48:20,869] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 16:48:20,870] [INFO] DQC Reference Directory: /var/lib/cwl/stg4ab47254-f9a0-4c5c-9b3a-f453e91da335/dqc_reference
[2023-06-28 16:48:23,015] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 16:48:23,016] [INFO] Task started: Prodigal
[2023-06-28 16:48:23,017] [INFO] Running command: gunzip -c /var/lib/cwl/stga0d99eed-7349-4a01-8207-51f7494a6197/GCA_020055045.1_ASM2005504v1_genomic.fna.gz | prodigal -d GCA_020055045.1_ASM2005504v1_genomic.fna/cds.fna -a GCA_020055045.1_ASM2005504v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 16:48:25,911] [INFO] Task succeeded: Prodigal
[2023-06-28 16:48:25,911] [INFO] Task started: HMMsearch
[2023-06-28 16:48:25,912] [INFO] Running command: hmmsearch --tblout GCA_020055045.1_ASM2005504v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4ab47254-f9a0-4c5c-9b3a-f453e91da335/dqc_reference/reference_markers.hmm GCA_020055045.1_ASM2005504v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 16:48:26,134] [INFO] Task succeeded: HMMsearch
[2023-06-28 16:48:26,136] [INFO] Found 6/6 markers.
[2023-06-28 16:48:26,159] [INFO] Query marker FASTA was written to GCA_020055045.1_ASM2005504v1_genomic.fna/markers.fasta
[2023-06-28 16:48:26,159] [INFO] Task started: Blastn
[2023-06-28 16:48:26,159] [INFO] Running command: blastn -query GCA_020055045.1_ASM2005504v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ab47254-f9a0-4c5c-9b3a-f453e91da335/dqc_reference/reference_markers.fasta -out GCA_020055045.1_ASM2005504v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:48:26,733] [INFO] Task succeeded: Blastn
[2023-06-28 16:48:26,737] [INFO] Selected 9 target genomes.
[2023-06-28 16:48:26,738] [INFO] Target genome list was writen to GCA_020055045.1_ASM2005504v1_genomic.fna/target_genomes.txt
[2023-06-28 16:48:26,742] [INFO] Task started: fastANI
[2023-06-28 16:48:26,742] [INFO] Running command: fastANI --query /var/lib/cwl/stga0d99eed-7349-4a01-8207-51f7494a6197/GCA_020055045.1_ASM2005504v1_genomic.fna.gz --refList GCA_020055045.1_ASM2005504v1_genomic.fna/target_genomes.txt --output GCA_020055045.1_ASM2005504v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 16:48:31,191] [INFO] Task succeeded: fastANI
[2023-06-28 16:48:31,191] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4ab47254-f9a0-4c5c-9b3a-f453e91da335/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 16:48:31,192] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4ab47254-f9a0-4c5c-9b3a-f453e91da335/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 16:48:31,204] [INFO] Found 6 fastANI hits (3 hits with ANI > threshold)
[2023-06-28 16:48:31,204] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2023-06-28 16:48:31,204] [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
Thermodesulfobacterium commune	strain=DSM 2178	GCA_000746435.1	1741	1741	type	True	98.68	522	551	95	inconclusive
Thermodesulfobacterium commune	strain=DSM 2178	GCA_000734015.1	1741	1741	type	True	98.6747	529	551	95	inconclusive
Thermodesulfobacterium thermophilum	strain=DSM 1276	GCA_000421605.1	886	886	type	True	96.2012	504	551	95	inconclusive
Thermodesulfobacterium hveragerdense	strain=DSM 12571	GCA_000423845.1	53424	53424	type	True	93.8562	495	551	95	below_threshold
Thermodesulfobacterium hydrogeniphilum	strain=DSM 14290	GCA_000746255.1	161156	161156	type	True	77.2352	112	551	95	below_threshold
Thermodesulfobacterium geofontis	strain=OPF15	GCA_000215975.1	1295609	1295609	type	True	76.728	88	551	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 16:48:31,207] [INFO] DFAST Taxonomy check result was written to GCA_020055045.1_ASM2005504v1_genomic.fna/tc_result.tsv
[2023-06-28 16:48:31,207] [INFO] ===== Taxonomy check completed =====
[2023-06-28 16:48:31,208] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 16:48:31,208] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4ab47254-f9a0-4c5c-9b3a-f453e91da335/dqc_reference/checkm_data
[2023-06-28 16:48:31,210] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 16:48:31,232] [INFO] Task started: CheckM
[2023-06-28 16:48:31,232] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020055045.1_ASM2005504v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020055045.1_ASM2005504v1_genomic.fna/checkm_input GCA_020055045.1_ASM2005504v1_genomic.fna/checkm_result
[2023-06-28 16:48:47,795] [INFO] Task succeeded: CheckM
[2023-06-28 16:48:47,797] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 16:48:47,823] [INFO] ===== Completeness check finished =====
[2023-06-28 16:48:47,824] [INFO] ===== Start GTDB Search =====
[2023-06-28 16:48:47,824] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020055045.1_ASM2005504v1_genomic.fna/markers.fasta)
[2023-06-28 16:48:47,824] [INFO] Task started: Blastn
[2023-06-28 16:48:47,824] [INFO] Running command: blastn -query GCA_020055045.1_ASM2005504v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ab47254-f9a0-4c5c-9b3a-f453e91da335/dqc_reference/reference_markers_gtdb.fasta -out GCA_020055045.1_ASM2005504v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:48:48,689] [INFO] Task succeeded: Blastn
[2023-06-28 16:48:48,693] [INFO] Selected 11 target genomes.
