[2023-06-29 12:18:18,123] [INFO] DFAST_QC pipeline started.
[2023-06-29 12:18:18,136] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 12:18:18,136] [INFO] DQC Reference Directory: /var/lib/cwl/stg07458d4f-68d6-4637-ae89-1db5a50a8cc3/dqc_reference
[2023-06-29 12:18:19,648] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 12:18:19,649] [INFO] Task started: Prodigal
[2023-06-29 12:18:19,649] [INFO] Running command: gunzip -c /var/lib/cwl/stg74e425cb-6a92-42ca-a1a0-5dcc757092a3/GCA_021737685.1_ASM2173768v1_genomic.fna.gz | prodigal -d GCA_021737685.1_ASM2173768v1_genomic.fna/cds.fna -a GCA_021737685.1_ASM2173768v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 12:18:26,404] [INFO] Task succeeded: Prodigal
[2023-06-29 12:18:26,404] [INFO] Task started: HMMsearch
[2023-06-29 12:18:26,404] [INFO] Running command: hmmsearch --tblout GCA_021737685.1_ASM2173768v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg07458d4f-68d6-4637-ae89-1db5a50a8cc3/dqc_reference/reference_markers.hmm GCA_021737685.1_ASM2173768v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 12:18:26,665] [INFO] Task succeeded: HMMsearch
[2023-06-29 12:18:26,667] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg74e425cb-6a92-42ca-a1a0-5dcc757092a3/GCA_021737685.1_ASM2173768v1_genomic.fna.gz]
[2023-06-29 12:18:26,694] [INFO] Query marker FASTA was written to GCA_021737685.1_ASM2173768v1_genomic.fna/markers.fasta
[2023-06-29 12:18:26,694] [INFO] Task started: Blastn
[2023-06-29 12:18:26,694] [INFO] Running command: blastn -query GCA_021737685.1_ASM2173768v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg07458d4f-68d6-4637-ae89-1db5a50a8cc3/dqc_reference/reference_markers.fasta -out GCA_021737685.1_ASM2173768v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:18:27,350] [INFO] Task succeeded: Blastn
[2023-06-29 12:18:27,354] [INFO] Selected 12 target genomes.
[2023-06-29 12:18:27,354] [INFO] Target genome list was writen to GCA_021737685.1_ASM2173768v1_genomic.fna/target_genomes.txt
[2023-06-29 12:18:27,355] [INFO] Task started: fastANI
[2023-06-29 12:18:27,355] [INFO] Running command: fastANI --query /var/lib/cwl/stg74e425cb-6a92-42ca-a1a0-5dcc757092a3/GCA_021737685.1_ASM2173768v1_genomic.fna.gz --refList GCA_021737685.1_ASM2173768v1_genomic.fna/target_genomes.txt --output GCA_021737685.1_ASM2173768v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 12:18:38,290] [INFO] Task succeeded: fastANI
[2023-06-29 12:18:38,290] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg07458d4f-68d6-4637-ae89-1db5a50a8cc3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 12:18:38,291] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg07458d4f-68d6-4637-ae89-1db5a50a8cc3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 12:18:38,298] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 12:18:38,299] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 12:18:38,299] [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	81.8953	514	721	95	below_threshold
Desulfotignum phosphitoxidans	strain=DSM 13687	GCA_000350545.1	190898	190898	type	True	81.734	517	721	95	below_threshold
Desulfospira joergensenii	strain=DSM 10085	GCA_000420085.1	53329	53329	type	True	77.5656	239	721	95	below_threshold
Desulfobacter vibrioformis	strain=DSM 8776	GCA_000745975.1	34031	34031	type	True	77.2967	149	721	95	below_threshold
Desulfobacter hydrogenophilus	strain=DSM 3380	GCA_010499545.1	2291	2291	type	True	76.878	115	721	95	below_threshold
Desulfobacula phenolica	strain=DSM 3384	GCA_900105645.1	90732	90732	type	True	76.803	111	721	95	below_threshold
Desulfobacula toluolica	strain=Tol2	GCA_000307105.1	28223	28223	type	True	76.7177	100	721	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 12:18:38,301] [INFO] DFAST Taxonomy check result was written to GCA_021737685.1_ASM2173768v1_genomic.fna/tc_result.tsv
[2023-06-29 12:18:38,302] [INFO] ===== Taxonomy check completed =====
[2023-06-29 12:18:38,302] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 12:18:38,302] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg07458d4f-68d6-4637-ae89-1db5a50a8cc3/dqc_reference/checkm_data
[2023-06-29 12:18:38,304] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 12:18:38,334] [INFO] Task started: CheckM
