[2023-06-19 07:49:39,734] [INFO] DFAST_QC pipeline started.
[2023-06-19 07:49:39,736] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 07:49:39,737] [INFO] DQC Reference Directory: /var/lib/cwl/stg9d67c758-f8df-49e1-93d0-7c900cac5d1b/dqc_reference
[2023-06-19 07:49:41,072] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 07:49:41,074] [INFO] Task started: Prodigal
[2023-06-19 07:49:41,074] [INFO] Running command: gunzip -c /var/lib/cwl/stgca882acf-3b6a-4ae1-864c-8a4d6424381b/GCA_018399285.1_ASM1839928v1_genomic.fna.gz | prodigal -d GCA_018399285.1_ASM1839928v1_genomic.fna/cds.fna -a GCA_018399285.1_ASM1839928v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 07:49:51,582] [INFO] Task succeeded: Prodigal
[2023-06-19 07:49:51,583] [INFO] Task started: HMMsearch
[2023-06-19 07:49:51,583] [INFO] Running command: hmmsearch --tblout GCA_018399285.1_ASM1839928v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9d67c758-f8df-49e1-93d0-7c900cac5d1b/dqc_reference/reference_markers.hmm GCA_018399285.1_ASM1839928v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 07:49:51,859] [INFO] Task succeeded: HMMsearch
[2023-06-19 07:49:51,860] [INFO] Found 6/6 markers.
[2023-06-19 07:49:51,890] [INFO] Query marker FASTA was written to GCA_018399285.1_ASM1839928v1_genomic.fna/markers.fasta
[2023-06-19 07:49:51,890] [INFO] Task started: Blastn
[2023-06-19 07:49:51,891] [INFO] Running command: blastn -query GCA_018399285.1_ASM1839928v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d67c758-f8df-49e1-93d0-7c900cac5d1b/dqc_reference/reference_markers.fasta -out GCA_018399285.1_ASM1839928v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 07:49:52,476] [INFO] Task succeeded: Blastn
[2023-06-19 07:49:52,480] [INFO] Selected 18 target genomes.
[2023-06-19 07:49:52,480] [INFO] Target genome list was writen to GCA_018399285.1_ASM1839928v1_genomic.fna/target_genomes.txt
[2023-06-19 07:49:52,484] [INFO] Task started: fastANI
[2023-06-19 07:49:52,484] [INFO] Running command: fastANI --query /var/lib/cwl/stgca882acf-3b6a-4ae1-864c-8a4d6424381b/GCA_018399285.1_ASM1839928v1_genomic.fna.gz --refList GCA_018399285.1_ASM1839928v1_genomic.fna/target_genomes.txt --output GCA_018399285.1_ASM1839928v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 07:50:06,675] [INFO] Task succeeded: fastANI
[2023-06-19 07:50:06,675] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9d67c758-f8df-49e1-93d0-7c900cac5d1b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 07:50:06,676] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9d67c758-f8df-49e1-93d0-7c900cac5d1b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 07:50:06,684] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 07:50:06,684] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 07:50:06,685] [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
Desulfotignum balticum	strain=DSM 7044	GCA_000421285.1	115781	115781	type	True	94.5632	909	1060	95	below_threshold
Desulfotignum phosphitoxidans	strain=DSM 13687	GCA_000350545.1	190898	190898	type	True	93.9777	894	1060	95	below_threshold
Desulfobacter postgatei	strain=2ac9	GCA_000233695.3	2293	2293	type	True	77.7589	114	1060	95	below_threshold
Desulfospira joergensenii	strain=DSM 10085	GCA_000420085.1	53329	53329	type	True	77.2889	278	1060	95	below_threshold
Desulfobacter latus	strain=AcRS2	GCA_013389365.1	2292	2292	type	True	77.1649	127	1060	95	below_threshold
Desulfobacter vibrioformis	strain=DSM 8776	GCA_000745975.1	34031	34031	type	True	76.8956	159	1060	95	below_threshold
Desulfobacter curvatus	strain=DSM 3379	GCA_000373985.1	2290	2290	type	True	76.6753	133	1060	95	below_threshold
Desulfosarcina ovata subsp. ovata	strain=oXyS1	GCA_009689005.1	2752305	83564	type	True	76.6343	65	1060	95	below_threshold
Desulfosarcina cetonica	strain=JCM 12296	GCA_001311845.1	90730	90730	type	True	76.2694	53	1060	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 07:50:06,687] [INFO] DFAST Taxonomy check result was written to GCA_018399285.1_ASM1839928v1_genomic.fna/tc_result.tsv
