[2024-01-24 13:22:10,603] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:10,606] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:10,606] [INFO] DQC Reference Directory: /var/lib/cwl/stged1e172d-2cee-4f03-854d-09c3610e455d/dqc_reference
[2024-01-24 13:22:11,927] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:11,928] [INFO] Task started: Prodigal
[2024-01-24 13:22:11,928] [INFO] Running command: gunzip -c /var/lib/cwl/stg2c67ca96-c14d-4dc2-a35b-6b4e7ed92105/GCF_001017655.1_ASM101765v1_genomic.fna.gz | prodigal -d GCF_001017655.1_ASM101765v1_genomic.fna/cds.fna -a GCF_001017655.1_ASM101765v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:20,649] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:20,650] [INFO] Task started: HMMsearch
[2024-01-24 13:22:20,650] [INFO] Running command: hmmsearch --tblout GCF_001017655.1_ASM101765v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stged1e172d-2cee-4f03-854d-09c3610e455d/dqc_reference/reference_markers.hmm GCF_001017655.1_ASM101765v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:20,889] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:20,891] [INFO] Found 6/6 markers.
[2024-01-24 13:22:20,919] [INFO] Query marker FASTA was written to GCF_001017655.1_ASM101765v1_genomic.fna/markers.fasta
[2024-01-24 13:22:20,919] [INFO] Task started: Blastn
[2024-01-24 13:22:20,919] [INFO] Running command: blastn -query GCF_001017655.1_ASM101765v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged1e172d-2cee-4f03-854d-09c3610e455d/dqc_reference/reference_markers.fasta -out GCF_001017655.1_ASM101765v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:21,615] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:21,621] [INFO] Selected 22 target genomes.
[2024-01-24 13:22:21,621] [INFO] Target genome list was writen to GCF_001017655.1_ASM101765v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:21,631] [INFO] Task started: fastANI
[2024-01-24 13:22:21,632] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c67ca96-c14d-4dc2-a35b-6b4e7ed92105/GCF_001017655.1_ASM101765v1_genomic.fna.gz --refList GCF_001017655.1_ASM101765v1_genomic.fna/target_genomes.txt --output GCF_001017655.1_ASM101765v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:40,262] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:40,263] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stged1e172d-2cee-4f03-854d-09c3610e455d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:40,263] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stged1e172d-2cee-4f03-854d-09c3610e455d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:40,268] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:22:40,268] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:40,268] [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
Kiritimatiella glycovorans	strain=L21-Fru-AB	GCA_001017655.1	1307763	1307763	type	True	100.0	983	983	95	conclusive
Pontiella desulfatans	strain=F1(T)	GCA_900890425.1	2750659	2750659	type	True	75.6442	66	983	95	below_threshold
Pseudonocardia kunmingensis	strain=DSM 45301	GCA_006716445.1	630975	630975	type	True	74.9382	61	983	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:40,270] [INFO] DFAST Taxonomy check result was written to GCF_001017655.1_ASM101765v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:40,271] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:40,271] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:40,271] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stged1e172d-2cee-4f03-854d-09c3610e455d/dqc_reference/checkm_data
[2024-01-24 13:22:40,272] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:40,313] [INFO] Task started: CheckM
[2024-01-24 13:22:40,314] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001017655.1_ASM101765v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001017655.1_ASM101765v1_genomic.fna/checkm_input GCF_001017655.1_ASM101765v1_genomic.fna/checkm_result
[2024-01-24 13:23:10,670] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:10,671] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:10,685] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:10,685] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:10,686] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001017655.1_ASM101765v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:10,686] [INFO] Task started: Blastn
[2024-01-24 13:23:10,686] [INFO] Running command: blastn -query GCF_001017655.1_ASM101765v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged1e172d-2cee-4f03-854d-09c3610e455d/dqc_reference/reference_markers_gtdb.fasta -out GCF_001017655.1_ASM101765v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:11,898] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:11,903] [INFO] Selected 26 target genomes.
[2024-01-24 13:23:11,903] [INFO] Target genome list was writen to GCF_001017655.1_ASM101765v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:11,989] [INFO] Task started: fastANI
[2024-01-24 13:23:11,990] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c67ca96-c14d-4dc2-a35b-6b4e7ed92105/GCF_001017655.1_ASM101765v1_genomic.fna.gz --refList GCF_001017655.1_ASM101765v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001017655.1_ASM101765v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:32,112] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:32,124] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:32,124] [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_001017655.1	s__Kiritimatiella glycovorans	100.0	983	983	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__Kiritimatiellales;f__Kiritimatiellaceae;g__Kiritimatiella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903896925.1	s__DP16D-bin41 sp903896925	76.179	71	983	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__LD1-PB3;f__CAIQIC01;g__DP16D-bin41	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016873715.1	s__VGWF01 sp016873715	76.1204	104	983	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__PWTM01;f__CAACVY01;g__VGWF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903889245.1	s__DP16D-bin41 sp903889245	75.8828	65	983	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__LD1-PB3;f__CAIQIC01;g__DP16D-bin41	95.0	99.95	99.92	0.98	0.98	5	-
GCF_006716445.1	s__Pseudonocardia kunmingensis	74.931	62	983	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002262885.1	s__Pseudonocardia sp002262885	74.5904	57	983	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:32,126] [INFO] GTDB search result was written to GCF_001017655.1_ASM101765v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:32,127] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:32,129] [INFO] DFAST_QC result json was written to GCF_001017655.1_ASM101765v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:32,129] [INFO] DFAST_QC completed!
[2024-01-24 13:23:32,129] [INFO] Total running time: 0h1m22s