[2024-01-24 14:22:01,149] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:01,151] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:01,151] [INFO] DQC Reference Directory: /var/lib/cwl/stg3e3d321c-d5a0-4c70-9b50-ca5cb95ae26c/dqc_reference
[2024-01-24 14:22:02,379] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:02,380] [INFO] Task started: Prodigal
[2024-01-24 14:22:02,380] [INFO] Running command: gunzip -c /var/lib/cwl/stgee1d6c4c-d2c1-4d17-beaa-93de91012c86/GCF_010669305.1_ASM1066930v1_genomic.fna.gz | prodigal -d GCF_010669305.1_ASM1066930v1_genomic.fna/cds.fna -a GCF_010669305.1_ASM1066930v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:10,681] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:10,681] [INFO] Task started: HMMsearch
[2024-01-24 14:22:10,682] [INFO] Running command: hmmsearch --tblout GCF_010669305.1_ASM1066930v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3e3d321c-d5a0-4c70-9b50-ca5cb95ae26c/dqc_reference/reference_markers.hmm GCF_010669305.1_ASM1066930v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:10,902] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:10,903] [INFO] Found 6/6 markers.
[2024-01-24 14:22:10,933] [INFO] Query marker FASTA was written to GCF_010669305.1_ASM1066930v1_genomic.fna/markers.fasta
[2024-01-24 14:22:10,934] [INFO] Task started: Blastn
[2024-01-24 14:22:10,934] [INFO] Running command: blastn -query GCF_010669305.1_ASM1066930v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e3d321c-d5a0-4c70-9b50-ca5cb95ae26c/dqc_reference/reference_markers.fasta -out GCF_010669305.1_ASM1066930v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:11,502] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:11,505] [INFO] Selected 16 target genomes.
[2024-01-24 14:22:11,506] [INFO] Target genome list was writen to GCF_010669305.1_ASM1066930v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:11,532] [INFO] Task started: fastANI
[2024-01-24 14:22:11,532] [INFO] Running command: fastANI --query /var/lib/cwl/stgee1d6c4c-d2c1-4d17-beaa-93de91012c86/GCF_010669305.1_ASM1066930v1_genomic.fna.gz --refList GCF_010669305.1_ASM1066930v1_genomic.fna/target_genomes.txt --output GCF_010669305.1_ASM1066930v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:19,677] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:19,677] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3e3d321c-d5a0-4c70-9b50-ca5cb95ae26c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:19,678] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3e3d321c-d5a0-4c70-9b50-ca5cb95ae26c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:19,683] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:22:19,684] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:19,684] [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
Aminipila butyrica	strain=DSM 103574	GCA_010669305.1	433296	433296	type	True	100.0	1110	1111	95	conclusive
Aminipila terrae	strain=CBA3637	GCA_010120715.1	2697030	2697030	type	True	79.3206	235	1111	95	below_threshold
Aminipila luticellarii	strain=JN-18	GCA_004103735.1	2507160	2507160	type	True	78.8718	265	1111	95	below_threshold
Emergencia timonensis	strain=SN18	GCA_900086585.1	1776384	1776384	type	True	77.9067	50	1111	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:19,685] [INFO] DFAST Taxonomy check result was written to GCF_010669305.1_ASM1066930v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:19,686] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:19,686] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:19,686] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3e3d321c-d5a0-4c70-9b50-ca5cb95ae26c/dqc_reference/checkm_data
[2024-01-24 14:22:19,687] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:19,725] [INFO] Task started: CheckM
[2024-01-24 14:22:19,725] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010669305.1_ASM1066930v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010669305.1_ASM1066930v1_genomic.fna/checkm_input GCF_010669305.1_ASM1066930v1_genomic.fna/checkm_result
[2024-01-24 14:22:49,692] [INFO] Task succeeded: CheckM
[2024-01-24 14:22:49,693] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:22:49,716] [INFO] ===== Completeness check finished =====
[2024-01-24 14:22:49,716] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:22:49,717] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010669305.1_ASM1066930v1_genomic.fna/markers.fasta)
[2024-01-24 14:22:49,717] [INFO] Task started: Blastn
[2024-01-24 14:22:49,717] [INFO] Running command: blastn -query GCF_010669305.1_ASM1066930v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e3d321c-d5a0-4c70-9b50-ca5cb95ae26c/dqc_reference/reference_markers_gtdb.fasta -out GCF_010669305.1_ASM1066930v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:50,511] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:50,515] [INFO] Selected 19 target genomes.
[2024-01-24 14:22:50,515] [INFO] Target genome list was writen to GCF_010669305.1_ASM1066930v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:22:50,529] [INFO] Task started: fastANI
[2024-01-24 14:22:50,529] [INFO] Running command: fastANI --query /var/lib/cwl/stgee1d6c4c-d2c1-4d17-beaa-93de91012c86/GCF_010669305.1_ASM1066930v1_genomic.fna.gz --refList GCF_010669305.1_ASM1066930v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010669305.1_ASM1066930v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:22:59,279] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:59,290] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:22:59,290] [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_010669305.1	s__Aminipila butyrica	100.0	1110	1111	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Aminipila	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_010120715.1	s__Aminipila terrae	79.3415	234	1111	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Aminipila	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004103735.1	s__Aminipila sp004103735	78.8628	265	1111	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Aminipila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002455605.1	s__Aminipila sp002455605	78.1892	161	1111	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Aminipila	95.0	99.31	99.31	0.92	0.92	2	-
GCF_017255415.1	s__Aminipila aminobutyricum	78.1186	107	1111	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Aminipila	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009936045.1	s__Emergencia sp009936045	77.776	52	1111	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Emergencia	95.0	98.32	98.24	0.87	0.87	6	-
--------------------------------------------------------------------------------
[2024-01-24 14:22:59,292] [INFO] GTDB search result was written to GCF_010669305.1_ASM1066930v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:22:59,292] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:22:59,295] [INFO] DFAST_QC result json was written to GCF_010669305.1_ASM1066930v1_genomic.fna/dqc_result.json
[2024-01-24 14:22:59,295] [INFO] DFAST_QC completed!
[2024-01-24 14:22:59,295] [INFO] Total running time: 0h0m58s