[2024-01-25 17:35:05,725] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:35:05,726] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:35:05,726] [INFO] DQC Reference Directory: /var/lib/cwl/stgccdd6668-6f79-43ea-a943-de3fb50fe45c/dqc_reference
[2024-01-25 17:35:06,879] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:35:06,880] [INFO] Task started: Prodigal
[2024-01-25 17:35:06,880] [INFO] Running command: gunzip -c /var/lib/cwl/stg9456be11-034f-4763-b096-394620ab731b/GCF_000231405.2_ASM23140v3_genomic.fna.gz | prodigal -d GCF_000231405.2_ASM23140v3_genomic.fna/cds.fna -a GCF_000231405.2_ASM23140v3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:35:12,915] [INFO] Task succeeded: Prodigal
[2024-01-25 17:35:12,916] [INFO] Task started: HMMsearch
[2024-01-25 17:35:12,916] [INFO] Running command: hmmsearch --tblout GCF_000231405.2_ASM23140v3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgccdd6668-6f79-43ea-a943-de3fb50fe45c/dqc_reference/reference_markers.hmm GCF_000231405.2_ASM23140v3_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:35:13,117] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:35:13,118] [INFO] Found 6/6 markers.
[2024-01-25 17:35:13,143] [INFO] Query marker FASTA was written to GCF_000231405.2_ASM23140v3_genomic.fna/markers.fasta
[2024-01-25 17:35:13,144] [INFO] Task started: Blastn
[2024-01-25 17:35:13,144] [INFO] Running command: blastn -query GCF_000231405.2_ASM23140v3_genomic.fna/markers.fasta -db /var/lib/cwl/stgccdd6668-6f79-43ea-a943-de3fb50fe45c/dqc_reference/reference_markers.fasta -out GCF_000231405.2_ASM23140v3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:35:13,711] [INFO] Task succeeded: Blastn
[2024-01-25 17:35:13,714] [INFO] Selected 18 target genomes.
[2024-01-25 17:35:13,715] [INFO] Target genome list was writen to GCF_000231405.2_ASM23140v3_genomic.fna/target_genomes.txt
[2024-01-25 17:35:13,720] [INFO] Task started: fastANI
[2024-01-25 17:35:13,720] [INFO] Running command: fastANI --query /var/lib/cwl/stg9456be11-034f-4763-b096-394620ab731b/GCF_000231405.2_ASM23140v3_genomic.fna.gz --refList GCF_000231405.2_ASM23140v3_genomic.fna/target_genomes.txt --output GCF_000231405.2_ASM23140v3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:35:26,030] [INFO] Task succeeded: fastANI
[2024-01-25 17:35:26,031] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgccdd6668-6f79-43ea-a943-de3fb50fe45c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:35:26,031] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgccdd6668-6f79-43ea-a943-de3fb50fe45c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:35:26,037] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:35:26,037] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:35:26,037] [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
Desulfitobacterium metallireducens	strain=853-15A	GCA_000231405.3	142877	142877	type	True	100.0	1057	1058	95	conclusive
Desulfosporosinus meridiei	strain=DSM 13257	GCA_000231385.3	79209	79209	type	True	79.1735	73	1058	95	below_threshold
Desulfosporosinus lacus	strain=DSM 15449	GCA_900129935.1	329936	329936	type	True	77.4598	67	1058	95	below_threshold
Desulfosporosinus hippei	strain=DSM 8344	GCA_900100785.1	569859	569859	type	True	77.1728	59	1058	95	below_threshold
Desulfitobacterium chlororespirans	strain=DSM 11544	GCA_900143285.1	51616	51616	type	True	77.1466	72	1058	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:35:26,039] [INFO] DFAST Taxonomy check result was written to GCF_000231405.2_ASM23140v3_genomic.fna/tc_result.tsv
[2024-01-25 17:35:26,040] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:35:26,040] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:35:26,040] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgccdd6668-6f79-43ea-a943-de3fb50fe45c/dqc_reference/checkm_data
[2024-01-25 17:35:26,041] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:35:26,073] [INFO] Task started: CheckM
[2024-01-25 17:35:26,073] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000231405.2_ASM23140v3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000231405.2_ASM23140v3_genomic.fna/checkm_input GCF_000231405.2_ASM23140v3_genomic.fna/checkm_result
[2024-01-25 17:35:49,063] [INFO] Task succeeded: CheckM
[2024-01-25 17:35:49,064] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:35:49,091] [INFO] ===== Completeness check finished =====
[2024-01-25 17:35:49,091] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:35:49,092] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000231405.2_ASM23140v3_genomic.fna/markers.fasta)
[2024-01-25 17:35:49,092] [INFO] Task started: Blastn
[2024-01-25 17:35:49,092] [INFO] Running command: blastn -query GCF_000231405.2_ASM23140v3_genomic.fna/markers.fasta -db /var/lib/cwl/stgccdd6668-6f79-43ea-a943-de3fb50fe45c/dqc_reference/reference_markers_gtdb.fasta -out GCF_000231405.2_ASM23140v3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:35:49,970] [INFO] Task succeeded: Blastn
[2024-01-25 17:35:49,973] [INFO] Selected 21 target genomes.
[2024-01-25 17:35:49,974] [INFO] Target genome list was writen to GCF_000231405.2_ASM23140v3_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:35:49,986] [INFO] Task started: fastANI
[2024-01-25 17:35:49,986] [INFO] Running command: fastANI --query /var/lib/cwl/stg9456be11-034f-4763-b096-394620ab731b/GCF_000231405.2_ASM23140v3_genomic.fna.gz --refList GCF_000231405.2_ASM23140v3_genomic.fna/target_genomes_gtdb.txt --output GCF_000231405.2_ASM23140v3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:36:02,198] [INFO] Task succeeded: fastANI
[2024-01-25 17:36:02,208] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:36:02,208] [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_000231405.2	s__Desulfitobacterium_A metallireducens	100.0	1058	1058	d__Bacteria;p__Firmicutes_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfitobacterium_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000231385.2	s__Desulfosporosinus meridiei	79.4538	74	1058	d__Bacteria;p__Firmicutes_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfosporosinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000224515.1	s__Desulfosporosinus sp000224515	77.7259	70	1058	d__Bacteria;p__Firmicutes_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfosporosinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129935.1	s__Desulfosporosinus lacus	77.3778	67	1058	d__Bacteria;p__Firmicutes_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfosporosinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900143285.1	s__Desulfitobacterium chlororespirans	77.1855	71	1058	d__Bacteria;p__Firmicutes_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfitobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000961805.1	s__Desulfosporosinus sp000961805	76.3308	52	1058	d__Bacteria;p__Firmicutes_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfosporosinus	95.0	99.79	99.68	0.91	0.86	3	-
--------------------------------------------------------------------------------
[2024-01-25 17:36:02,210] [INFO] GTDB search result was written to GCF_000231405.2_ASM23140v3_genomic.fna/result_gtdb.tsv
[2024-01-25 17:36:02,211] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:36:02,213] [INFO] DFAST_QC result json was written to GCF_000231405.2_ASM23140v3_genomic.fna/dqc_result.json
[2024-01-25 17:36:02,213] [INFO] DFAST_QC completed!
[2024-01-25 17:36:02,213] [INFO] Total running time: 0h0m56s