[2024-01-24 13:56:26,615] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:56:26,617] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:56:26,617] [INFO] DQC Reference Directory: /var/lib/cwl/stg511b1ed3-854c-4ed1-a138-5034847d64f4/dqc_reference
[2024-01-24 13:56:27,882] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:56:27,883] [INFO] Task started: Prodigal
[2024-01-24 13:56:27,883] [INFO] Running command: gunzip -c /var/lib/cwl/stgd5ac1931-6a1d-444e-a209-3e810e2d5a30/GCF_914768045.1_LMG_28360_genomic.fna.gz | prodigal -d GCF_914768045.1_LMG_28360_genomic.fna/cds.fna -a GCF_914768045.1_LMG_28360_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:33,260] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:33,260] [INFO] Task started: HMMsearch
[2024-01-24 13:56:33,260] [INFO] Running command: hmmsearch --tblout GCF_914768045.1_LMG_28360_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg511b1ed3-854c-4ed1-a138-5034847d64f4/dqc_reference/reference_markers.hmm GCF_914768045.1_LMG_28360_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:33,488] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:33,489] [INFO] Found 6/6 markers.
[2024-01-24 13:56:33,510] [INFO] Query marker FASTA was written to GCF_914768045.1_LMG_28360_genomic.fna/markers.fasta
[2024-01-24 13:56:33,511] [INFO] Task started: Blastn
[2024-01-24 13:56:33,511] [INFO] Running command: blastn -query GCF_914768045.1_LMG_28360_genomic.fna/markers.fasta -db /var/lib/cwl/stg511b1ed3-854c-4ed1-a138-5034847d64f4/dqc_reference/reference_markers.fasta -out GCF_914768045.1_LMG_28360_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:34,173] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:34,177] [INFO] Selected 17 target genomes.
[2024-01-24 13:56:34,178] [INFO] Target genome list was writen to GCF_914768045.1_LMG_28360_genomic.fna/target_genomes.txt
[2024-01-24 13:56:34,211] [INFO] Task started: fastANI
[2024-01-24 13:56:34,211] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5ac1931-6a1d-444e-a209-3e810e2d5a30/GCF_914768045.1_LMG_28360_genomic.fna.gz --refList GCF_914768045.1_LMG_28360_genomic.fna/target_genomes.txt --output GCF_914768045.1_LMG_28360_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:41,883] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:41,884] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg511b1ed3-854c-4ed1-a138-5034847d64f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:41,884] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg511b1ed3-854c-4ed1-a138-5034847d64f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:41,896] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:56:41,896] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:56:41,896] [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
Snodgrassella communis	strain=LMG 28360	GCA_914768045.1	2946699	2946699	type	True	100.0	754	755	95	conclusive
Snodgrassella gandavensis	strain=LMG 30236	GCA_914768025.1	2946698	2946698	type	True	88.4232	663	755	95	below_threshold
Snodgrassella alvi	strain=wkB2	GCA_000600005.1	1196083	1196083	type	True	81.1343	510	755	95	below_threshold
Snodgrassella alvi	strain=wkB2	GCA_022870965.1	1196083	1196083	type	True	80.9599	530	755	95	below_threshold
Stenoxybacter acetivorans	strain=DSM 19021	GCA_000745895.1	422441	422441	type	True	76.865	59	755	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:41,898] [INFO] DFAST Taxonomy check result was written to GCF_914768045.1_LMG_28360_genomic.fna/tc_result.tsv
[2024-01-24 13:56:41,899] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:41,899] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:41,899] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg511b1ed3-854c-4ed1-a138-5034847d64f4/dqc_reference/checkm_data
[2024-01-24 13:56:41,900] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:41,925] [INFO] Task started: CheckM
[2024-01-24 13:56:41,925] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_914768045.1_LMG_28360_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_914768045.1_LMG_28360_genomic.fna/checkm_input GCF_914768045.1_LMG_28360_genomic.fna/checkm_result
[2024-01-24 13:57:04,729] [INFO] Task succeeded: CheckM
[2024-01-24 13:57:04,731] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:57:04,754] [INFO] ===== Completeness check finished =====
[2024-01-24 13:57:04,754] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:57:04,755] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_914768045.1_LMG_28360_genomic.fna/markers.fasta)
[2024-01-24 13:57:04,755] [INFO] Task started: Blastn
[2024-01-24 13:57:04,756] [INFO] Running command: blastn -query GCF_914768045.1_LMG_28360_genomic.fna/markers.fasta -db /var/lib/cwl/stg511b1ed3-854c-4ed1-a138-5034847d64f4/dqc_reference/reference_markers_gtdb.fasta -out GCF_914768045.1_LMG_28360_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:05,798] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:05,803] [INFO] Selected 7 target genomes.
[2024-01-24 13:57:05,803] [INFO] Target genome list was writen to GCF_914768045.1_LMG_28360_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:57:05,810] [INFO] Task started: fastANI
[2024-01-24 13:57:05,811] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5ac1931-6a1d-444e-a209-3e810e2d5a30/GCF_914768045.1_LMG_28360_genomic.fna.gz --refList GCF_914768045.1_LMG_28360_genomic.fna/target_genomes_gtdb.txt --output GCF_914768045.1_LMG_28360_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:57:09,784] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:09,791] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:57:09,791] [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_900094895.1	s__Snodgrassella sp900094895	99.9694	747	755	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Snodgrassella	95.0	96.52	95.92	0.91	0.89	11	conclusive
GCF_002777425.1	s__Snodgrassella alvi_B	88.6687	631	755	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Snodgrassella	95.0	98.37	97.04	0.91	0.85	4	-
GCF_002777825.1	s__Snodgrassella alvi_C	87.8995	621	755	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Snodgrassella	95.0	98.79	98.79	0.90	0.90	2	-
GCF_002777745.1	s__Snodgrassella alvi_D	86.0147	644	755	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Snodgrassella	95.0	98.59	98.58	0.91	0.90	4	-
GCF_000600005.1	s__Snodgrassella alvi	81.1343	510	755	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Snodgrassella	95.0	97.18	95.11	0.93	0.85	47	-
GCF_002777855.1	s__Snodgrassella alvi_E	80.3331	454	755	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Snodgrassella	95.0	98.27	98.21	0.94	0.93	3	-
GCA_000725195.1	s__Snodgrassella alvi_G	78.6438	132	755	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Snodgrassella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:57:09,794] [INFO] GTDB search result was written to GCF_914768045.1_LMG_28360_genomic.fna/result_gtdb.tsv
[2024-01-24 13:57:09,796] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:57:09,798] [INFO] DFAST_QC result json was written to GCF_914768045.1_LMG_28360_genomic.fna/dqc_result.json
[2024-01-24 13:57:09,799] [INFO] DFAST_QC completed!
[2024-01-24 13:57:09,799] [INFO] Total running time: 0h0m43s