[2023-06-28 04:58:47,975] [INFO] DFAST_QC pipeline started.
[2023-06-28 04:58:47,980] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 04:58:47,980] [INFO] DQC Reference Directory: /var/lib/cwl/stgbbdba627-aec3-42b6-a670-c579bf9d6fd7/dqc_reference
[2023-06-28 04:58:49,282] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 04:58:49,283] [INFO] Task started: Prodigal
[2023-06-28 04:58:49,284] [INFO] Running command: gunzip -c /var/lib/cwl/stgd466f1d4-5225-450a-a937-9e5ad0d6021a/GCA_017984845.1_ASM1798484v1_genomic.fna.gz | prodigal -d GCA_017984845.1_ASM1798484v1_genomic.fna/cds.fna -a GCA_017984845.1_ASM1798484v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 04:58:51,560] [INFO] Task succeeded: Prodigal
[2023-06-28 04:58:51,561] [INFO] Task started: HMMsearch
[2023-06-28 04:58:51,561] [INFO] Running command: hmmsearch --tblout GCA_017984845.1_ASM1798484v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbbdba627-aec3-42b6-a670-c579bf9d6fd7/dqc_reference/reference_markers.hmm GCA_017984845.1_ASM1798484v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 04:58:51,774] [INFO] Task succeeded: HMMsearch
[2023-06-28 04:58:51,776] [WARNING] Found 1/6 markers. [/var/lib/cwl/stgd466f1d4-5225-450a-a937-9e5ad0d6021a/GCA_017984845.1_ASM1798484v1_genomic.fna.gz]
[2023-06-28 04:58:51,795] [INFO] Query marker FASTA was written to GCA_017984845.1_ASM1798484v1_genomic.fna/markers.fasta
[2023-06-28 04:58:51,796] [INFO] Task started: Blastn
[2023-06-28 04:58:51,796] [INFO] Running command: blastn -query GCA_017984845.1_ASM1798484v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbbdba627-aec3-42b6-a670-c579bf9d6fd7/dqc_reference/reference_markers.fasta -out GCA_017984845.1_ASM1798484v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 04:58:52,277] [INFO] Task succeeded: Blastn
[2023-06-28 04:58:52,281] [INFO] Selected 5 target genomes.
[2023-06-28 04:58:52,281] [INFO] Target genome list was writen to GCA_017984845.1_ASM1798484v1_genomic.fna/target_genomes.txt
[2023-06-28 04:58:52,282] [INFO] Task started: fastANI
[2023-06-28 04:58:52,282] [INFO] Running command: fastANI --query /var/lib/cwl/stgd466f1d4-5225-450a-a937-9e5ad0d6021a/GCA_017984845.1_ASM1798484v1_genomic.fna.gz --refList GCA_017984845.1_ASM1798484v1_genomic.fna/target_genomes.txt --output GCA_017984845.1_ASM1798484v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 04:58:55,449] [INFO] Task succeeded: fastANI
[2023-06-28 04:58:55,450] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbbdba627-aec3-42b6-a670-c579bf9d6fd7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 04:58:55,450] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbbdba627-aec3-42b6-a670-c579bf9d6fd7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 04:58:55,461] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2023-06-28 04:58:55,461] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-28 04:58:55,461] [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
Blautia wexlerae	strain=DSM 19850	GCA_025148125.1	418240	418240	suspected-type	True	98.4886	287	315	95	conclusive
Blautia wexlerae	strain=DSM 19850	GCA_000484655.1	418240	418240	suspected-type	True	98.4467	274	315	95	conclusive
Blautia luti	strain=DSM 14534	GCA_009707925.1	89014	89014	suspected-type	True	84.646	198	315	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	79.4869	107	315	95	below_threshold
Blautia caecimuris	strain=DSM 29492	GCA_024622975.1	1796615	1796615	type	True	78.3002	98	315	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 04:58:55,463] [INFO] DFAST Taxonomy check result was written to GCA_017984845.1_ASM1798484v1_genomic.fna/tc_result.tsv
[2023-06-28 04:58:55,464] [INFO] ===== Taxonomy check completed =====
[2023-06-28 04:58:55,464] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 04:58:55,465] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbbdba627-aec3-42b6-a670-c579bf9d6fd7/dqc_reference/checkm_data
[2023-06-28 04:58:55,466] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 04:58:55,487] [INFO] Task started: CheckM
[2023-06-28 04:58:55,487] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017984845.1_ASM1798484v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017984845.1_ASM1798484v1_genomic.fna/checkm_input GCA_017984845.1_ASM1798484v1_genomic.fna/checkm_result
[2023-06-28 04:59:10,567] [INFO] Task succeeded: CheckM
[2023-06-28 04:59:10,568] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 20.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 04:59:10,588] [INFO] ===== Completeness check finished =====
[2023-06-28 04:59:10,588] [INFO] ===== Start GTDB Search =====
[2023-06-28 04:59:10,589] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017984845.1_ASM1798484v1_genomic.fna/markers.fasta)
[2023-06-28 04:59:10,589] [INFO] Task started: Blastn
[2023-06-28 04:59:10,589] [INFO] Running command: blastn -query GCA_017984845.1_ASM1798484v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbbdba627-aec3-42b6-a670-c579bf9d6fd7/dqc_reference/reference_markers_gtdb.fasta -out GCA_017984845.1_ASM1798484v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 04:59:11,066] [INFO] Task succeeded: Blastn
[2023-06-28 04:59:11,071] [INFO] Selected 5 target genomes.
[2023-06-28 04:59:11,071] [INFO] Target genome list was writen to GCA_017984845.1_ASM1798484v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 04:59:11,072] [INFO] Task started: fastANI
[2023-06-28 04:59:11,072] [INFO] Running command: fastANI --query /var/lib/cwl/stgd466f1d4-5225-450a-a937-9e5ad0d6021a/GCA_017984845.1_ASM1798484v1_genomic.fna.gz --refList GCA_017984845.1_ASM1798484v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017984845.1_ASM1798484v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 04:59:14,559] [INFO] Task succeeded: fastANI
[2023-06-28 04:59:14,566] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 04:59:14,566] [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_000484655.1	s__Blautia_A wexlerae	98.4467	274	315	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	97.38	96.15	0.76	0.65	140	conclusive
GCF_013300825.1	s__Blautia_A wexlerae_B	94.1709	259	315	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.68	98.07	0.89	0.86	5	-
GCF_003471165.1	s__Blautia_A sp003471165	86.8355	255	315	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.40	97.74	0.83	0.79	20	-
GCA_905209435.1	s__Blautia_A sp905209435	84.7029	216	315	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009707925.1	s__Blautia_A luti	84.6843	197	315	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.33	97.04	0.87	0.84	5	-
--------------------------------------------------------------------------------
[2023-06-28 04:59:14,568] [INFO] GTDB search result was written to GCA_017984845.1_ASM1798484v1_genomic.fna/result_gtdb.tsv
[2023-06-28 04:59:14,568] [INFO] ===== GTDB Search completed =====
[2023-06-28 04:59:14,572] [INFO] DFAST_QC result json was written to GCA_017984845.1_ASM1798484v1_genomic.fna/dqc_result.json
[2023-06-28 04:59:14,572] [INFO] DFAST_QC completed!
[2023-06-28 04:59:14,572] [INFO] Total running time: 0h0m27s