[2024-01-24 13:49:55,294] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:55,296] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:55,296] [INFO] DQC Reference Directory: /var/lib/cwl/stg3f71397c-f5b3-47bc-a80a-2de41258fa9a/dqc_reference
[2024-01-24 13:49:56,544] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:56,544] [INFO] Task started: Prodigal
[2024-01-24 13:49:56,545] [INFO] Running command: gunzip -c /var/lib/cwl/stg86a6efd2-ed8f-475e-a863-97c575a564d6/GCF_000025845.1_ASM2584v1_genomic.fna.gz | prodigal -d GCF_000025845.1_ASM2584v1_genomic.fna/cds.fna -a GCF_000025845.1_ASM2584v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:58,068] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:58,069] [INFO] Task started: HMMsearch
[2024-01-24 13:49:58,069] [INFO] Running command: hmmsearch --tblout GCF_000025845.1_ASM2584v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3f71397c-f5b3-47bc-a80a-2de41258fa9a/dqc_reference/reference_markers.hmm GCF_000025845.1_ASM2584v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:58,289] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:58,291] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg86a6efd2-ed8f-475e-a863-97c575a564d6/GCF_000025845.1_ASM2584v1_genomic.fna.gz]
[2024-01-24 13:49:58,309] [INFO] Query marker FASTA was written to GCF_000025845.1_ASM2584v1_genomic.fna/markers.fasta
[2024-01-24 13:49:58,310] [INFO] Task started: Blastn
[2024-01-24 13:49:58,310] [INFO] Running command: blastn -query GCF_000025845.1_ASM2584v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f71397c-f5b3-47bc-a80a-2de41258fa9a/dqc_reference/reference_markers.fasta -out GCF_000025845.1_ASM2584v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:58,812] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:58,816] [INFO] Selected 12 target genomes.
[2024-01-24 13:49:58,817] [INFO] Target genome list was writen to GCF_000025845.1_ASM2584v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:58,909] [INFO] Task started: fastANI
[2024-01-24 13:49:58,909] [INFO] Running command: fastANI --query /var/lib/cwl/stg86a6efd2-ed8f-475e-a863-97c575a564d6/GCF_000025845.1_ASM2584v1_genomic.fna.gz --refList GCF_000025845.1_ASM2584v1_genomic.fna/target_genomes.txt --output GCF_000025845.1_ASM2584v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:01,004] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:01,005] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3f71397c-f5b3-47bc-a80a-2de41258fa9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:01,006] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3f71397c-f5b3-47bc-a80a-2de41258fa9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:01,014] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:50:01,014] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:50:01,014] [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
Mycoplasmopsis anatis	strain=NCTC10156	GCA_900660655.1	171279	171279	type	True	78.0354	65	311	95	below_threshold
Mycoplasmopsis anatis	strain=NCTC 10156	GCA_003285065.1	171279	171279	type	True	77.7663	62	311	95	below_threshold
Mycoplasmopsis cynos	strain=NCTC10142	GCA_900660545.1	171284	171284	type	True	77.4213	50	311	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:01,017] [INFO] DFAST Taxonomy check result was written to GCF_000025845.1_ASM2584v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:01,018] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:01,018] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:01,018] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3f71397c-f5b3-47bc-a80a-2de41258fa9a/dqc_reference/checkm_data
[2024-01-24 13:50:01,019] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:01,033] [INFO] Task started: CheckM
[2024-01-24 13:50:01,033] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000025845.1_ASM2584v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000025845.1_ASM2584v1_genomic.fna/checkm_input GCF_000025845.1_ASM2584v1_genomic.fna/checkm_result
[2024-01-24 13:50:14,025] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:14,026] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:14,044] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:14,044] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:14,045] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000025845.1_ASM2584v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:14,045] [INFO] Task started: Blastn
[2024-01-24 13:50:14,045] [INFO] Running command: blastn -query GCF_000025845.1_ASM2584v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f71397c-f5b3-47bc-a80a-2de41258fa9a/dqc_reference/reference_markers_gtdb.fasta -out GCF_000025845.1_ASM2584v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:14,501] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:14,505] [INFO] Selected 16 target genomes.
[2024-01-24 13:50:14,506] [INFO] Target genome list was writen to GCF_000025845.1_ASM2584v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:14,552] [INFO] Task started: fastANI
[2024-01-24 13:50:14,553] [INFO] Running command: fastANI --query /var/lib/cwl/stg86a6efd2-ed8f-475e-a863-97c575a564d6/GCF_000025845.1_ASM2584v1_genomic.fna.gz --refList GCF_000025845.1_ASM2584v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000025845.1_ASM2584v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:17,696] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:17,704] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:17,705] [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_000025845.1	s__Mycoplasmopsis_A crocodyli	100.0	311	311	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000178375.1	s__Mycoplasmopsis_A alligatoris	79.4468	131	311	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900660545.1	s__Mycoplasmopsis_A cynos	77.4213	50	311	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis_A	95.0	99.10	98.35	0.95	0.90	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:17,707] [INFO] GTDB search result was written to GCF_000025845.1_ASM2584v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:17,708] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:17,710] [INFO] DFAST_QC result json was written to GCF_000025845.1_ASM2584v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:17,711] [INFO] DFAST_QC completed!
[2024-01-24 13:50:17,711] [INFO] Total running time: 0h0m22s