[2024-01-25 19:51:20,521] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:51:20,522] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:51:20,523] [INFO] DQC Reference Directory: /var/lib/cwl/stg52092014-5447-4507-93b4-5f0108a5856d/dqc_reference
[2024-01-25 19:51:21,698] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:51:21,698] [INFO] Task started: Prodigal
[2024-01-25 19:51:21,699] [INFO] Running command: gunzip -c /var/lib/cwl/stgbb8fcbb4-ed3e-4bd0-9426-25179f2510a8/GCF_024918955.1_ASM2491895v1_genomic.fna.gz | prodigal -d GCF_024918955.1_ASM2491895v1_genomic.fna/cds.fna -a GCF_024918955.1_ASM2491895v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:51:22,800] [INFO] Task succeeded: Prodigal
[2024-01-25 19:51:22,800] [INFO] Task started: HMMsearch
[2024-01-25 19:51:22,801] [INFO] Running command: hmmsearch --tblout GCF_024918955.1_ASM2491895v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg52092014-5447-4507-93b4-5f0108a5856d/dqc_reference/reference_markers.hmm GCF_024918955.1_ASM2491895v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:51:22,963] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:51:22,964] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgbb8fcbb4-ed3e-4bd0-9426-25179f2510a8/GCF_024918955.1_ASM2491895v1_genomic.fna.gz]
[2024-01-25 19:51:22,975] [INFO] Query marker FASTA was written to GCF_024918955.1_ASM2491895v1_genomic.fna/markers.fasta
[2024-01-25 19:51:22,975] [INFO] Task started: Blastn
[2024-01-25 19:51:22,975] [INFO] Running command: blastn -query GCF_024918955.1_ASM2491895v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52092014-5447-4507-93b4-5f0108a5856d/dqc_reference/reference_markers.fasta -out GCF_024918955.1_ASM2491895v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:51:23,437] [INFO] Task succeeded: Blastn
[2024-01-25 19:51:23,440] [INFO] Selected 13 target genomes.
[2024-01-25 19:51:23,440] [INFO] Target genome list was writen to GCF_024918955.1_ASM2491895v1_genomic.fna/target_genomes.txt
[2024-01-25 19:51:23,446] [INFO] Task started: fastANI
[2024-01-25 19:51:23,446] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb8fcbb4-ed3e-4bd0-9426-25179f2510a8/GCF_024918955.1_ASM2491895v1_genomic.fna.gz --refList GCF_024918955.1_ASM2491895v1_genomic.fna/target_genomes.txt --output GCF_024918955.1_ASM2491895v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:51:27,139] [INFO] Task succeeded: fastANI
[2024-01-25 19:51:27,139] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg52092014-5447-4507-93b4-5f0108a5856d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:51:27,140] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg52092014-5447-4507-93b4-5f0108a5856d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:51:27,144] [INFO] Found 4 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:51:27,145] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:51:27,145] [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
Mesomycoplasma molare	strain=H 542	GCA_024918955.1	171288	171288	type	True	100.0	288	289	95	conclusive
Mesomycoplasma molare	strain=ATCC 27746	GCA_000622165.1	171288	171288	type	True	99.8415	268	289	95	conclusive
Mycoplasma procyoni	strain=LR5794	GCA_017052595.1	568784	568784	type	True	78.3926	69	289	95	below_threshold
Mesomycoplasma neurolyticum	strain=NCTC10166	GCA_900660485.1	2120	2120	type	True	77.5041	88	289	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:51:27,146] [INFO] DFAST Taxonomy check result was written to GCF_024918955.1_ASM2491895v1_genomic.fna/tc_result.tsv
[2024-01-25 19:51:27,146] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:51:27,147] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:51:27,147] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg52092014-5447-4507-93b4-5f0108a5856d/dqc_reference/checkm_data
[2024-01-25 19:51:27,148] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:51:27,160] [INFO] Task started: CheckM
[2024-01-25 19:51:27,160] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024918955.1_ASM2491895v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024918955.1_ASM2491895v1_genomic.fna/checkm_input GCF_024918955.1_ASM2491895v1_genomic.fna/checkm_result
[2024-01-25 19:51:38,260] [INFO] Task succeeded: CheckM
[2024-01-25 19:51:38,261] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:51:38,282] [INFO] ===== Completeness check finished =====
[2024-01-25 19:51:38,282] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:51:38,282] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024918955.1_ASM2491895v1_genomic.fna/markers.fasta)
[2024-01-25 19:51:38,283] [INFO] Task started: Blastn
[2024-01-25 19:51:38,283] [INFO] Running command: blastn -query GCF_024918955.1_ASM2491895v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52092014-5447-4507-93b4-5f0108a5856d/dqc_reference/reference_markers_gtdb.fasta -out GCF_024918955.1_ASM2491895v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:51:38,763] [INFO] Task succeeded: Blastn
[2024-01-25 19:51:38,766] [INFO] Selected 20 target genomes.
[2024-01-25 19:51:38,766] [INFO] Target genome list was writen to GCF_024918955.1_ASM2491895v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:51:38,787] [INFO] Task started: fastANI
[2024-01-25 19:51:38,787] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb8fcbb4-ed3e-4bd0-9426-25179f2510a8/GCF_024918955.1_ASM2491895v1_genomic.fna.gz --refList GCF_024918955.1_ASM2491895v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024918955.1_ASM2491895v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:51:42,453] [INFO] Task succeeded: fastANI
[2024-01-25 19:51:42,457] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:51:42,457] [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_000622165.1	s__Mesomycoplasma molare	99.8415	268	289	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mesomycoplasma	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017052595.1	s__Mesomycoplasma procyoni	78.5099	67	289	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mesomycoplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900660485.1	s__Mesomycoplasma neurolyticum	77.5041	88	289	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mesomycoplasma	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:51:42,458] [INFO] GTDB search result was written to GCF_024918955.1_ASM2491895v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:51:42,459] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:51:42,461] [INFO] DFAST_QC result json was written to GCF_024918955.1_ASM2491895v1_genomic.fna/dqc_result.json
[2024-01-25 19:51:42,461] [INFO] DFAST_QC completed!
[2024-01-25 19:51:42,461] [INFO] Total running time: 0h0m22s