[2024-01-24 13:27:31,747] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:31,752] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:31,753] [INFO] DQC Reference Directory: /var/lib/cwl/stg85a40083-839d-4203-aafc-1dfbcaac15a8/dqc_reference
[2024-01-24 13:27:33,194] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:33,195] [INFO] Task started: Prodigal
[2024-01-24 13:27:33,195] [INFO] Running command: gunzip -c /var/lib/cwl/stg83c0aca4-0482-49af-bf18-b6e72a911050/GCF_900015215.1_CRIB_assembly_V1_genomic.fna.gz | prodigal -d GCF_900015215.1_CRIB_assembly_V1_genomic.fna/cds.fna -a GCF_900015215.1_CRIB_assembly_V1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:27:37,158] [INFO] Task succeeded: Prodigal
[2024-01-24 13:27:37,158] [INFO] Task started: HMMsearch
[2024-01-24 13:27:37,158] [INFO] Running command: hmmsearch --tblout GCF_900015215.1_CRIB_assembly_V1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg85a40083-839d-4203-aafc-1dfbcaac15a8/dqc_reference/reference_markers.hmm GCF_900015215.1_CRIB_assembly_V1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:27:37,389] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:27:37,391] [INFO] Found 6/6 markers.
[2024-01-24 13:27:37,414] [INFO] Query marker FASTA was written to GCF_900015215.1_CRIB_assembly_V1_genomic.fna/markers.fasta
[2024-01-24 13:27:37,414] [INFO] Task started: Blastn
[2024-01-24 13:27:37,414] [INFO] Running command: blastn -query GCF_900015215.1_CRIB_assembly_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stg85a40083-839d-4203-aafc-1dfbcaac15a8/dqc_reference/reference_markers.fasta -out GCF_900015215.1_CRIB_assembly_V1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:38,004] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:38,009] [INFO] Selected 7 target genomes.
[2024-01-24 13:27:38,009] [INFO] Target genome list was writen to GCF_900015215.1_CRIB_assembly_V1_genomic.fna/target_genomes.txt
[2024-01-24 13:27:38,043] [INFO] Task started: fastANI
[2024-01-24 13:27:38,043] [INFO] Running command: fastANI --query /var/lib/cwl/stg83c0aca4-0482-49af-bf18-b6e72a911050/GCF_900015215.1_CRIB_assembly_V1_genomic.fna.gz --refList GCF_900015215.1_CRIB_assembly_V1_genomic.fna/target_genomes.txt --output GCF_900015215.1_CRIB_assembly_V1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:27:44,305] [INFO] Task succeeded: fastANI
[2024-01-24 13:27:44,305] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg85a40083-839d-4203-aafc-1dfbcaac15a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:27:44,306] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg85a40083-839d-4203-aafc-1dfbcaac15a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:27:44,318] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:27:44,319] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:27:44,319] [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
Romboutsia ilealis	strain=CRIB	GCA_900015215.1	1115758	1115758	type	True	100.0	860	862	95	conclusive
Romboutsia timonensis	strain=Marseille-P326	GCA_900106845.1	1776391	1776391	type	True	92.1636	688	862	95	below_threshold
Romboutsia hominis	strain=FRIFI	GCA_900002575.1	1507512	1507512	type	True	81.3988	429	862	95	below_threshold
Romboutsia lituseburensis	strain=A25K	GCA_900002825.1	1537	1537	type	True	81.1152	462	862	95	below_threshold
[Clostridium] dakarense	strain=FF1	GCA_000499525.1	1301100	1301100	type	True	80.7321	421	862	95	below_threshold
Romboutsia lituseburensis	strain=DSM 797	GCA_900103615.1	1537	1537	type	True	80.5499	445	862	95	below_threshold
Paraclostridium bifermentans	strain=ATCC 638	GCA_006802875.1	1490	1490	type	True	79.1318	323	862	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:27:44,321] [INFO] DFAST Taxonomy check result was written to GCF_900015215.1_CRIB_assembly_V1_genomic.fna/tc_result.tsv
[2024-01-24 13:27:44,322] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:27:44,322] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:27:44,322] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg85a40083-839d-4203-aafc-1dfbcaac15a8/dqc_reference/checkm_data
[2024-01-24 13:27:44,323] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:27:44,351] [INFO] Task started: CheckM
[2024-01-24 13:27:44,351] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900015215.1_CRIB_assembly_V1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900015215.1_CRIB_assembly_V1_genomic.fna/checkm_input GCF_900015215.1_CRIB_assembly_V1_genomic.fna/checkm_result
[2024-01-24 13:28:04,421] [INFO] Task succeeded: CheckM
[2024-01-24 13:28:04,423] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:28:04,443] [INFO] ===== Completeness check finished =====
[2024-01-24 13:28:04,444] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:28:04,444] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900015215.1_CRIB_assembly_V1_genomic.fna/markers.fasta)
[2024-01-24 13:28:04,444] [INFO] Task started: Blastn
[2024-01-24 13:28:04,445] [INFO] Running command: blastn -query GCF_900015215.1_CRIB_assembly_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stg85a40083-839d-4203-aafc-1dfbcaac15a8/dqc_reference/reference_markers_gtdb.fasta -out GCF_900015215.1_CRIB_assembly_V1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:05,239] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:05,242] [INFO] Selected 8 target genomes.
[2024-01-24 13:28:05,242] [INFO] Target genome list was writen to GCF_900015215.1_CRIB_assembly_V1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:28:05,270] [INFO] Task started: fastANI
[2024-01-24 13:28:05,270] [INFO] Running command: fastANI --query /var/lib/cwl/stg83c0aca4-0482-49af-bf18-b6e72a911050/GCF_900015215.1_CRIB_assembly_V1_genomic.fna.gz --refList GCF_900015215.1_CRIB_assembly_V1_genomic.fna/target_genomes_gtdb.txt --output GCF_900015215.1_CRIB_assembly_V1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:28:11,901] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:11,908] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:28:11,909] [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_900015215.1	s__Romboutsia ilealis	100.0	860	862	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Romboutsia	95.0	98.59	98.59	0.90	0.90	2	conclusive
GCF_900106845.1	s__Romboutsia timonensis	92.1905	687	862	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Romboutsia	95.0	98.20	98.12	0.88	0.86	5	-
GCA_904418825.1	s__Romboutsia sp904418825	89.3933	538	862	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Romboutsia	95.0	99.17	99.17	0.88	0.88	2	-
GCA_018336475.1	s__Romboutsia sp018336475	87.1826	690	862	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Romboutsia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900002575.1	s__Romboutsia_C hominis	81.3955	428	862	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Romboutsia_C	95.0	98.29	95.25	0.93	0.90	6	-
GCA_017425305.1	s__Paraclostridium sp017425305	80.8723	156	862	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Paraclostridium	95.0	97.54	97.54	0.79	0.79	2	-
GCF_000499525.1	s__CCUG-7971 spG000499525	80.7316	421	862	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__CCUG-7971	95.0	100.00	100.00	0.99	0.99	2	-
GCF_017590215.1	s__CCUG-7971 sp017590215	80.7282	419	862	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__CCUG-7971	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:28:11,910] [INFO] GTDB search result was written to GCF_900015215.1_CRIB_assembly_V1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:28:11,911] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:28:11,913] [INFO] DFAST_QC result json was written to GCF_900015215.1_CRIB_assembly_V1_genomic.fna/dqc_result.json
[2024-01-24 13:28:11,914] [INFO] DFAST_QC completed!
[2024-01-24 13:28:11,914] [INFO] Total running time: 0h0m40s