[2024-01-24 14:05:59,949] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:59,951] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:59,951] [INFO] DQC Reference Directory: /var/lib/cwl/stgafab94e6-8c9a-4dcc-848e-cf357a6da5f5/dqc_reference
[2024-01-24 14:06:01,206] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:01,207] [INFO] Task started: Prodigal
[2024-01-24 14:06:01,207] [INFO] Running command: gunzip -c /var/lib/cwl/stg4a19112e-4804-468a-ac21-31213dce9055/GCF_000209735.1_ASM20973v1_genomic.fna.gz | prodigal -d GCF_000209735.1_ASM20973v1_genomic.fna/cds.fna -a GCF_000209735.1_ASM20973v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:02,814] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:02,815] [INFO] Task started: HMMsearch
[2024-01-24 14:06:02,815] [INFO] Running command: hmmsearch --tblout GCF_000209735.1_ASM20973v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgafab94e6-8c9a-4dcc-848e-cf357a6da5f5/dqc_reference/reference_markers.hmm GCF_000209735.1_ASM20973v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:03,024] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:03,026] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg4a19112e-4804-468a-ac21-31213dce9055/GCF_000209735.1_ASM20973v1_genomic.fna.gz]
[2024-01-24 14:06:03,040] [INFO] Query marker FASTA was written to GCF_000209735.1_ASM20973v1_genomic.fna/markers.fasta
[2024-01-24 14:06:03,041] [INFO] Task started: Blastn
[2024-01-24 14:06:03,041] [INFO] Running command: blastn -query GCF_000209735.1_ASM20973v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgafab94e6-8c9a-4dcc-848e-cf357a6da5f5/dqc_reference/reference_markers.fasta -out GCF_000209735.1_ASM20973v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:03,636] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:03,648] [INFO] Selected 13 target genomes.
[2024-01-24 14:06:03,649] [INFO] Target genome list was writen to GCF_000209735.1_ASM20973v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:03,657] [INFO] Task started: fastANI
[2024-01-24 14:06:03,658] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a19112e-4804-468a-ac21-31213dce9055/GCF_000209735.1_ASM20973v1_genomic.fna.gz --refList GCF_000209735.1_ASM20973v1_genomic.fna/target_genomes.txt --output GCF_000209735.1_ASM20973v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:06,770] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:06,771] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgafab94e6-8c9a-4dcc-848e-cf357a6da5f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:06,772] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgafab94e6-8c9a-4dcc-848e-cf357a6da5f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:06,782] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:06,783] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:06,783] [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 fermentans	strain=PG18	GCA_000209735.1	2115	2115	type	True	100.0	334	334	95	conclusive
Mycoplasmopsis caviae	strain=NCTC10126	GCA_900631685.1	55603	55603	type	True	81.7173	182	334	95	below_threshold
Mycoplasmopsis caviae	strain=G122	GCA_024498215.1	55603	55603	type	True	81.588	182	334	95	below_threshold
Mycoplasmopsis lipofaciens	strain=ATCC 35015	GCA_000686585.1	114884	114884	type	True	78.3521	84	334	95	below_threshold
Mycoplasmopsis felifaucium	strain=ATCC 43428	GCA_000687775.1	35768	35768	type	True	77.986	74	334	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:06,787] [INFO] DFAST Taxonomy check result was written to GCF_000209735.1_ASM20973v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:06,787] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:06,788] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:06,788] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgafab94e6-8c9a-4dcc-848e-cf357a6da5f5/dqc_reference/checkm_data
[2024-01-24 14:06:06,789] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:06,802] [INFO] Task started: CheckM
[2024-01-24 14:06:06,802] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000209735.1_ASM20973v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000209735.1_ASM20973v1_genomic.fna/checkm_input GCF_000209735.1_ASM20973v1_genomic.fna/checkm_result
[2024-01-24 14:06:21,124] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:21,125] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:21,147] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:21,147] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:21,148] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000209735.1_ASM20973v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:21,148] [INFO] Task started: Blastn
[2024-01-24 14:06:21,148] [INFO] Running command: blastn -query GCF_000209735.1_ASM20973v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgafab94e6-8c9a-4dcc-848e-cf357a6da5f5/dqc_reference/reference_markers_gtdb.fasta -out GCF_000209735.1_ASM20973v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:21,992] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:21,997] [INFO] Selected 21 target genomes.
[2024-01-24 14:06:21,997] [INFO] Target genome list was writen to GCF_000209735.1_ASM20973v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:22,031] [INFO] Task started: fastANI
[2024-01-24 14:06:22,031] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a19112e-4804-468a-ac21-31213dce9055/GCF_000209735.1_ASM20973v1_genomic.fna.gz --refList GCF_000209735.1_ASM20973v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000209735.1_ASM20973v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:25,799] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:25,810] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:06:25,810] [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_000209735.1	s__Mycoplasmopsis fermentans	100.0	334	334	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis	95.0	99.32	98.97	0.96	0.92	5	conclusive
GCF_900631685.1	s__Mycoplasmopsis caviae	81.7574	181	334	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000686585.1	s__Mycoplasmopsis lipofaciens	78.2477	85	334	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000687775.1	s__Mycoplasmopsis felifaucium	77.986	74	334	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000621085.1	s__Mycoplasmopsis gallinarum	77.3974	59	334	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis	95.0	96.67	96.67	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:06:25,812] [INFO] GTDB search result was written to GCF_000209735.1_ASM20973v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:25,812] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:25,815] [INFO] DFAST_QC result json was written to GCF_000209735.1_ASM20973v1_genomic.fna/dqc_result.json
[2024-01-24 14:06:25,815] [INFO] DFAST_QC completed!
[2024-01-24 14:06:25,816] [INFO] Total running time: 0h0m26s