[2024-01-24 15:02:23,240] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:23,242] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:23,242] [INFO] DQC Reference Directory: /var/lib/cwl/stg53b10a66-37b6-4e45-960f-d02e6df23448/dqc_reference
[2024-01-24 15:02:24,444] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:24,445] [INFO] Task started: Prodigal
[2024-01-24 15:02:24,445] [INFO] Running command: gunzip -c /var/lib/cwl/stg6a9cf675-f64f-428b-aa79-519af8e47875/GCF_900660485.1_50648_E01-3_genomic.fna.gz | prodigal -d GCF_900660485.1_50648_E01-3_genomic.fna/cds.fna -a GCF_900660485.1_50648_E01-3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:25,996] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:25,996] [INFO] Task started: HMMsearch
[2024-01-24 15:02:25,997] [INFO] Running command: hmmsearch --tblout GCF_900660485.1_50648_E01-3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg53b10a66-37b6-4e45-960f-d02e6df23448/dqc_reference/reference_markers.hmm GCF_900660485.1_50648_E01-3_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:26,308] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:26,310] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg6a9cf675-f64f-428b-aa79-519af8e47875/GCF_900660485.1_50648_E01-3_genomic.fna.gz]
[2024-01-24 15:02:26,331] [INFO] Query marker FASTA was written to GCF_900660485.1_50648_E01-3_genomic.fna/markers.fasta
[2024-01-24 15:02:26,332] [INFO] Task started: Blastn
[2024-01-24 15:02:26,332] [INFO] Running command: blastn -query GCF_900660485.1_50648_E01-3_genomic.fna/markers.fasta -db /var/lib/cwl/stg53b10a66-37b6-4e45-960f-d02e6df23448/dqc_reference/reference_markers.fasta -out GCF_900660485.1_50648_E01-3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:29,551] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:29,555] [INFO] Selected 16 target genomes.
[2024-01-24 15:02:29,555] [INFO] Target genome list was writen to GCF_900660485.1_50648_E01-3_genomic.fna/target_genomes.txt
[2024-01-24 15:02:29,643] [INFO] Task started: fastANI
[2024-01-24 15:02:29,643] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a9cf675-f64f-428b-aa79-519af8e47875/GCF_900660485.1_50648_E01-3_genomic.fna.gz --refList GCF_900660485.1_50648_E01-3_genomic.fna/target_genomes.txt --output GCF_900660485.1_50648_E01-3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:02:33,413] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:33,414] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg53b10a66-37b6-4e45-960f-d02e6df23448/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:02:33,414] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg53b10a66-37b6-4e45-960f-d02e6df23448/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:02:33,423] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:02:33,423] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:02:33,423] [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 neurolyticum	strain=NCTC10166	GCA_900660485.1	2120	2120	type	True	100.0	341	345	95	conclusive
Mesomycoplasma collis	strain=ATCC 35278	GCA_000701825.1	2127	2127	type	True	79.2669	178	345	95	below_threshold
Mesomycoplasma molare	strain=ATCC 27746	GCA_000622165.1	171288	171288	type	True	77.1612	85	345	95	below_threshold
Mesomycoplasma molare	strain=H 542	GCA_024918955.1	171288	171288	type	True	77.1226	85	345	95	below_threshold
Mycoplasma procyoni	strain=LR5794	GCA_017052595.1	568784	568784	type	True	77.0881	51	345	95	below_threshold
Mycoplasmopsis cricetuli	strain=ATCC 35279	GCA_000526955.1	171283	171283	type	True	75.844	75	345	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:02:33,425] [INFO] DFAST Taxonomy check result was written to GCF_900660485.1_50648_E01-3_genomic.fna/tc_result.tsv
[2024-01-24 15:02:33,425] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:02:33,426] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:02:33,426] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg53b10a66-37b6-4e45-960f-d02e6df23448/dqc_reference/checkm_data
[2024-01-24 15:02:33,427] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:02:33,440] [INFO] Task started: CheckM
[2024-01-24 15:02:33,441] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900660485.1_50648_E01-3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900660485.1_50648_E01-3_genomic.fna/checkm_input GCF_900660485.1_50648_E01-3_genomic.fna/checkm_result
[2024-01-24 15:02:50,890] [INFO] Task succeeded: CheckM
[2024-01-24 15:02:50,891] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:02:50,910] [INFO] ===== Completeness check finished =====
[2024-01-24 15:02:50,910] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:02:50,911] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900660485.1_50648_E01-3_genomic.fna/markers.fasta)
[2024-01-24 15:02:50,911] [INFO] Task started: Blastn
[2024-01-24 15:02:50,911] [INFO] Running command: blastn -query GCF_900660485.1_50648_E01-3_genomic.fna/markers.fasta -db /var/lib/cwl/stg53b10a66-37b6-4e45-960f-d02e6df23448/dqc_reference/reference_markers_gtdb.fasta -out GCF_900660485.1_50648_E01-3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:51,445] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:51,466] [INFO] Selected 13 target genomes.
[2024-01-24 15:02:51,466] [INFO] Target genome list was writen to GCF_900660485.1_50648_E01-3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:02:51,600] [INFO] Task started: fastANI
[2024-01-24 15:02:51,600] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a9cf675-f64f-428b-aa79-519af8e47875/GCF_900660485.1_50648_E01-3_genomic.fna.gz --refList GCF_900660485.1_50648_E01-3_genomic.fna/target_genomes_gtdb.txt --output GCF_900660485.1_50648_E01-3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:02:54,621] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:54,630] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:02:54,631] [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_900660485.1	s__Mesomycoplasma neurolyticum	100.0	343	345	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_000701825.1	s__Mesomycoplasma collis	79.2013	180	345	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mesomycoplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017052595.1	s__Mesomycoplasma procyoni	77.1406	50	345	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mesomycoplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000622165.1	s__Mesomycoplasma molare	77.1358	85	345	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mesomycoplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000526955.1	s__Mycoplasmopsis_A cricetuli	75.8609	74	345	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:02:54,634] [INFO] GTDB search result was written to GCF_900660485.1_50648_E01-3_genomic.fna/result_gtdb.tsv
[2024-01-24 15:02:54,634] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:02:54,637] [INFO] DFAST_QC result json was written to GCF_900660485.1_50648_E01-3_genomic.fna/dqc_result.json
[2024-01-24 15:02:54,637] [INFO] DFAST_QC completed!
[2024-01-24 15:02:54,638] [INFO] Total running time: 0h0m31s