[2024-01-24 13:57:31,783] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:31,785] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:31,785] [INFO] DQC Reference Directory: /var/lib/cwl/stg1b537f8e-bad5-4652-a89b-4bf71077ccc7/dqc_reference
[2024-01-24 13:57:33,124] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:33,125] [INFO] Task started: Prodigal
[2024-01-24 13:57:33,126] [INFO] Running command: gunzip -c /var/lib/cwl/stg784f9657-9853-4996-a0c7-566466b2624a/GCF_928097925.1_Q5883_genomic.fna.gz | prodigal -d GCF_928097925.1_Q5883_genomic.fna/cds.fna -a GCF_928097925.1_Q5883_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:36,986] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:36,987] [INFO] Task started: HMMsearch
[2024-01-24 13:57:36,987] [INFO] Running command: hmmsearch --tblout GCF_928097925.1_Q5883_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1b537f8e-bad5-4652-a89b-4bf71077ccc7/dqc_reference/reference_markers.hmm GCF_928097925.1_Q5883_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:37,197] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:37,198] [INFO] Found 6/6 markers.
[2024-01-24 13:57:37,217] [INFO] Query marker FASTA was written to GCF_928097925.1_Q5883_genomic.fna/markers.fasta
[2024-01-24 13:57:37,218] [INFO] Task started: Blastn
[2024-01-24 13:57:37,218] [INFO] Running command: blastn -query GCF_928097925.1_Q5883_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b537f8e-bad5-4652-a89b-4bf71077ccc7/dqc_reference/reference_markers.fasta -out GCF_928097925.1_Q5883_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:37,884] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:37,887] [INFO] Selected 16 target genomes.
[2024-01-24 13:57:37,888] [INFO] Target genome list was writen to GCF_928097925.1_Q5883_genomic.fna/target_genomes.txt
[2024-01-24 13:57:37,901] [INFO] Task started: fastANI
[2024-01-24 13:57:37,901] [INFO] Running command: fastANI --query /var/lib/cwl/stg784f9657-9853-4996-a0c7-566466b2624a/GCF_928097925.1_Q5883_genomic.fna.gz --refList GCF_928097925.1_Q5883_genomic.fna/target_genomes.txt --output GCF_928097925.1_Q5883_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:45,299] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:45,300] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1b537f8e-bad5-4652-a89b-4bf71077ccc7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:45,300] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1b537f8e-bad5-4652-a89b-4bf71077ccc7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:45,306] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:57:45,306] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:57:45,307] [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
Lagierella massiliensis	strain=SIT14	GCA_001407835.1	1689303	1689303	type	True	86.6941	473	663	95	below_threshold
Lagierella massiliensis	strain=Marseille-P2012	GCA_902375645.1	1689303	1689303	type	True	86.6493	475	663	95	below_threshold
Anaerococcus vaginalis	strain=FDAARGOS_988	GCA_016127475.1	33037	33037	type	True	86.1154	76	663	95	below_threshold
Miniphocaeibacter halophilus	strain=AMB_01	GCA_016458825.1	2931922	2931922	type	True	77.9684	67	663	95	below_threshold
Miniphocaeibacter massiliensis	strain=Marseille-P4678	GCA_900232905.1	2041841	2041841	type	True	77.1641	61	663	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:45,308] [INFO] DFAST Taxonomy check result was written to GCF_928097925.1_Q5883_genomic.fna/tc_result.tsv
[2024-01-24 13:57:45,309] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:45,309] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:45,309] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1b537f8e-bad5-4652-a89b-4bf71077ccc7/dqc_reference/checkm_data
[2024-01-24 13:57:45,310] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:45,336] [INFO] Task started: CheckM
[2024-01-24 13:57:45,337] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_928097925.1_Q5883_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_928097925.1_Q5883_genomic.fna/checkm_input GCF_928097925.1_Q5883_genomic.fna/checkm_result
[2024-01-24 13:58:04,918] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:04,919] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:04,937] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:04,937] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:04,937] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_928097925.1_Q5883_genomic.fna/markers.fasta)
[2024-01-24 13:58:04,938] [INFO] Task started: Blastn
[2024-01-24 13:58:04,938] [INFO] Running command: blastn -query GCF_928097925.1_Q5883_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b537f8e-bad5-4652-a89b-4bf71077ccc7/dqc_reference/reference_markers_gtdb.fasta -out GCF_928097925.1_Q5883_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:05,787] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:05,790] [INFO] Selected 22 target genomes.
[2024-01-24 13:58:05,790] [INFO] Target genome list was writen to GCF_928097925.1_Q5883_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:05,811] [INFO] Task started: fastANI
[2024-01-24 13:58:05,811] [INFO] Running command: fastANI --query /var/lib/cwl/stg784f9657-9853-4996-a0c7-566466b2624a/GCF_928097925.1_Q5883_genomic.fna.gz --refList GCF_928097925.1_Q5883_genomic.fna/target_genomes_gtdb.txt --output GCF_928097925.1_Q5883_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:14,090] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:14,096] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:58:14,096] [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_001407835.1	s__Lagierella massiliensis	86.6702	474	663	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Lagierella	95.0	100.00	100.00	0.99	0.99	2	-
GCA_016458825.1	s__Miniphocibacter sp016458825	78.0169	69	663	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Miniphocibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900232905.1	s__Miniphocibacter massiliensis	77.1641	61	663	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Miniphocibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001552895.1	s__Parvimonas sp001552895	76.8424	54	663	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Parvimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012841535.1	s__Miniphocibacter sp012841535	76.5763	81	663	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Miniphocibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:14,098] [INFO] GTDB search result was written to GCF_928097925.1_Q5883_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:14,098] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:14,101] [INFO] DFAST_QC result json was written to GCF_928097925.1_Q5883_genomic.fna/dqc_result.json
[2024-01-24 13:58:14,101] [INFO] DFAST_QC completed!
[2024-01-24 13:58:14,101] [INFO] Total running time: 0h0m42s