[2024-01-24 14:39:34,335] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:34,337] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:34,337] [INFO] DQC Reference Directory: /var/lib/cwl/stgfc24a679-17e3-4e35-928d-dfb4a55b5032/dqc_reference
[2024-01-24 14:39:36,896] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:36,897] [INFO] Task started: Prodigal
[2024-01-24 14:39:36,897] [INFO] Running command: gunzip -c /var/lib/cwl/stg10e06c59-c84d-4e2a-b369-8d0069e76ab3/GCF_003253435.1_ASM325343v1_genomic.fna.gz | prodigal -d GCF_003253435.1_ASM325343v1_genomic.fna/cds.fna -a GCF_003253435.1_ASM325343v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:38,160] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:38,160] [INFO] Task started: HMMsearch
[2024-01-24 14:39:38,160] [INFO] Running command: hmmsearch --tblout GCF_003253435.1_ASM325343v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfc24a679-17e3-4e35-928d-dfb4a55b5032/dqc_reference/reference_markers.hmm GCF_003253435.1_ASM325343v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:38,460] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:38,461] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg10e06c59-c84d-4e2a-b369-8d0069e76ab3/GCF_003253435.1_ASM325343v1_genomic.fna.gz]
[2024-01-24 14:39:38,481] [INFO] Query marker FASTA was written to GCF_003253435.1_ASM325343v1_genomic.fna/markers.fasta
[2024-01-24 14:39:38,485] [INFO] Task started: Blastn
[2024-01-24 14:39:38,486] [INFO] Running command: blastn -query GCF_003253435.1_ASM325343v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc24a679-17e3-4e35-928d-dfb4a55b5032/dqc_reference/reference_markers.fasta -out GCF_003253435.1_ASM325343v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:42,598] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:42,602] [INFO] Selected 18 target genomes.
[2024-01-24 14:39:42,602] [INFO] Target genome list was writen to GCF_003253435.1_ASM325343v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:42,744] [INFO] Task started: fastANI
[2024-01-24 14:39:42,745] [INFO] Running command: fastANI --query /var/lib/cwl/stg10e06c59-c84d-4e2a-b369-8d0069e76ab3/GCF_003253435.1_ASM325343v1_genomic.fna.gz --refList GCF_003253435.1_ASM325343v1_genomic.fna/target_genomes.txt --output GCF_003253435.1_ASM325343v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:46,876] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:46,877] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfc24a679-17e3-4e35-928d-dfb4a55b5032/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:46,877] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfc24a679-17e3-4e35-928d-dfb4a55b5032/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:46,945] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:39:46,946] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:39:46,946] [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
Metamycoplasma auris	strain=ATCC 51348	GCA_003253435.1	51363	51363	type	True	100.0	230	231	95	conclusive
Metamycoplasma alkalescens	strain=ATCC 29103	GCA_003208575.1	45363	45363	type	True	80.1643	117	231	95	below_threshold
Metamycoplasma alkalescens	strain=NCTC10135	GCA_900476125.1	45363	45363	type	True	80.0301	130	231	95	below_threshold
Metamycoplasma anseris	strain=ATCC 49234	GCA_003285045.1	92400	92400	type	True	78.3867	55	231	95	below_threshold
Metamycoplasma anseris	strain=ATCC 49234	GCA_000702805.1	92400	92400	type	True	78.3468	53	231	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:46,947] [INFO] DFAST Taxonomy check result was written to GCF_003253435.1_ASM325343v1_genomic.fna/tc_result.tsv
[2024-01-24 14:39:46,948] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:46,948] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:46,948] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfc24a679-17e3-4e35-928d-dfb4a55b5032/dqc_reference/checkm_data
[2024-01-24 14:39:46,956] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:46,968] [INFO] Task started: CheckM
[2024-01-24 14:39:46,968] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003253435.1_ASM325343v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003253435.1_ASM325343v1_genomic.fna/checkm_input GCF_003253435.1_ASM325343v1_genomic.fna/checkm_result
[2024-01-24 14:40:03,862] [INFO] Task succeeded: CheckM
[2024-01-24 14:40:03,863] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:40:03,884] [INFO] ===== Completeness check finished =====
[2024-01-24 14:40:03,884] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:40:03,885] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003253435.1_ASM325343v1_genomic.fna/markers.fasta)
[2024-01-24 14:40:03,886] [INFO] Task started: Blastn
[2024-01-24 14:40:03,886] [INFO] Running command: blastn -query GCF_003253435.1_ASM325343v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc24a679-17e3-4e35-928d-dfb4a55b5032/dqc_reference/reference_markers_gtdb.fasta -out GCF_003253435.1_ASM325343v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:05,240] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:05,244] [INFO] Selected 19 target genomes.
[2024-01-24 14:40:05,244] [INFO] Target genome list was writen to GCF_003253435.1_ASM325343v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:40:05,271] [INFO] Task started: fastANI
[2024-01-24 14:40:05,271] [INFO] Running command: fastANI --query /var/lib/cwl/stg10e06c59-c84d-4e2a-b369-8d0069e76ab3/GCF_003253435.1_ASM325343v1_genomic.fna.gz --refList GCF_003253435.1_ASM325343v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003253435.1_ASM325343v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:40:09,683] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:09,710] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:40:09,711] [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_003253435.1	s__Metamycoplasma auris	100.0	230	231	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000367765.1	s__Metamycoplasma auris_A	84.0941	187	231	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900476125.1	s__Metamycoplasma alkalescens	80.0714	129	231	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	99.14	98.30	0.97	0.94	3	-
GCF_900660725.1	s__Metamycoplasma arginini	79.0975	104	231	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	98.27	98.11	0.94	0.92	6	-
GCF_000828855.1	s__Metamycoplasma canadense	79.0852	98	231	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003383595.3	s__Metamycoplasma phocicerebrale	78.6071	78	231	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017116825.1	s__Metamycoplasma enhydrae	78.5454	77	231	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003855455.1	s__Metamycoplasma struthionis	78.443	56	231	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	98.82	98.82	0.96	0.96	2	-
GCF_000702805.1	s__Metamycoplasma anseris	78.3468	53	231	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:40:09,712] [INFO] GTDB search result was written to GCF_003253435.1_ASM325343v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:40:09,713] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:40:09,716] [INFO] DFAST_QC result json was written to GCF_003253435.1_ASM325343v1_genomic.fna/dqc_result.json
[2024-01-24 14:40:09,716] [INFO] DFAST_QC completed!
[2024-01-24 14:40:09,717] [INFO] Total running time: 0h0m35s