[2024-01-24 12:54:05,363] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:54:05,366] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:54:05,367] [INFO] DQC Reference Directory: /var/lib/cwl/stgd493db4e-ca93-4531-a35f-1847a605ca00/dqc_reference
[2024-01-24 12:54:07,724] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:54:07,725] [INFO] Task started: Prodigal
[2024-01-24 12:54:07,725] [INFO] Running command: gunzip -c /var/lib/cwl/stg3505f8e0-97bd-42bb-a0fc-4f7ad13bc84e/GCF_000021925.1_ASM2192v1_genomic.fna.gz | prodigal -d GCF_000021925.1_ASM2192v1_genomic.fna/cds.fna -a GCF_000021925.1_ASM2192v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:21,952] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:21,953] [INFO] Task started: HMMsearch
[2024-01-24 12:54:21,953] [INFO] Running command: hmmsearch --tblout GCF_000021925.1_ASM2192v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd493db4e-ca93-4531-a35f-1847a605ca00/dqc_reference/reference_markers.hmm GCF_000021925.1_ASM2192v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:22,355] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:22,357] [INFO] Found 6/6 markers.
[2024-01-24 12:54:22,413] [INFO] Query marker FASTA was written to GCF_000021925.1_ASM2192v1_genomic.fna/markers.fasta
[2024-01-24 12:54:22,414] [INFO] Task started: Blastn
[2024-01-24 12:54:22,414] [INFO] Running command: blastn -query GCF_000021925.1_ASM2192v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd493db4e-ca93-4531-a35f-1847a605ca00/dqc_reference/reference_markers.fasta -out GCF_000021925.1_ASM2192v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:22,996] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:23,000] [INFO] Selected 17 target genomes.
[2024-01-24 12:54:23,001] [INFO] Target genome list was writen to GCF_000021925.1_ASM2192v1_genomic.fna/target_genomes.txt
[2024-01-24 12:54:23,021] [INFO] Task started: fastANI
[2024-01-24 12:54:23,021] [INFO] Running command: fastANI --query /var/lib/cwl/stg3505f8e0-97bd-42bb-a0fc-4f7ad13bc84e/GCF_000021925.1_ASM2192v1_genomic.fna.gz --refList GCF_000021925.1_ASM2192v1_genomic.fna/target_genomes.txt --output GCF_000021925.1_ASM2192v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:38,492] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:38,493] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd493db4e-ca93-4531-a35f-1847a605ca00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:38,493] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd493db4e-ca93-4531-a35f-1847a605ca00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:38,502] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:54:38,503] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:38,503] [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 hafniense	strain=DCB-2	GCA_000021925.1	49338	49338	type	True	100.0	1759	1759	95	conclusive
Desulfitobacterium chlororespirans	strain=DSM 11544	GCA_900143285.1	51616	51616	type	True	93.995	1412	1759	95	below_threshold
Desulfitobacterium dehalogenans	strain=ATCC 51507	GCA_000243155.3	36854	36854	type	True	85.4586	1050	1759	95	below_threshold
Desulfosporosinus orientis	strain=DSM 765	GCA_000235605.1	1563	1563	type	True	78.0119	93	1759	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:38,506] [INFO] DFAST Taxonomy check result was written to GCF_000021925.1_ASM2192v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:38,507] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:38,507] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:38,508] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd493db4e-ca93-4531-a35f-1847a605ca00/dqc_reference/checkm_data
[2024-01-24 12:54:38,509] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:38,567] [INFO] Task started: CheckM
[2024-01-24 12:54:38,567] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000021925.1_ASM2192v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000021925.1_ASM2192v1_genomic.fna/checkm_input GCF_000021925.1_ASM2192v1_genomic.fna/checkm_result
[2024-01-24 12:55:23,032] [INFO] Task succeeded: CheckM
[2024-01-24 12:55:23,034] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:55:23,059] [INFO] ===== Completeness check finished =====
[2024-01-24 12:55:23,059] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:55:23,060] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000021925.1_ASM2192v1_genomic.fna/markers.fasta)
[2024-01-24 12:55:23,060] [INFO] Task started: Blastn
[2024-01-24 12:55:23,060] [INFO] Running command: blastn -query GCF_000021925.1_ASM2192v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd493db4e-ca93-4531-a35f-1847a605ca00/dqc_reference/reference_markers_gtdb.fasta -out GCF_000021925.1_ASM2192v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:55:23,802] [INFO] Task succeeded: Blastn
[2024-01-24 12:55:23,806] [INFO] Selected 11 target genomes.
[2024-01-24 12:55:23,806] [INFO] Target genome list was writen to GCF_000021925.1_ASM2192v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:55:23,827] [INFO] Task started: fastANI
[2024-01-24 12:55:23,827] [INFO] Running command: fastANI --query /var/lib/cwl/stg3505f8e0-97bd-42bb-a0fc-4f7ad13bc84e/GCF_000021925.1_ASM2192v1_genomic.fna.gz --refList GCF_000021925.1_ASM2192v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000021925.1_ASM2192v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:55:33,715] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:33,726] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:55:33,726] [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_000021925.1	s__Desulfitobacterium hafniense	100.0	1759	1759	d__Bacteria;p__Firmicutes_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfitobacterium	95.0	97.85	96.87	0.87	0.83	9	conclusive
GCF_900143285.1	s__Desulfitobacterium chlororespirans	93.995	1412	1759	d__Bacteria;p__Firmicutes_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfitobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000243155.2	s__Desulfitobacterium dehalogenans	85.4837	1046	1759	d__Bacteria;p__Firmicutes_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfitobacterium	95.0	97.36	95.71	0.90	0.87	3	-
GCF_000243135.2	s__Desulfitobacterium dichloroeliminans	78.9234	411	1759	d__Bacteria;p__Firmicutes_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfitobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000235605.1	s__Desulfosporosinus orientis	77.9989	93	1759	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_002196705.1	s__Desulfosporosinus sp002196705	77.7677	54	1759	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	77.6794	71	1759	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_001707885.1	s__Desulfosporosinus sp001707885	77.073	52	1759	d__Bacteria;p__Firmicutes_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfosporosinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012799495.1	s__Desulfitobacterium sp012799495	76.731	68	1759	d__Bacteria;p__Firmicutes_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfitobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:55:33,728] [INFO] GTDB search result was written to GCF_000021925.1_ASM2192v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:55:33,728] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:55:33,731] [INFO] DFAST_QC result json was written to GCF_000021925.1_ASM2192v1_genomic.fna/dqc_result.json
[2024-01-24 12:55:33,731] [INFO] DFAST_QC completed!
[2024-01-24 12:55:33,731] [INFO] Total running time: 0h1m28s