[2024-01-24 14:38:45,551] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:38:45,553] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:38:45,554] [INFO] DQC Reference Directory: /var/lib/cwl/stgb514c6b7-c1d5-4c9c-a7a5-63f64ba87f2c/dqc_reference
[2024-01-24 14:38:48,275] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:38:48,277] [INFO] Task started: Prodigal
[2024-01-24 14:38:48,278] [INFO] Running command: gunzip -c /var/lib/cwl/stg5235135c-872e-4590-a522-91eb172be05b/GCF_004335995.1_5H_genomic.fna.gz | prodigal -d GCF_004335995.1_5H_genomic.fna/cds.fna -a GCF_004335995.1_5H_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:38:51,250] [INFO] Task succeeded: Prodigal
[2024-01-24 14:38:51,250] [INFO] Task started: HMMsearch
[2024-01-24 14:38:51,251] [INFO] Running command: hmmsearch --tblout GCF_004335995.1_5H_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb514c6b7-c1d5-4c9c-a7a5-63f64ba87f2c/dqc_reference/reference_markers.hmm GCF_004335995.1_5H_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:38:51,557] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:38:51,558] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg5235135c-872e-4590-a522-91eb172be05b/GCF_004335995.1_5H_genomic.fna.gz]
[2024-01-24 14:38:51,574] [INFO] Query marker FASTA was written to GCF_004335995.1_5H_genomic.fna/markers.fasta
[2024-01-24 14:38:51,575] [INFO] Task started: Blastn
[2024-01-24 14:38:51,575] [INFO] Running command: blastn -query GCF_004335995.1_5H_genomic.fna/markers.fasta -db /var/lib/cwl/stgb514c6b7-c1d5-4c9c-a7a5-63f64ba87f2c/dqc_reference/reference_markers.fasta -out GCF_004335995.1_5H_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:38:55,135] [INFO] Task succeeded: Blastn
[2024-01-24 14:38:55,139] [INFO] Selected 12 target genomes.
[2024-01-24 14:38:55,139] [INFO] Target genome list was writen to GCF_004335995.1_5H_genomic.fna/target_genomes.txt
[2024-01-24 14:38:55,280] [INFO] Task started: fastANI
[2024-01-24 14:38:55,280] [INFO] Running command: fastANI --query /var/lib/cwl/stg5235135c-872e-4590-a522-91eb172be05b/GCF_004335995.1_5H_genomic.fna.gz --refList GCF_004335995.1_5H_genomic.fna/target_genomes.txt --output GCF_004335995.1_5H_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:38:58,428] [INFO] Task succeeded: fastANI
[2024-01-24 14:38:58,428] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb514c6b7-c1d5-4c9c-a7a5-63f64ba87f2c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:38:58,428] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb514c6b7-c1d5-4c9c-a7a5-63f64ba87f2c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:38:58,435] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:38:58,435] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:38:58,435] [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
Mycoplasma todarodis	strain=5H	GCA_004335995.1	1937191	1937191	type	True	100.0	295	296	95	conclusive
Mycoplasma marinum	strain=PE	GCA_004335975.1	1937190	1937190	type	True	79.5355	101	296	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:38:58,436] [INFO] DFAST Taxonomy check result was written to GCF_004335995.1_5H_genomic.fna/tc_result.tsv
[2024-01-24 14:38:58,437] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:38:58,437] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:38:58,437] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb514c6b7-c1d5-4c9c-a7a5-63f64ba87f2c/dqc_reference/checkm_data
[2024-01-24 14:38:58,439] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:38:58,453] [INFO] Task started: CheckM
[2024-01-24 14:38:58,454] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004335995.1_5H_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004335995.1_5H_genomic.fna/checkm_input GCF_004335995.1_5H_genomic.fna/checkm_result
[2024-01-24 14:39:20,313] [INFO] Task succeeded: CheckM
[2024-01-24 14:39:20,314] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.20%
Contamintation: 0.93%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2024-01-24 14:39:20,333] [INFO] ===== Completeness check finished =====
[2024-01-24 14:39:20,333] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:39:20,334] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004335995.1_5H_genomic.fna/markers.fasta)
[2024-01-24 14:39:20,334] [INFO] Task started: Blastn
[2024-01-24 14:39:20,334] [INFO] Running command: blastn -query GCF_004335995.1_5H_genomic.fna/markers.fasta -db /var/lib/cwl/stgb514c6b7-c1d5-4c9c-a7a5-63f64ba87f2c/dqc_reference/reference_markers_gtdb.fasta -out GCF_004335995.1_5H_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:20,805] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:20,809] [INFO] Selected 12 target genomes.
[2024-01-24 14:39:20,809] [INFO] Target genome list was writen to GCF_004335995.1_5H_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:39:20,819] [INFO] Task started: fastANI
[2024-01-24 14:39:20,819] [INFO] Running command: fastANI --query /var/lib/cwl/stg5235135c-872e-4590-a522-91eb172be05b/GCF_004335995.1_5H_genomic.fna.gz --refList GCF_004335995.1_5H_genomic.fna/target_genomes_gtdb.txt --output GCF_004335995.1_5H_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:39:23,949] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:23,954] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:39:23,955] [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_004335995.1	s__Mycoplasma_K todarodis	100.0	295	296	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasma_K	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013215715.1	s__Mycoplasma_K sp013215715	83.4674	169	296	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasma_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004335975.1	s__Mycoplasma_K marinum	79.5355	101	296	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasma_K	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:39:23,956] [INFO] GTDB search result was written to GCF_004335995.1_5H_genomic.fna/result_gtdb.tsv
[2024-01-24 14:39:23,957] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:39:23,959] [INFO] DFAST_QC result json was written to GCF_004335995.1_5H_genomic.fna/dqc_result.json
[2024-01-24 14:39:23,959] [INFO] DFAST_QC completed!
[2024-01-24 14:39:23,959] [INFO] Total running time: 0h0m38s