[2023-06-28 12:02:02,177] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:02:02,179] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:02:02,180] [INFO] DQC Reference Directory: /var/lib/cwl/stg06e64f35-9df9-4531-b92a-218d48eb4303/dqc_reference
[2023-06-28 12:02:03,518] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:02:03,519] [INFO] Task started: Prodigal
[2023-06-28 12:02:03,519] [INFO] Running command: gunzip -c /var/lib/cwl/stg4e67db32-f080-433c-94ed-57dd5e5ed211/GCA_027403545.1_ASM2740354v1_genomic.fna.gz | prodigal -d GCA_027403545.1_ASM2740354v1_genomic.fna/cds.fna -a GCA_027403545.1_ASM2740354v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:02:18,017] [INFO] Task succeeded: Prodigal
[2023-06-28 12:02:18,017] [INFO] Task started: HMMsearch
[2023-06-28 12:02:18,018] [INFO] Running command: hmmsearch --tblout GCA_027403545.1_ASM2740354v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg06e64f35-9df9-4531-b92a-218d48eb4303/dqc_reference/reference_markers.hmm GCA_027403545.1_ASM2740354v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:02:18,342] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:02:18,343] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4e67db32-f080-433c-94ed-57dd5e5ed211/GCA_027403545.1_ASM2740354v1_genomic.fna.gz]
[2023-06-28 12:02:18,399] [INFO] Query marker FASTA was written to GCA_027403545.1_ASM2740354v1_genomic.fna/markers.fasta
[2023-06-28 12:02:18,400] [INFO] Task started: Blastn
[2023-06-28 12:02:18,400] [INFO] Running command: blastn -query GCA_027403545.1_ASM2740354v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg06e64f35-9df9-4531-b92a-218d48eb4303/dqc_reference/reference_markers.fasta -out GCA_027403545.1_ASM2740354v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:02:19,046] [INFO] Task succeeded: Blastn
[2023-06-28 12:02:19,051] [INFO] Selected 19 target genomes.
[2023-06-28 12:02:19,052] [INFO] Target genome list was writen to GCA_027403545.1_ASM2740354v1_genomic.fna/target_genomes.txt
[2023-06-28 12:02:19,062] [INFO] Task started: fastANI
[2023-06-28 12:02:19,062] [INFO] Running command: fastANI --query /var/lib/cwl/stg4e67db32-f080-433c-94ed-57dd5e5ed211/GCA_027403545.1_ASM2740354v1_genomic.fna.gz --refList GCA_027403545.1_ASM2740354v1_genomic.fna/target_genomes.txt --output GCA_027403545.1_ASM2740354v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:02:31,928] [INFO] Task succeeded: fastANI
[2023-06-28 12:02:31,928] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg06e64f35-9df9-4531-b92a-218d48eb4303/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:02:31,928] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg06e64f35-9df9-4531-b92a-218d48eb4303/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:02:31,933] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 12:02:31,934] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 12:02:31,934] [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
Desulfacinum infernum	strain=DSM 9756	GCA_900129305.1	35837	35837	type	True	75.4474	53	1702	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 12:02:31,936] [INFO] DFAST Taxonomy check result was written to GCA_027403545.1_ASM2740354v1_genomic.fna/tc_result.tsv
[2023-06-28 12:02:31,937] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:02:31,937] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:02:31,937] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg06e64f35-9df9-4531-b92a-218d48eb4303/dqc_reference/checkm_data
[2023-06-28 12:02:31,939] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:02:32,005] [INFO] Task started: CheckM
[2023-06-28 12:02:32,005] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027403545.1_ASM2740354v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027403545.1_ASM2740354v1_genomic.fna/checkm_input GCA_027403545.1_ASM2740354v1_genomic.fna/checkm_result
[2023-06-28 12:03:17,760] [INFO] Task succeeded: CheckM
[2023-06-28 12:03:17,763] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 12:03:17,792] [INFO] ===== Completeness check finished =====
[2023-06-28 12:03:17,792] [INFO] ===== Start GTDB Search =====
[2023-06-28 12:03:17,794] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027403545.1_ASM2740354v1_genomic.fna/markers.fasta)
[2023-06-28 12:03:17,794] [INFO] Task started: Blastn
[2023-06-28 12:03:17,794] [INFO] Running command: blastn -query GCA_027403545.1_ASM2740354v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg06e64f35-9df9-4531-b92a-218d48eb4303/dqc_reference/reference_markers_gtdb.fasta -out GCA_027403545.1_ASM2740354v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:03:18,713] [INFO] Task succeeded: Blastn
[2023-06-28 12:03:18,719] [INFO] Selected 15 target genomes.
[2023-06-28 12:03:18,719] [INFO] Target genome list was writen to GCA_027403545.1_ASM2740354v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 12:03:18,728] [INFO] Task started: fastANI
[2023-06-28 12:03:18,728] [INFO] Running command: fastANI --query /var/lib/cwl/stg4e67db32-f080-433c-94ed-57dd5e5ed211/GCA_027403545.1_ASM2740354v1_genomic.fna.gz --refList GCA_027403545.1_ASM2740354v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027403545.1_ASM2740354v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 12:03:27,548] [INFO] Task succeeded: fastANI
[2023-06-28 12:03:27,564] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 12:03:27,564] [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_900290385.1	s__SbD1 sp900290385	77.6423	137	1702	d__Bacteria;p__Desulfobacterota;c__Syntrophobacteria;o__Syntrophobacterales;f__Syntrophobacteraceae;g__SbD1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003165235.1	s__SbD1 sp003165235	77.5576	387	1702	d__Bacteria;p__Desulfobacterota;c__Syntrophobacteria;o__Syntrophobacterales;f__Syntrophobacteraceae;g__SbD1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900290365.1	s__SbD1 sp900290365	77.1346	321	1702	d__Bacteria;p__Desulfobacterota;c__Syntrophobacteria;o__Syntrophobacterales;f__Syntrophobacteraceae;g__SbD1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001603845.1	s__SbD1 sp001603845	76.3307	89	1702	d__Bacteria;p__Desulfobacterota;c__Syntrophobacteria;o__Syntrophobacterales;f__Syntrophobacteraceae;g__SbD1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002298995.1	s__SbD1 sp002298995	76.2431	101	1702	d__Bacteria;p__Desulfobacterota;c__Syntrophobacteria;o__Syntrophobacterales;f__Syntrophobacteraceae;g__SbD1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002298165.1	s__SbD1 sp002298165	75.9326	79	1702	d__Bacteria;p__Desulfobacterota;c__Syntrophobacteria;o__Syntrophobacterales;f__Syntrophobacteraceae;g__SbD1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129305.1	s__Desulfacinum infernum	75.4474	53	1702	d__Bacteria;p__Desulfobacterota;c__Syntrophobacteria;o__Syntrophobacterales;f__DSM-9756;g__Desulfacinum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 12:03:27,566] [INFO] GTDB search result was written to GCA_027403545.1_ASM2740354v1_genomic.fna/result_gtdb.tsv
[2023-06-28 12:03:27,567] [INFO] ===== GTDB Search completed =====
[2023-06-28 12:03:27,570] [INFO] DFAST_QC result json was written to GCA_027403545.1_ASM2740354v1_genomic.fna/dqc_result.json
[2023-06-28 12:03:27,570] [INFO] DFAST_QC completed!
[2023-06-28 12:03:27,570] [INFO] Total running time: 0h1m25s