[2024-01-24 15:18:51,281] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:51,288] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:51,289] [INFO] DQC Reference Directory: /var/lib/cwl/stge68e0e4e-0e4f-4adc-93a8-be8fcd596dcd/dqc_reference
[2024-01-24 15:18:52,656] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:52,657] [INFO] Task started: Prodigal
[2024-01-24 15:18:52,657] [INFO] Running command: gunzip -c /var/lib/cwl/stgb0d3bba5-7446-439b-b8cb-65dce5b5fe0f/GCF_004103715.1_ASM410371v1_genomic.fna.gz | prodigal -d GCF_004103715.1_ASM410371v1_genomic.fna/cds.fna -a GCF_004103715.1_ASM410371v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:19:00,430] [INFO] Task succeeded: Prodigal
[2024-01-24 15:19:00,430] [INFO] Task started: HMMsearch
[2024-01-24 15:19:00,430] [INFO] Running command: hmmsearch --tblout GCF_004103715.1_ASM410371v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge68e0e4e-0e4f-4adc-93a8-be8fcd596dcd/dqc_reference/reference_markers.hmm GCF_004103715.1_ASM410371v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:19:00,730] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:19:00,731] [INFO] Found 6/6 markers.
[2024-01-24 15:19:00,764] [INFO] Query marker FASTA was written to GCF_004103715.1_ASM410371v1_genomic.fna/markers.fasta
[2024-01-24 15:19:00,764] [INFO] Task started: Blastn
[2024-01-24 15:19:00,764] [INFO] Running command: blastn -query GCF_004103715.1_ASM410371v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge68e0e4e-0e4f-4adc-93a8-be8fcd596dcd/dqc_reference/reference_markers.fasta -out GCF_004103715.1_ASM410371v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:01,428] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:01,433] [INFO] Selected 19 target genomes.
[2024-01-24 15:19:01,434] [INFO] Target genome list was writen to GCF_004103715.1_ASM410371v1_genomic.fna/target_genomes.txt
[2024-01-24 15:19:01,439] [INFO] Task started: fastANI
[2024-01-24 15:19:01,440] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0d3bba5-7446-439b-b8cb-65dce5b5fe0f/GCF_004103715.1_ASM410371v1_genomic.fna.gz --refList GCF_004103715.1_ASM410371v1_genomic.fna/target_genomes.txt --output GCF_004103715.1_ASM410371v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:11,395] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:11,396] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge68e0e4e-0e4f-4adc-93a8-be8fcd596dcd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:11,396] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge68e0e4e-0e4f-4adc-93a8-be8fcd596dcd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:11,403] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:19:11,403] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:19:11,403] [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
Proteiniborus ethanoligenes	strain=DSM 21650	GCA_900107485.1	415015	415015	type	True	77.6059	67	1247	95	below_threshold
Sporanaerobacter acetigenes	strain=DSM 13106	GCA_900130025.1	165813	165813	type	True	77.5408	99	1247	95	below_threshold
Keratinibaculum paraultunense	strain=KD-1	GCA_016767175.1	1278232	1278232	type	True	77.0052	70	1247	95	below_threshold
Tissierella praeacuta	strain=NCTC11158	GCA_900460335.1	43131	43131	type	True	76.9703	55	1247	95	below_threshold
Clostridium manihotivorum	strain=CT4	GCA_004015185.1	2320868	2320868	type	True	76.402	54	1247	95	below_threshold
Keratinibaculum paraultunense	strain=DSM 26752	GCA_004343355.1	1278232	1278232	type	True	76.043	62	1247	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:11,405] [INFO] DFAST Taxonomy check result was written to GCF_004103715.1_ASM410371v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:11,406] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:11,406] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:11,406] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge68e0e4e-0e4f-4adc-93a8-be8fcd596dcd/dqc_reference/checkm_data
[2024-01-24 15:19:11,408] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:11,448] [INFO] Task started: CheckM
[2024-01-24 15:19:11,448] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004103715.1_ASM410371v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004103715.1_ASM410371v1_genomic.fna/checkm_input GCF_004103715.1_ASM410371v1_genomic.fna/checkm_result
[2024-01-24 15:19:39,707] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:39,709] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:39,733] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:39,734] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:39,734] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004103715.1_ASM410371v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:39,735] [INFO] Task started: Blastn
[2024-01-24 15:19:39,735] [INFO] Running command: blastn -query GCF_004103715.1_ASM410371v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge68e0e4e-0e4f-4adc-93a8-be8fcd596dcd/dqc_reference/reference_markers_gtdb.fasta -out GCF_004103715.1_ASM410371v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:40,533] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:40,537] [INFO] Selected 20 target genomes.
[2024-01-24 15:19:40,537] [INFO] Target genome list was writen to GCF_004103715.1_ASM410371v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:40,551] [INFO] Task started: fastANI
[2024-01-24 15:19:40,551] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0d3bba5-7446-439b-b8cb-65dce5b5fe0f/GCF_004103715.1_ASM410371v1_genomic.fna.gz --refList GCF_004103715.1_ASM410371v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004103715.1_ASM410371v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:52,125] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:52,144] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:52,144] [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_004103715.1	s__PP17-6a sp900095615	100.0	1246	1247	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__PP17-6a;g__PP17-6a	95.0	98.35	97.94	0.90	0.87	4	conclusive
GCA_018434075.1	s__Soehngenia_A sp018434075	82.3988	62	1247	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tissierellaceae;g__Soehngenia_A	95.0	97.20	97.20	0.85	0.85	2	-
GCA_014385195.1	s__BX21 sp014385195	79.1316	77	1247	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tissierellaceae;g__BX21	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107485.1	s__Proteiniborus ethanoligenes	77.5962	68	1247	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Proteiniboraceae;g__Proteiniborus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900130025.1	s__Sporanaerobacter acetigenes	77.5408	99	1247	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sporanaerobacteraceae;g__Sporanaerobacter	95.0	99.49	99.49	0.90	0.90	2	-
GCF_016767175.1	s__Keratinibaculum paraultunense	77.1605	69	1247	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tepidimicrobiaceae;g__Keratinibaculum	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004015185.1	s__Clostridium_AR sp004015185	76.4094	53	1247	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AR	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000751555.1	s__Anaerosalibacter massiliensis	76.2887	88	1247	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sporanaerobacteraceae;g__Anaerosalibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002266425.1	s__Tissierella carlieri	76.0446	69	1247	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tissierellaceae;g__Tissierella	95.0	97.51	96.78	0.86	0.84	3	-
GCA_002398845.1	s__Mt11 sp002398845	75.7755	50	1247	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tepidimicrobiaceae;g__Mt11	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:19:52,147] [INFO] GTDB search result was written to GCF_004103715.1_ASM410371v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:52,147] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:52,151] [INFO] DFAST_QC result json was written to GCF_004103715.1_ASM410371v1_genomic.fna/dqc_result.json
[2024-01-24 15:19:52,151] [INFO] DFAST_QC completed!
[2024-01-24 15:19:52,151] [INFO] Total running time: 0h1m1s