[2024-01-24 13:17:05,498] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:05,503] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:05,503] [INFO] DQC Reference Directory: /var/lib/cwl/stg643fa834-abac-4b53-a1e6-98931af27351/dqc_reference
[2024-01-24 13:17:06,976] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:06,977] [INFO] Task started: Prodigal
[2024-01-24 13:17:06,977] [INFO] Running command: gunzip -c /var/lib/cwl/stg010ec2d6-5b52-48f3-9223-d719513edd8e/GCF_000423145.1_ASM42314v1_genomic.fna.gz | prodigal -d GCF_000423145.1_ASM42314v1_genomic.fna/cds.fna -a GCF_000423145.1_ASM42314v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:09,470] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:09,470] [INFO] Task started: HMMsearch
[2024-01-24 13:17:09,470] [INFO] Running command: hmmsearch --tblout GCF_000423145.1_ASM42314v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg643fa834-abac-4b53-a1e6-98931af27351/dqc_reference/reference_markers.hmm GCF_000423145.1_ASM42314v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:09,712] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:09,713] [INFO] Found 6/6 markers.
[2024-01-24 13:17:09,737] [INFO] Query marker FASTA was written to GCF_000423145.1_ASM42314v1_genomic.fna/markers.fasta
[2024-01-24 13:17:09,737] [INFO] Task started: Blastn
[2024-01-24 13:17:09,738] [INFO] Running command: blastn -query GCF_000423145.1_ASM42314v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg643fa834-abac-4b53-a1e6-98931af27351/dqc_reference/reference_markers.fasta -out GCF_000423145.1_ASM42314v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:10,346] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:10,349] [INFO] Selected 18 target genomes.
[2024-01-24 13:17:10,349] [INFO] Target genome list was writen to GCF_000423145.1_ASM42314v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:10,359] [INFO] Task started: fastANI
[2024-01-24 13:17:10,359] [INFO] Running command: fastANI --query /var/lib/cwl/stg010ec2d6-5b52-48f3-9223-d719513edd8e/GCF_000423145.1_ASM42314v1_genomic.fna.gz --refList GCF_000423145.1_ASM42314v1_genomic.fna/target_genomes.txt --output GCF_000423145.1_ASM42314v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:17,149] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:17,150] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg643fa834-abac-4b53-a1e6-98931af27351/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:17,150] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg643fa834-abac-4b53-a1e6-98931af27351/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:17,156] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:17:17,156] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:17,156] [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
Helcococcus sueciensis	strain=DSM 17243	GCA_000423145.1	241555	241555	type	True	100.0	503	505	95	conclusive
Helcococcus massiliensis	strain=Marseille-P4590	GCA_900258485.1	2040290	2040290	type	True	80.2298	126	505	95	below_threshold
Anaerococcus ihuae	strain=Marseille-Q5893	GCA_928368155.1	2899519	2899519	type	True	78.5727	55	505	95	below_threshold
Helcococcus kunzii	strain=ATCC 51366	GCA_000245755.1	40091	40091	type	True	78.4781	161	505	95	below_threshold
Anaerococcus obesiensis	strain=ph10	GCA_000311745.1	1287640	1287640	type	True	78.1426	50	505	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:17,158] [INFO] DFAST Taxonomy check result was written to GCF_000423145.1_ASM42314v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:17,159] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:17,159] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:17,159] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg643fa834-abac-4b53-a1e6-98931af27351/dqc_reference/checkm_data
[2024-01-24 13:17:17,160] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:17,178] [INFO] Task started: CheckM
[2024-01-24 13:17:17,179] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000423145.1_ASM42314v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000423145.1_ASM42314v1_genomic.fna/checkm_input GCF_000423145.1_ASM42314v1_genomic.fna/checkm_result
[2024-01-24 13:17:33,150] [INFO] Task succeeded: CheckM
[2024-01-24 13:17:33,151] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:17:33,174] [INFO] ===== Completeness check finished =====
[2024-01-24 13:17:33,174] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:17:33,175] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000423145.1_ASM42314v1_genomic.fna/markers.fasta)
[2024-01-24 13:17:33,175] [INFO] Task started: Blastn
[2024-01-24 13:17:33,175] [INFO] Running command: blastn -query GCF_000423145.1_ASM42314v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg643fa834-abac-4b53-a1e6-98931af27351/dqc_reference/reference_markers_gtdb.fasta -out GCF_000423145.1_ASM42314v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:34,019] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:34,023] [INFO] Selected 16 target genomes.
[2024-01-24 13:17:34,023] [INFO] Target genome list was writen to GCF_000423145.1_ASM42314v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:17:34,047] [INFO] Task started: fastANI
[2024-01-24 13:17:34,048] [INFO] Running command: fastANI --query /var/lib/cwl/stg010ec2d6-5b52-48f3-9223-d719513edd8e/GCF_000423145.1_ASM42314v1_genomic.fna.gz --refList GCF_000423145.1_ASM42314v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000423145.1_ASM42314v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:17:39,420] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:39,426] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:17:39,427] [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_000423145.1	s__Helcococcus sueciensis	100.0	503	505	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Helcococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900258485.1	s__Helcococcus massiliensis	80.1641	128	505	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Helcococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000245755.1	s__Helcococcus kunzii	78.4781	161	505	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Helcococcus	95.0	99.14	99.14	0.93	0.93	2	-
GCF_000311745.1	s__Anaerococcus obesiensis	78.1426	50	505	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	96.6984	97.99	96.80	0.92	0.85	6	-
GCF_004524775.1	s__Helcococcus ovis	78.0603	127	505	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Helcococcus	95.0	99.42	99.12	0.95	0.90	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:17:39,428] [INFO] GTDB search result was written to GCF_000423145.1_ASM42314v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:17:39,429] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:17:39,432] [INFO] DFAST_QC result json was written to GCF_000423145.1_ASM42314v1_genomic.fna/dqc_result.json
[2024-01-24 13:17:39,432] [INFO] DFAST_QC completed!
[2024-01-24 13:17:39,432] [INFO] Total running time: 0h0m34s