[2024-01-25 20:06:50,635] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:06:50,636] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:06:50,637] [INFO] DQC Reference Directory: /var/lib/cwl/stg9c83d83a-43d9-4f61-a536-ecf38ba53325/dqc_reference
[2024-01-25 20:06:51,746] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:06:51,747] [INFO] Task started: Prodigal
[2024-01-25 20:06:51,747] [INFO] Running command: gunzip -c /var/lib/cwl/stg51ff02ca-bd6f-4efd-9db1-eccd13fcf9b5/GCF_009362815.1_ASM936281v1_genomic.fna.gz | prodigal -d GCF_009362815.1_ASM936281v1_genomic.fna/cds.fna -a GCF_009362815.1_ASM936281v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:06:56,881] [INFO] Task succeeded: Prodigal
[2024-01-25 20:06:56,882] [INFO] Task started: HMMsearch
[2024-01-25 20:06:56,882] [INFO] Running command: hmmsearch --tblout GCF_009362815.1_ASM936281v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9c83d83a-43d9-4f61-a536-ecf38ba53325/dqc_reference/reference_markers.hmm GCF_009362815.1_ASM936281v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:06:57,118] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:06:57,119] [INFO] Found 6/6 markers.
[2024-01-25 20:06:57,146] [INFO] Query marker FASTA was written to GCF_009362815.1_ASM936281v1_genomic.fna/markers.fasta
[2024-01-25 20:06:57,146] [INFO] Task started: Blastn
[2024-01-25 20:06:57,146] [INFO] Running command: blastn -query GCF_009362815.1_ASM936281v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c83d83a-43d9-4f61-a536-ecf38ba53325/dqc_reference/reference_markers.fasta -out GCF_009362815.1_ASM936281v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:06:57,680] [INFO] Task succeeded: Blastn
[2024-01-25 20:06:57,683] [INFO] Selected 17 target genomes.
[2024-01-25 20:06:57,683] [INFO] Target genome list was writen to GCF_009362815.1_ASM936281v1_genomic.fna/target_genomes.txt
[2024-01-25 20:06:57,695] [INFO] Task started: fastANI
[2024-01-25 20:06:57,696] [INFO] Running command: fastANI --query /var/lib/cwl/stg51ff02ca-bd6f-4efd-9db1-eccd13fcf9b5/GCF_009362815.1_ASM936281v1_genomic.fna.gz --refList GCF_009362815.1_ASM936281v1_genomic.fna/target_genomes.txt --output GCF_009362815.1_ASM936281v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:07:05,240] [INFO] Task succeeded: fastANI
[2024-01-25 20:07:05,241] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9c83d83a-43d9-4f61-a536-ecf38ba53325/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:07:05,241] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9c83d83a-43d9-4f61-a536-ecf38ba53325/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:07:05,245] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:07:05,245] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:07:05,245] [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
Alkalibaculum sporogenes	strain=M08 DMB	GCA_009362815.1	2655001	2655001	type	True	100.0	1121	1125	95	conclusive
Alkalibaculum bacchi	strain=DSM 22112	GCA_003317055.1	645887	645887	type	True	76.9698	113	1125	95	below_threshold
Clostridium thermobutyricum	strain=DSM 4928	GCA_002050515.1	29372	29372	type	True	74.9556	52	1125	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:07:05,247] [INFO] DFAST Taxonomy check result was written to GCF_009362815.1_ASM936281v1_genomic.fna/tc_result.tsv
[2024-01-25 20:07:05,247] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:07:05,247] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:07:05,247] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9c83d83a-43d9-4f61-a536-ecf38ba53325/dqc_reference/checkm_data
[2024-01-25 20:07:05,248] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:07:05,284] [INFO] Task started: CheckM
[2024-01-25 20:07:05,285] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009362815.1_ASM936281v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009362815.1_ASM936281v1_genomic.fna/checkm_input GCF_009362815.1_ASM936281v1_genomic.fna/checkm_result
[2024-01-25 20:07:26,014] [INFO] Task succeeded: CheckM
[2024-01-25 20:07:26,015] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:07:26,031] [INFO] ===== Completeness check finished =====
[2024-01-25 20:07:26,031] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:07:26,032] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009362815.1_ASM936281v1_genomic.fna/markers.fasta)
[2024-01-25 20:07:26,032] [INFO] Task started: Blastn
[2024-01-25 20:07:26,032] [INFO] Running command: blastn -query GCF_009362815.1_ASM936281v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c83d83a-43d9-4f61-a536-ecf38ba53325/dqc_reference/reference_markers_gtdb.fasta -out GCF_009362815.1_ASM936281v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:07:26,781] [INFO] Task succeeded: Blastn
[2024-01-25 20:07:26,784] [INFO] Selected 23 target genomes.
[2024-01-25 20:07:26,784] [INFO] Target genome list was writen to GCF_009362815.1_ASM936281v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:07:26,803] [INFO] Task started: fastANI
[2024-01-25 20:07:26,803] [INFO] Running command: fastANI --query /var/lib/cwl/stg51ff02ca-bd6f-4efd-9db1-eccd13fcf9b5/GCF_009362815.1_ASM936281v1_genomic.fna.gz --refList GCF_009362815.1_ASM936281v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009362815.1_ASM936281v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:07:36,776] [INFO] Task succeeded: fastANI
[2024-01-25 20:07:36,780] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:07:36,780] [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_009362815.1	s__M08DMB sp009362815	100.0	1121	1125	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Eubacteriales;f__Alkalibacteraceae;g__M08DMB	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003317055.1	s__Alkalibaculum bacchi	76.9698	113	1125	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Eubacteriales;f__Alkalibacteraceae;g__Alkalibaculum	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900626135.1	s__Senegalia massiliensis	75.845	50	1125	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__SIT17;g__Senegalia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:07:36,781] [INFO] GTDB search result was written to GCF_009362815.1_ASM936281v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:07:36,782] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:07:36,784] [INFO] DFAST_QC result json was written to GCF_009362815.1_ASM936281v1_genomic.fna/dqc_result.json
[2024-01-25 20:07:36,785] [INFO] DFAST_QC completed!
[2024-01-25 20:07:36,785] [INFO] Total running time: 0h0m46s