[2024-01-25 17:40:50,934] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:40:50,936] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:40:50,936] [INFO] DQC Reference Directory: /var/lib/cwl/stgfb48e37a-dd78-47a2-94fd-4521c8e8d893/dqc_reference
[2024-01-25 17:40:52,159] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:40:52,160] [INFO] Task started: Prodigal
[2024-01-25 17:40:52,160] [INFO] Running command: gunzip -c /var/lib/cwl/stgbb597947-9b05-4a6e-a67a-e0cd8bf1fa8e/GCF_000468535.1_ASM46853v1_genomic.fna.gz | prodigal -d GCF_000468535.1_ASM46853v1_genomic.fna/cds.fna -a GCF_000468535.1_ASM46853v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:40:54,503] [INFO] Task succeeded: Prodigal
[2024-01-25 17:40:54,503] [INFO] Task started: HMMsearch
[2024-01-25 17:40:54,503] [INFO] Running command: hmmsearch --tblout GCF_000468535.1_ASM46853v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfb48e37a-dd78-47a2-94fd-4521c8e8d893/dqc_reference/reference_markers.hmm GCF_000468535.1_ASM46853v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:40:54,677] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:40:54,678] [INFO] Found 6/6 markers.
[2024-01-25 17:40:54,693] [INFO] Query marker FASTA was written to GCF_000468535.1_ASM46853v1_genomic.fna/markers.fasta
[2024-01-25 17:40:54,694] [INFO] Task started: Blastn
[2024-01-25 17:40:54,694] [INFO] Running command: blastn -query GCF_000468535.1_ASM46853v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb48e37a-dd78-47a2-94fd-4521c8e8d893/dqc_reference/reference_markers.fasta -out GCF_000468535.1_ASM46853v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:40:55,256] [INFO] Task succeeded: Blastn
[2024-01-25 17:40:55,258] [INFO] Selected 17 target genomes.
[2024-01-25 17:40:55,259] [INFO] Target genome list was writen to GCF_000468535.1_ASM46853v1_genomic.fna/target_genomes.txt
[2024-01-25 17:40:55,277] [INFO] Task started: fastANI
[2024-01-25 17:40:55,277] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb597947-9b05-4a6e-a67a-e0cd8bf1fa8e/GCF_000468535.1_ASM46853v1_genomic.fna.gz --refList GCF_000468535.1_ASM46853v1_genomic.fna/target_genomes.txt --output GCF_000468535.1_ASM46853v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:41:01,886] [INFO] Task succeeded: fastANI
[2024-01-25 17:41:01,886] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfb48e37a-dd78-47a2-94fd-4521c8e8d893/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:41:01,887] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfb48e37a-dd78-47a2-94fd-4521c8e8d893/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:41:01,893] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:41:01,893] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:41:01,893] [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
Peptoniphilus mikwangii	strain=ChDC B134	GCA_000468535.1	1354300	1354300	type	True	100.0	496	497	95	conclusive
Peptoniphilus asaccharolyticus	strain=FDAARGOS_1135	GCA_016791605.1	1258	1258	type	True	78.2099	107	497	95	below_threshold
Peptoniphilus asaccharolyticus	strain=DSM 20463	GCA_900176115.1	1258	1258	type	True	77.7835	104	497	95	below_threshold
Anaerosphaera aminiphila	strain=DSM 21120	GCA_900129925.1	1120994	1120994	type	True	77.5372	116	497	95	below_threshold
Anaerosphaera massiliensis	strain=Marseille-P4592	GCA_902167235.1	2040296	2040296	type	True	77.2252	144	497	95	below_threshold
Peptoniphilus stercorisuis	strain=DSM 27563	GCA_017874395.1	1436965	1436965	type	True	77.1328	129	497	95	below_threshold
Anaerosphaera multitolerans	strain=GS7-6-2	GCA_004006535.1	2487351	2487351	type	True	77.0176	122	497	95	below_threshold
Peptoniphilus obesi	strain=ph1	GCA_000311865.1	1472765	1472765	type	True	76.6723	84	497	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:41:01,894] [INFO] DFAST Taxonomy check result was written to GCF_000468535.1_ASM46853v1_genomic.fna/tc_result.tsv
[2024-01-25 17:41:01,895] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:41:01,895] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:41:01,895] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfb48e37a-dd78-47a2-94fd-4521c8e8d893/dqc_reference/checkm_data
[2024-01-25 17:41:01,896] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:41:01,913] [INFO] Task started: CheckM
[2024-01-25 17:41:01,913] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000468535.1_ASM46853v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000468535.1_ASM46853v1_genomic.fna/checkm_input GCF_000468535.1_ASM46853v1_genomic.fna/checkm_result
[2024-01-25 17:41:15,856] [INFO] Task succeeded: CheckM
[2024-01-25 17:41:15,857] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:41:15,872] [INFO] ===== Completeness check finished =====
[2024-01-25 17:41:15,872] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:41:15,872] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000468535.1_ASM46853v1_genomic.fna/markers.fasta)
[2024-01-25 17:41:15,872] [INFO] Task started: Blastn
[2024-01-25 17:41:15,872] [INFO] Running command: blastn -query GCF_000468535.1_ASM46853v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb48e37a-dd78-47a2-94fd-4521c8e8d893/dqc_reference/reference_markers_gtdb.fasta -out GCF_000468535.1_ASM46853v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:41:16,684] [INFO] Task succeeded: Blastn
[2024-01-25 17:41:16,687] [INFO] Selected 18 target genomes.
[2024-01-25 17:41:16,687] [INFO] Target genome list was writen to GCF_000468535.1_ASM46853v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:41:16,700] [INFO] Task started: fastANI
[2024-01-25 17:41:16,701] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb597947-9b05-4a6e-a67a-e0cd8bf1fa8e/GCF_000468535.1_ASM46853v1_genomic.fna.gz --refList GCF_000468535.1_ASM46853v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000468535.1_ASM46853v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:41:23,051] [INFO] Task succeeded: fastANI
[2024-01-25 17:41:23,057] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:41:23,057] [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_000468535.1	s__Anaerosphaera mikwangii	100.0	495	497	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerosphaera	95.0	99.03	99.03	0.96	0.96	2	conclusive
GCF_900176115.1	s__Peptoniphilus asaccharolyticus	77.7835	104	497	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus	95.0	99.97	99.97	0.98	0.98	2	-
GCF_900129925.1	s__Anaerosphaera aminiphila	77.5214	118	497	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerosphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000952975.1	s__Peptoniphilus_E sp000952975	77.4375	76	497	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_901447155.2	s__Peptoniphilus_E catoniae	77.3213	89	497	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017874395.1	s__Anaerosphaera stercorisuis	77.1537	128	497	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerosphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004006535.1	s__Anaerosphaera multitolerans	77.0176	122	497	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerosphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000311865.1	s__Peptoniphilus_E obesi	76.6723	84	497	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_E	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:41:23,059] [INFO] GTDB search result was written to GCF_000468535.1_ASM46853v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:41:23,059] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:41:23,062] [INFO] DFAST_QC result json was written to GCF_000468535.1_ASM46853v1_genomic.fna/dqc_result.json
[2024-01-25 17:41:23,062] [INFO] DFAST_QC completed!
[2024-01-25 17:41:23,062] [INFO] Total running time: 0h0m32s