[2023-06-28 16:48:48,693] [INFO] Target genome list was writen to GCA_020055045.1_ASM2005504v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 16:48:48,714] [INFO] Task started: fastANI
[2023-06-28 16:48:48,715] [INFO] Running command: fastANI --query /var/lib/cwl/stga0d99eed-7349-4a01-8207-51f7494a6197/GCA_020055045.1_ASM2005504v1_genomic.fna.gz --refList GCA_020055045.1_ASM2005504v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020055045.1_ASM2005504v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 16:48:53,361] [INFO] Task succeeded: fastANI
[2023-06-28 16:48:53,372] [INFO] Found 7 fastANI hits (2 hits with ANI > circumscription radius)
[2023-06-28 16:48:53,372] [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_000734015.1	s__Thermodesulfobacterium commune	98.6373	530	551	d__Bacteria;p__Desulfobacterota;c__Thermodesulfobacteria;o__Thermodesulfobacteriales;f__Thermodesulfobacteriaceae;g__Thermodesulfobacterium	95.9677	99.11	98.83	0.97	0.93	10	inconclusive
GCF_000421605.1	s__Thermodesulfobacterium thermophilum	96.2012	504	551	d__Bacteria;p__Desulfobacterota;c__Thermodesulfobacteria;o__Thermodesulfobacteriales;f__Thermodesulfobacteriaceae;g__Thermodesulfobacterium	95.9677	N/A	N/A	N/A	N/A	1	inconclusive
GCF_000423845.1	s__Thermodesulfobacterium hveragerdense	93.8224	496	551	d__Bacteria;p__Desulfobacterota;c__Thermodesulfobacteria;o__Thermodesulfobacteriales;f__Thermodesulfobacteriaceae;g__Thermodesulfobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008630935.1	s__Thermodesulfobacterium sp008630935	80.1913	377	551	d__Bacteria;p__Desulfobacterota;c__Thermodesulfobacteria;o__Thermodesulfobacteriales;f__Thermodesulfobacteriaceae;g__Thermodesulfobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000746255.1	s__Thermodesulfobacterium hydrogeniphilum	77.2352	112	551	d__Bacteria;p__Desulfobacterota;c__Thermodesulfobacteria;o__Thermodesulfobacteriales;f__Thermodesulfobacteriaceae;g__Thermodesulfobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011361985.1	s__Thermodesulfobacterium geofontis_D	76.7884	77	551	d__Bacteria;p__Desulfobacterota;c__Thermodesulfobacteria;o__Thermodesulfobacteriales;f__Thermodesulfobacteriaceae;g__Thermodesulfobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000215975.1	s__Thermodesulfobacterium geofontis	76.728	88	551	d__Bacteria;p__Desulfobacterota;c__Thermodesulfobacteria;o__Thermodesulfobacteriales;f__Thermodesulfobacteriaceae;g__Thermodesulfobacterium	95.0	96.03	96.03	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2023-06-28 16:48:53,374] [INFO] GTDB search result was written to GCA_020055045.1_ASM2005504v1_genomic.fna/result_gtdb.tsv
[2023-06-28 16:48:53,375] [INFO] ===== GTDB Search completed =====
[2023-06-28 16:48:53,378] [INFO] DFAST_QC result json was written to GCA_020055045.1_ASM2005504v1_genomic.fna/dqc_result.json
[2023-06-28 16:48:53,378] [INFO] DFAST_QC completed!
[2023-06-28 16:48:53,378] [INFO] Total running time: 0h0m33s