[2024-01-24 13:46:40,481] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:40,483] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:40,483] [INFO] DQC Reference Directory: /var/lib/cwl/stgf10d18fa-b75e-4654-823d-e9a4707cc88c/dqc_reference
[2024-01-24 13:46:41,725] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:41,726] [INFO] Task started: Prodigal
[2024-01-24 13:46:41,726] [INFO] Running command: gunzip -c /var/lib/cwl/stgcd54f1fd-fb47-4234-a67a-7858bc85f1d8/GCF_000243155.2_ASM24315v3_genomic.fna.gz | prodigal -d GCF_000243155.2_ASM24315v3_genomic.fna/cds.fna -a GCF_000243155.2_ASM24315v3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:52,450] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:52,450] [INFO] Task started: HMMsearch
[2024-01-24 13:46:52,451] [INFO] Running command: hmmsearch --tblout GCF_000243155.2_ASM24315v3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf10d18fa-b75e-4654-823d-e9a4707cc88c/dqc_reference/reference_markers.hmm GCF_000243155.2_ASM24315v3_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:52,798] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:52,800] [INFO] Found 6/6 markers.
[2024-01-24 13:46:52,842] [INFO] Query marker FASTA was written to GCF_000243155.2_ASM24315v3_genomic.fna/markers.fasta
[2024-01-24 13:46:52,843] [INFO] Task started: Blastn
[2024-01-24 13:46:52,843] [INFO] Running command: blastn -query GCF_000243155.2_ASM24315v3_genomic.fna/markers.fasta -db /var/lib/cwl/stgf10d18fa-b75e-4654-823d-e9a4707cc88c/dqc_reference/reference_markers.fasta -out GCF_000243155.2_ASM24315v3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:53,474] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:53,479] [INFO] Selected 15 target genomes.
[2024-01-24 13:46:53,479] [INFO] Target genome list was writen to GCF_000243155.2_ASM24315v3_genomic.fna/target_genomes.txt
[2024-01-24 13:46:53,489] [INFO] Task started: fastANI
[2024-01-24 13:46:53,489] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd54f1fd-fb47-4234-a67a-7858bc85f1d8/GCF_000243155.2_ASM24315v3_genomic.fna.gz --refList GCF_000243155.2_ASM24315v3_genomic.fna/target_genomes.txt --output GCF_000243155.2_ASM24315v3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:06,283] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:06,284] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf10d18fa-b75e-4654-823d-e9a4707cc88c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:06,284] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf10d18fa-b75e-4654-823d-e9a4707cc88c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:06,291] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:47:06,291] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:47:06,291] [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 dehalogenans	strain=ATCC 51507	GCA_000243155.3	36854	36854	type	True	100.0	1439	1440	95	conclusive
Desulfitobacterium chlororespirans	strain=DSM 11544	GCA_900143285.1	51616	51616	type	True	85.5669	1074	1440	95	below_threshold
Desulfitobacterium hafniense	strain=DCB-2	GCA_000021925.1	49338	49338	type	True	85.4588	1054	1440	95	below_threshold
Desulfosporosinus youngiae	strain=DSM 17734	GCA_000244895.1	339862	339862	type	True	78.8077	113	1440	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:47:06,294] [INFO] DFAST Taxonomy check result was written to GCF_000243155.2_ASM24315v3_genomic.fna/tc_result.tsv
[2024-01-24 13:47:06,294] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:06,294] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:06,295] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf10d18fa-b75e-4654-823d-e9a4707cc88c/dqc_reference/checkm_data
[2024-01-24 13:47:06,296] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:06,345] [INFO] Task started: CheckM
[2024-01-24 13:47:06,345] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000243155.2_ASM24315v3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000243155.2_ASM24315v3_genomic.fna/checkm_input GCF_000243155.2_ASM24315v3_genomic.fna/checkm_result
[2024-01-24 13:47:42,841] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:42,843] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:42,871] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:42,872] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:42,872] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000243155.2_ASM24315v3_genomic.fna/markers.fasta)
[2024-01-24 13:47:42,873] [INFO] Task started: Blastn
[2024-01-24 13:47:42,873] [INFO] Running command: blastn -query GCF_000243155.2_ASM24315v3_genomic.fna/markers.fasta -db /var/lib/cwl/stgf10d18fa-b75e-4654-823d-e9a4707cc88c/dqc_reference/reference_markers_gtdb.fasta -out GCF_000243155.2_ASM24315v3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:43,704] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:43,708] [INFO] Selected 10 target genomes.
[2024-01-24 13:47:43,709] [INFO] Target genome list was writen to GCF_000243155.2_ASM24315v3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:43,718] [INFO] Task started: fastANI
[2024-01-24 13:47:43,718] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd54f1fd-fb47-4234-a67a-7858bc85f1d8/GCF_000243155.2_ASM24315v3_genomic.fna.gz --refList GCF_000243155.2_ASM24315v3_genomic.fna/target_genomes_gtdb.txt --output GCF_000243155.2_ASM24315v3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:53,067] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:53,079] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:53,080] [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_000243155.2	s__Desulfitobacterium dehalogenans	100.0	1440	1440	d__Bacteria;p__Firmicutes_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfitobacterium	95.0	97.36	95.71	0.90	0.87	3	conclusive
GCF_900143285.1	s__Desulfitobacterium chlororespirans	85.5705	1073	1440	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_000021925.1	s__Desulfitobacterium hafniense	85.457	1056	1440	d__Bacteria;p__Firmicutes_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfitobacterium	95.0	97.85	96.87	0.87	0.83	9	-
GCF_000243135.2	s__Desulfitobacterium dichloroeliminans	79.2333	408	1440	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_000224515.1	s__Desulfosporosinus sp000224515	77.2739	76	1440	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	76.9519	63	1440	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	76.6698	84	1440	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 13:47:53,082] [INFO] GTDB search result was written to GCF_000243155.2_ASM24315v3_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:53,086] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:53,090] [INFO] DFAST_QC result json was written to GCF_000243155.2_ASM24315v3_genomic.fna/dqc_result.json
[2024-01-24 13:47:53,091] [INFO] DFAST_QC completed!
[2024-01-24 13:47:53,091] [INFO] Total running time: 0h1m13s