[2024-01-25 18:28:50,471] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:28:50,472] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:28:50,473] [INFO] DQC Reference Directory: /var/lib/cwl/stg34f57274-adc6-480a-8755-11a92a114c2b/dqc_reference
[2024-01-25 18:28:51,558] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:28:51,559] [INFO] Task started: Prodigal
[2024-01-25 18:28:51,559] [INFO] Running command: gunzip -c /var/lib/cwl/stgb715fa4d-0c19-42ad-8d25-0f8a9e0c24ac/GCF_009883755.2_ASM988375v2_genomic.fna.gz | prodigal -d GCF_009883755.2_ASM988375v2_genomic.fna/cds.fna -a GCF_009883755.2_ASM988375v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:28:53,388] [INFO] Task succeeded: Prodigal
[2024-01-25 18:28:53,388] [INFO] Task started: HMMsearch
[2024-01-25 18:28:53,388] [INFO] Running command: hmmsearch --tblout GCF_009883755.2_ASM988375v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg34f57274-adc6-480a-8755-11a92a114c2b/dqc_reference/reference_markers.hmm GCF_009883755.2_ASM988375v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:28:53,649] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:28:53,650] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgb715fa4d-0c19-42ad-8d25-0f8a9e0c24ac/GCF_009883755.2_ASM988375v2_genomic.fna.gz]
[2024-01-25 18:28:53,666] [INFO] Query marker FASTA was written to GCF_009883755.2_ASM988375v2_genomic.fna/markers.fasta
[2024-01-25 18:28:53,666] [INFO] Task started: Blastn
[2024-01-25 18:28:53,666] [INFO] Running command: blastn -query GCF_009883755.2_ASM988375v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg34f57274-adc6-480a-8755-11a92a114c2b/dqc_reference/reference_markers.fasta -out GCF_009883755.2_ASM988375v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:28:54,168] [INFO] Task succeeded: Blastn
[2024-01-25 18:28:54,171] [INFO] Selected 14 target genomes.
[2024-01-25 18:28:54,171] [INFO] Target genome list was writen to GCF_009883755.2_ASM988375v2_genomic.fna/target_genomes.txt
[2024-01-25 18:28:54,172] [INFO] Task started: fastANI
[2024-01-25 18:28:54,172] [INFO] Running command: fastANI --query /var/lib/cwl/stgb715fa4d-0c19-42ad-8d25-0f8a9e0c24ac/GCF_009883755.2_ASM988375v2_genomic.fna.gz --refList GCF_009883755.2_ASM988375v2_genomic.fna/target_genomes.txt --output GCF_009883755.2_ASM988375v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:29:00,092] [INFO] Task succeeded: fastANI
[2024-01-25 18:29:00,092] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg34f57274-adc6-480a-8755-11a92a114c2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:29:00,093] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg34f57274-adc6-480a-8755-11a92a114c2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:29:00,098] [INFO] Found 5 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 18:29:00,098] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:29:00,098] [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
Malacoplasma iowae	strain=NCTC10185	GCA_900660615.1	2116	2116	type	True	99.998	426	438	95	conclusive
Malacoplasma iowae	strain=695	GCA_009883755.1	2116	2116	type	True	99.9958	438	438	95	conclusive
Malacoplasma iowae	strain=695	GCA_000227355.2	2116	2116	type	True	99.749	358	438	95	conclusive
Mycoplasmoides pirum	strain=ATCC 25960	GCA_000685905.1	2122	2122	type	True	76.0036	50	438	95	below_threshold
Mycoplasmoides pirum	strain=MPI25960	GCA_000686245.1	2122	2122	type	True	75.9184	53	438	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:29:00,099] [INFO] DFAST Taxonomy check result was written to GCF_009883755.2_ASM988375v2_genomic.fna/tc_result.tsv
[2024-01-25 18:29:00,100] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:29:00,100] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:29:00,100] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg34f57274-adc6-480a-8755-11a92a114c2b/dqc_reference/checkm_data
[2024-01-25 18:29:00,101] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:29:00,116] [INFO] Task started: CheckM
[2024-01-25 18:29:00,117] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009883755.2_ASM988375v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009883755.2_ASM988375v2_genomic.fna/checkm_input GCF_009883755.2_ASM988375v2_genomic.fna/checkm_result
[2024-01-25 18:29:12,548] [INFO] Task succeeded: CheckM
[2024-01-25 18:29:12,548] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:29:12,563] [INFO] ===== Completeness check finished =====
[2024-01-25 18:29:12,564] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:29:12,564] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009883755.2_ASM988375v2_genomic.fna/markers.fasta)
[2024-01-25 18:29:12,564] [INFO] Task started: Blastn
[2024-01-25 18:29:12,564] [INFO] Running command: blastn -query GCF_009883755.2_ASM988375v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg34f57274-adc6-480a-8755-11a92a114c2b/dqc_reference/reference_markers_gtdb.fasta -out GCF_009883755.2_ASM988375v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:29:13,199] [INFO] Task succeeded: Blastn
[2024-01-25 18:29:13,207] [INFO] Selected 17 target genomes.
[2024-01-25 18:29:13,207] [INFO] Target genome list was writen to GCF_009883755.2_ASM988375v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:29:13,208] [INFO] Task started: fastANI
[2024-01-25 18:29:13,209] [INFO] Running command: fastANI --query /var/lib/cwl/stgb715fa4d-0c19-42ad-8d25-0f8a9e0c24ac/GCF_009883755.2_ASM988375v2_genomic.fna.gz --refList GCF_009883755.2_ASM988375v2_genomic.fna/target_genomes_gtdb.txt --output GCF_009883755.2_ASM988375v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:29:18,073] [INFO] Task succeeded: fastANI
[2024-01-25 18:29:18,077] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:29:18,077] [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_900660615.1	s__Malacoplasma iowae	99.998	426	438	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmoidaceae;g__Malacoplasma	95.0	99.59	98.93	0.99	0.96	4	conclusive
GCF_000011225.1	s__Malacoplasma penetrans	76.9665	79	438	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmoidaceae;g__Malacoplasma	95.0	99.90	99.90	1.00	1.00	2	-
GCF_000685905.1	s__Mycoplasmoides pirum	75.9755	51	438	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmoidaceae;g__Mycoplasmoides	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:29:18,079] [INFO] GTDB search result was written to GCF_009883755.2_ASM988375v2_genomic.fna/result_gtdb.tsv
[2024-01-25 18:29:18,079] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:29:18,081] [INFO] DFAST_QC result json was written to GCF_009883755.2_ASM988375v2_genomic.fna/dqc_result.json
[2024-01-25 18:29:18,081] [INFO] DFAST_QC completed!
[2024-01-25 18:29:18,081] [INFO] Total running time: 0h0m28s