[2023-06-29 12:18:38,335] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021737685.1_ASM2173768v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021737685.1_ASM2173768v1_genomic.fna/checkm_input GCA_021737685.1_ASM2173768v1_genomic.fna/checkm_result
[2023-06-29 12:19:04,887] [INFO] Task succeeded: CheckM
[2023-06-29 12:19:04,888] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.29%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 12:19:04,912] [INFO] ===== Completeness check finished =====
[2023-06-29 12:19:04,913] [INFO] ===== Start GTDB Search =====
[2023-06-29 12:19:04,913] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021737685.1_ASM2173768v1_genomic.fna/markers.fasta)
[2023-06-29 12:19:04,914] [INFO] Task started: Blastn
[2023-06-29 12:19:04,914] [INFO] Running command: blastn -query GCA_021737685.1_ASM2173768v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg07458d4f-68d6-4637-ae89-1db5a50a8cc3/dqc_reference/reference_markers_gtdb.fasta -out GCA_021737685.1_ASM2173768v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:19:05,935] [INFO] Task succeeded: Blastn
[2023-06-29 12:19:05,939] [INFO] Selected 13 target genomes.
[2023-06-29 12:19:05,939] [INFO] Target genome list was writen to GCA_021737685.1_ASM2173768v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 12:19:05,946] [INFO] Task started: fastANI
[2023-06-29 12:19:05,946] [INFO] Running command: fastANI --query /var/lib/cwl/stg74e425cb-6a92-42ca-a1a0-5dcc757092a3/GCA_021737685.1_ASM2173768v1_genomic.fna.gz --refList GCA_021737685.1_ASM2173768v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021737685.1_ASM2173768v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 12:19:14,571] [INFO] Task succeeded: fastANI
[2023-06-29 12:19:14,595] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 12:19:14,595] [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_011390335.1	s__Desulfotignum sp011390335	85.9701	541	721	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfotignum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011390615.1	s__Desulfotignum sp011390615	85.3184	415	721	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfotignum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011389715.1	s__Desulfotignum sp011389715	85.0125	346	721	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	84.2053	456	721	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfotignum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011390635.1	s__Desulfotignum sp011390635	83.5127	517	721	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfotignum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011390235.1	s__Desulfotignum sp011390235	83.1016	274	721	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	82.9899	275	721	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfotignum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011389555.1	s__Desulfotignum sp011389555	81.9382	454	721	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfotignum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000421285.1	s__Desulfotignum balticum	81.8953	514	721	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	81.74	516	721	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfotignum	96.875	N/A	N/A	N/A	N/A	1	-
GCA_018399285.1	s__Desulfotignum sp018399285	81.2613	436	721	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	81.1651	384	721	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfotignum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013792075.1	s__NBML01 sp013792075	77.1166	199	721	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__NBML01	95.0	99.85	99.75	0.95	0.94	3	-
--------------------------------------------------------------------------------
[2023-06-29 12:19:14,597] [INFO] GTDB search result was written to GCA_021737685.1_ASM2173768v1_genomic.fna/result_gtdb.tsv
[2023-06-29 12:19:14,598] [INFO] ===== GTDB Search completed =====
[2023-06-29 12:19:14,601] [INFO] DFAST_QC result json was written to GCA_021737685.1_ASM2173768v1_genomic.fna/dqc_result.json
[2023-06-29 12:19:14,601] [INFO] DFAST_QC completed!
[2023-06-29 12:19:14,601] [INFO] Total running time: 0h0m56s