[2024-01-24 14:39:14,624] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:14,627] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:14,627] [INFO] DQC Reference Directory: /var/lib/cwl/stgf83b968e-9ab7-474c-8d9f-66cd3d2a275a/dqc_reference
[2024-01-24 14:39:16,035] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:16,036] [INFO] Task started: Prodigal
[2024-01-24 14:39:16,037] [INFO] Running command: gunzip -c /var/lib/cwl/stg7c2e5f18-b603-497e-815d-849e56d8905f/GCF_014068355.1_ASM1406835v1_genomic.fna.gz | prodigal -d GCF_014068355.1_ASM1406835v1_genomic.fna/cds.fna -a GCF_014068355.1_ASM1406835v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:17,565] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:17,565] [INFO] Task started: HMMsearch
[2024-01-24 14:39:17,566] [INFO] Running command: hmmsearch --tblout GCF_014068355.1_ASM1406835v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf83b968e-9ab7-474c-8d9f-66cd3d2a275a/dqc_reference/reference_markers.hmm GCF_014068355.1_ASM1406835v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:17,757] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:17,759] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg7c2e5f18-b603-497e-815d-849e56d8905f/GCF_014068355.1_ASM1406835v1_genomic.fna.gz]
[2024-01-24 14:39:17,775] [INFO] Query marker FASTA was written to GCF_014068355.1_ASM1406835v1_genomic.fna/markers.fasta
[2024-01-24 14:39:17,776] [INFO] Task started: Blastn
[2024-01-24 14:39:17,776] [INFO] Running command: blastn -query GCF_014068355.1_ASM1406835v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf83b968e-9ab7-474c-8d9f-66cd3d2a275a/dqc_reference/reference_markers.fasta -out GCF_014068355.1_ASM1406835v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:18,410] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:18,414] [INFO] Selected 16 target genomes.
[2024-01-24 14:39:18,414] [INFO] Target genome list was writen to GCF_014068355.1_ASM1406835v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:18,420] [INFO] Task started: fastANI
[2024-01-24 14:39:18,421] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c2e5f18-b603-497e-815d-849e56d8905f/GCF_014068355.1_ASM1406835v1_genomic.fna.gz --refList GCF_014068355.1_ASM1406835v1_genomic.fna/target_genomes.txt --output GCF_014068355.1_ASM1406835v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:25,301] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:25,301] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf83b968e-9ab7-474c-8d9f-66cd3d2a275a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:25,301] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf83b968e-9ab7-474c-8d9f-66cd3d2a275a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:25,306] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:39:25,306] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:39:25,307] [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
Mycoplasmoides gallisepticum	strain=ATCC 19610	GCA_000428645.1	2096	2096	type	True	86.9169	233	289	95	below_threshold
Mycoplasmoides gallisepticum	strain=NCTC10115	GCA_900476085.1	2096	2096	type	True	86.7407	247	289	95	below_threshold
Mycoplasma imitans	strain=ATCC 51306	GCA_000518305.1	29560	29560	type	True	82.4429	224	289	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:25,308] [INFO] DFAST Taxonomy check result was written to GCF_014068355.1_ASM1406835v1_genomic.fna/tc_result.tsv
[2024-01-24 14:39:25,309] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:25,309] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:25,309] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf83b968e-9ab7-474c-8d9f-66cd3d2a275a/dqc_reference/checkm_data
[2024-01-24 14:39:25,310] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:25,322] [INFO] Task started: CheckM
[2024-01-24 14:39:25,323] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014068355.1_ASM1406835v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014068355.1_ASM1406835v1_genomic.fna/checkm_input GCF_014068355.1_ASM1406835v1_genomic.fna/checkm_result
[2024-01-24 14:39:39,103] [INFO] Task succeeded: CheckM
[2024-01-24 14:39:39,107] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:39:39,136] [INFO] ===== Completeness check finished =====
[2024-01-24 14:39:39,136] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:39:39,137] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014068355.1_ASM1406835v1_genomic.fna/markers.fasta)
[2024-01-24 14:39:39,137] [INFO] Task started: Blastn
[2024-01-24 14:39:39,137] [INFO] Running command: blastn -query GCF_014068355.1_ASM1406835v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf83b968e-9ab7-474c-8d9f-66cd3d2a275a/dqc_reference/reference_markers_gtdb.fasta -out GCF_014068355.1_ASM1406835v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:39,972] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:39,976] [INFO] Selected 14 target genomes.
[2024-01-24 14:39:39,977] [INFO] Target genome list was writen to GCF_014068355.1_ASM1406835v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:39:40,009] [INFO] Task started: fastANI
[2024-01-24 14:39:40,009] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c2e5f18-b603-497e-815d-849e56d8905f/GCF_014068355.1_ASM1406835v1_genomic.fna.gz --refList GCF_014068355.1_ASM1406835v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014068355.1_ASM1406835v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:39:43,988] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:43,993] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:39:43,993] [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_014068355.1	s__Mycoplasmoides tullyi	100.0	289	289	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmoidaceae;g__Mycoplasmoides	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900476085.1	s__Mycoplasmoides gallisepticum	86.7739	246	289	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmoidaceae;g__Mycoplasmoides	95.0	98.49	97.87	0.96	0.93	28	-
GCF_000518305.1	s__Mycoplasmoides imitans	82.4429	224	289	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmoidaceae;g__Mycoplasmoides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:39:43,995] [INFO] GTDB search result was written to GCF_014068355.1_ASM1406835v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:39:43,995] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:39:43,998] [INFO] DFAST_QC result json was written to GCF_014068355.1_ASM1406835v1_genomic.fna/dqc_result.json
[2024-01-24 14:39:43,998] [INFO] DFAST_QC completed!
[2024-01-24 14:39:43,998] [INFO] Total running time: 0h0m29s