[2023-06-19 07:50:06,687] [INFO] ===== Taxonomy check completed =====
[2023-06-19 07:50:06,688] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 07:50:06,688] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9d67c758-f8df-49e1-93d0-7c900cac5d1b/dqc_reference/checkm_data
[2023-06-19 07:50:06,689] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 07:50:06,724] [INFO] Task started: CheckM
[2023-06-19 07:50:06,724] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018399285.1_ASM1839928v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018399285.1_ASM1839928v1_genomic.fna/checkm_input GCA_018399285.1_ASM1839928v1_genomic.fna/checkm_result
[2023-06-19 07:50:42,217] [INFO] Task succeeded: CheckM
[2023-06-19 07:50:42,218] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.12%
Contamintation: 1.39%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-19 07:50:42,241] [INFO] ===== Completeness check finished =====
[2023-06-19 07:50:42,241] [INFO] ===== Start GTDB Search =====
[2023-06-19 07:50:42,242] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018399285.1_ASM1839928v1_genomic.fna/markers.fasta)
[2023-06-19 07:50:42,242] [INFO] Task started: Blastn
[2023-06-19 07:50:42,242] [INFO] Running command: blastn -query GCA_018399285.1_ASM1839928v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d67c758-f8df-49e1-93d0-7c900cac5d1b/dqc_reference/reference_markers_gtdb.fasta -out GCA_018399285.1_ASM1839928v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 07:50:43,045] [INFO] Task succeeded: Blastn
[2023-06-19 07:50:43,050] [INFO] Selected 7 target genomes.
[2023-06-19 07:50:43,050] [INFO] Target genome list was writen to GCA_018399285.1_ASM1839928v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 07:50:43,054] [INFO] Task started: fastANI
[2023-06-19 07:50:43,054] [INFO] Running command: fastANI --query /var/lib/cwl/stgca882acf-3b6a-4ae1-864c-8a4d6424381b/GCA_018399285.1_ASM1839928v1_genomic.fna.gz --refList GCA_018399285.1_ASM1839928v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018399285.1_ASM1839928v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 07:50:48,701] [INFO] Task succeeded: fastANI
[2023-06-19 07:50:48,714] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 07:50:48,714] [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
GCA_018399285.1	s__Desulfotignum sp018399285	100.0	1052	1060	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfotignum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000421285.1	s__Desulfotignum balticum	94.5771	908	1060	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfotignum	96.875	N/A	N/A	N/A	N/A	1	-
GCF_000350545.1	s__Desulfotignum phosphitoxidans	93.9766	895	1060	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfotignum	96.875	N/A	N/A	N/A	N/A	1	-
GCA_011389555.1	s__Desulfotignum sp011389555	87.1625	690	1060	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfotignum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011389835.1	s__Desulfotignum sp011389835	84.4253	632	1060	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfotignum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011390695.1	s__Desulfotignum sp011390695	81.2535	281	1060	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfotignum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011389575.1	s__Desulfotignum sp011389575	80.488	504	1060	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfotignum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 07:50:48,716] [INFO] GTDB search result was written to GCA_018399285.1_ASM1839928v1_genomic.fna/result_gtdb.tsv
[2023-06-19 07:50:48,717] [INFO] ===== GTDB Search completed =====
[2023-06-19 07:50:48,720] [INFO] DFAST_QC result json was written to GCA_018399285.1_ASM1839928v1_genomic.fna/dqc_result.json
[2023-06-19 07:50:48,720] [INFO] DFAST_QC completed!
[2023-06-19 07:50:48,720] [INFO] Total running time: 0h1m9s