[2024-01-24 11:26:03,027] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:03,028] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:03,028] [INFO] DQC Reference Directory: /var/lib/cwl/stgf6fb1bcd-e2a3-4319-80ba-b852e9834986/dqc_reference
[2024-01-24 11:26:04,161] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:04,162] [INFO] Task started: Prodigal
[2024-01-24 11:26:04,162] [INFO] Running command: gunzip -c /var/lib/cwl/stg858fda72-cae4-40c9-be86-9653be549377/GCF_004006535.1_ASM400653v1_genomic.fna.gz | prodigal -d GCF_004006535.1_ASM400653v1_genomic.fna/cds.fna -a GCF_004006535.1_ASM400653v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:07,843] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:07,844] [INFO] Task started: HMMsearch
[2024-01-24 11:26:07,844] [INFO] Running command: hmmsearch --tblout GCF_004006535.1_ASM400653v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf6fb1bcd-e2a3-4319-80ba-b852e9834986/dqc_reference/reference_markers.hmm GCF_004006535.1_ASM400653v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:08,023] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:08,024] [INFO] Found 6/6 markers.
[2024-01-24 11:26:08,044] [INFO] Query marker FASTA was written to GCF_004006535.1_ASM400653v1_genomic.fna/markers.fasta
[2024-01-24 11:26:08,045] [INFO] Task started: Blastn
[2024-01-24 11:26:08,045] [INFO] Running command: blastn -query GCF_004006535.1_ASM400653v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6fb1bcd-e2a3-4319-80ba-b852e9834986/dqc_reference/reference_markers.fasta -out GCF_004006535.1_ASM400653v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:08,611] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:08,615] [INFO] Selected 15 target genomes.
[2024-01-24 11:26:08,616] [INFO] Target genome list was writen to GCF_004006535.1_ASM400653v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:08,671] [INFO] Task started: fastANI
[2024-01-24 11:26:08,671] [INFO] Running command: fastANI --query /var/lib/cwl/stg858fda72-cae4-40c9-be86-9653be549377/GCF_004006535.1_ASM400653v1_genomic.fna.gz --refList GCF_004006535.1_ASM400653v1_genomic.fna/target_genomes.txt --output GCF_004006535.1_ASM400653v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:15,506] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:15,506] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf6fb1bcd-e2a3-4319-80ba-b852e9834986/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:15,507] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf6fb1bcd-e2a3-4319-80ba-b852e9834986/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:15,514] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:26:15,514] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:26:15,514] [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
Anaerosphaera multitolerans	strain=GS7-6-2	GCA_004006535.1	2487351	2487351	type	True	100.0	720	722	95	conclusive
Anaerosphaera aminiphila	strain=DSM 21120	GCA_900129925.1	1120994	1120994	type	True	78.9277	291	722	95	below_threshold
Anaerosphaera massiliensis	strain=Marseille-P4592	GCA_902167235.1	2040296	2040296	type	True	78.1459	246	722	95	below_threshold
Peptoniphilus ovalis	strain=MSJ-1	GCA_018919265.1	2841503	2841503	type	True	78.0579	77	722	95	below_threshold
Peptoniphilus mikwangii	strain=ChDC B134	GCA_000468535.1	1354300	1354300	type	True	77.404	119	722	95	below_threshold
Peptoniphilus stercorisuis	strain=DSM 27563	GCA_017874395.1	1436965	1436965	type	True	77.2499	115	722	95	below_threshold
Peptoniphilus asaccharolyticus	strain=FDAARGOS_1135	GCA_016791605.1	1258	1258	type	True	77.1797	67	722	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:15,516] [INFO] DFAST Taxonomy check result was written to GCF_004006535.1_ASM400653v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:15,516] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:15,516] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:15,516] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf6fb1bcd-e2a3-4319-80ba-b852e9834986/dqc_reference/checkm_data
[2024-01-24 11:26:15,517] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:15,541] [INFO] Task started: CheckM
[2024-01-24 11:26:15,541] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004006535.1_ASM400653v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004006535.1_ASM400653v1_genomic.fna/checkm_input GCF_004006535.1_ASM400653v1_genomic.fna/checkm_result
[2024-01-24 11:26:34,268] [INFO] Task succeeded: CheckM
[2024-01-24 11:26:34,269] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:26:34,286] [INFO] ===== Completeness check finished =====
[2024-01-24 11:26:34,287] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:26:34,287] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004006535.1_ASM400653v1_genomic.fna/markers.fasta)
[2024-01-24 11:26:34,287] [INFO] Task started: Blastn
[2024-01-24 11:26:34,287] [INFO] Running command: blastn -query GCF_004006535.1_ASM400653v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6fb1bcd-e2a3-4319-80ba-b852e9834986/dqc_reference/reference_markers_gtdb.fasta -out GCF_004006535.1_ASM400653v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:35,073] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:35,076] [INFO] Selected 17 target genomes.
[2024-01-24 11:26:35,076] [INFO] Target genome list was writen to GCF_004006535.1_ASM400653v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:26:35,104] [INFO] Task started: fastANI
[2024-01-24 11:26:35,104] [INFO] Running command: fastANI --query /var/lib/cwl/stg858fda72-cae4-40c9-be86-9653be549377/GCF_004006535.1_ASM400653v1_genomic.fna.gz --refList GCF_004006535.1_ASM400653v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004006535.1_ASM400653v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:26:42,091] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:42,098] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:26:42,098] [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_004006535.1	s__Anaerosphaera multitolerans	100.0	720	722	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerosphaera	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900129925.1	s__Anaerosphaera aminiphila	78.9279	291	722	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	78.5625	77	722	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	-
GCF_018919265.1	s__Peptoniphilus_A sp018919265	78.0579	77	722	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176115.1	s__Peptoniphilus asaccharolyticus	77.4574	66	722	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_000468535.1	s__Anaerosphaera mikwangii	77.404	119	722	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerosphaera	95.0	99.03	99.03	0.96	0.96	2	-
GCF_017874395.1	s__Anaerosphaera stercorisuis	77.2732	114	722	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerosphaera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:26:42,100] [INFO] GTDB search result was written to GCF_004006535.1_ASM400653v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:26:42,100] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:26:42,103] [INFO] DFAST_QC result json was written to GCF_004006535.1_ASM400653v1_genomic.fna/dqc_result.json
[2024-01-24 11:26:42,103] [INFO] DFAST_QC completed!
[2024-01-24 11:26:42,103] [INFO] Total running time: 0h0m39s