[2024-01-24 14:30:34,061] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:34,066] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:34,066] [INFO] DQC Reference Directory: /var/lib/cwl/stg13e4211f-3ad8-481a-a7be-0f4e9e547dac/dqc_reference
[2024-01-24 14:30:35,476] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:35,477] [INFO] Task started: Prodigal
[2024-01-24 14:30:35,477] [INFO] Running command: gunzip -c /var/lib/cwl/stgcdcbaf8a-1c22-4b75-9a38-d94cbdb1c99a/GCF_006385185.1_ASM638518v1_genomic.fna.gz | prodigal -d GCF_006385185.1_ASM638518v1_genomic.fna/cds.fna -a GCF_006385185.1_ASM638518v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:30:36,776] [INFO] Task succeeded: Prodigal
[2024-01-24 14:30:36,776] [INFO] Task started: HMMsearch
[2024-01-24 14:30:36,776] [INFO] Running command: hmmsearch --tblout GCF_006385185.1_ASM638518v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg13e4211f-3ad8-481a-a7be-0f4e9e547dac/dqc_reference/reference_markers.hmm GCF_006385185.1_ASM638518v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:30:37,023] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:30:37,025] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgcdcbaf8a-1c22-4b75-9a38-d94cbdb1c99a/GCF_006385185.1_ASM638518v1_genomic.fna.gz]
[2024-01-24 14:30:37,039] [INFO] Query marker FASTA was written to GCF_006385185.1_ASM638518v1_genomic.fna/markers.fasta
[2024-01-24 14:30:37,039] [INFO] Task started: Blastn
[2024-01-24 14:30:37,039] [INFO] Running command: blastn -query GCF_006385185.1_ASM638518v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg13e4211f-3ad8-481a-a7be-0f4e9e547dac/dqc_reference/reference_markers.fasta -out GCF_006385185.1_ASM638518v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:37,628] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:37,631] [INFO] Selected 10 target genomes.
[2024-01-24 14:30:37,631] [INFO] Target genome list was writen to GCF_006385185.1_ASM638518v1_genomic.fna/target_genomes.txt
[2024-01-24 14:30:37,636] [INFO] Task started: fastANI
[2024-01-24 14:30:37,636] [INFO] Running command: fastANI --query /var/lib/cwl/stgcdcbaf8a-1c22-4b75-9a38-d94cbdb1c99a/GCF_006385185.1_ASM638518v1_genomic.fna.gz --refList GCF_006385185.1_ASM638518v1_genomic.fna/target_genomes.txt --output GCF_006385185.1_ASM638518v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:30:39,468] [INFO] Task succeeded: fastANI
[2024-01-24 14:30:39,468] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg13e4211f-3ad8-481a-a7be-0f4e9e547dac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:30:39,469] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg13e4211f-3ad8-481a-a7be-0f4e9e547dac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:30:39,474] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:30:39,475] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:30:39,475] [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 anseris	strain=ATCC 49234	GCA_000702805.1	92400	92400	type	True	77.9782	62	225	95	below_threshold
Metamycoplasma orale	strain=NCTC10112	GCA_900660435.1	2121	2121	type	True	77.8966	50	225	95	below_threshold
Metamycoplasma orale	strain=ATCC 23714	GCA_000420105.1	2121	2121	type	True	77.8756	51	225	95	below_threshold
Metamycoplasma anseris	strain=ATCC 49234	GCA_003285045.1	92400	92400	type	True	77.7423	63	225	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:30:39,476] [INFO] DFAST Taxonomy check result was written to GCF_006385185.1_ASM638518v1_genomic.fna/tc_result.tsv
[2024-01-24 14:30:39,477] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:30:39,477] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:30:39,477] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg13e4211f-3ad8-481a-a7be-0f4e9e547dac/dqc_reference/checkm_data
[2024-01-24 14:30:39,478] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:30:39,489] [INFO] Task started: CheckM
[2024-01-24 14:30:39,489] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006385185.1_ASM638518v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006385185.1_ASM638518v1_genomic.fna/checkm_input GCF_006385185.1_ASM638518v1_genomic.fna/checkm_result
[2024-01-24 14:30:53,032] [INFO] Task succeeded: CheckM
[2024-01-24 14:30:53,034] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:30:53,051] [INFO] ===== Completeness check finished =====
[2024-01-24 14:30:53,051] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:30:53,051] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006385185.1_ASM638518v1_genomic.fna/markers.fasta)
[2024-01-24 14:30:53,052] [INFO] Task started: Blastn
[2024-01-24 14:30:53,052] [INFO] Running command: blastn -query GCF_006385185.1_ASM638518v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg13e4211f-3ad8-481a-a7be-0f4e9e547dac/dqc_reference/reference_markers_gtdb.fasta -out GCF_006385185.1_ASM638518v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:53,810] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:53,813] [INFO] Selected 16 target genomes.
[2024-01-24 14:30:53,814] [INFO] Target genome list was writen to GCF_006385185.1_ASM638518v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:30:53,841] [INFO] Task started: fastANI
[2024-01-24 14:30:53,841] [INFO] Running command: fastANI --query /var/lib/cwl/stgcdcbaf8a-1c22-4b75-9a38-d94cbdb1c99a/GCF_006385185.1_ASM638518v1_genomic.fna.gz --refList GCF_006385185.1_ASM638518v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006385185.1_ASM638518v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:30:57,563] [INFO] Task succeeded: fastANI
[2024-01-24 14:30:57,571] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:30:57,571] [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_006385185.1	s__Metamycoplasma equirhinis	100.0	225	225	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_003332325.1	s__Metamycoplasma phocidae	78.959	83	225	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006385795.1	s__Metamycoplasma falconis	78.6493	61	225	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000828855.1	s__Metamycoplasma canadense	78.6435	66	225	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620005.1	s__Metamycoplasma spumans	78.2921	75	225	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000702805.1	s__Metamycoplasma anseris	77.9995	61	225	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000420105.1	s__Metamycoplasma orale	77.8756	51	225	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006491995.1	s__Metamycoplasma neophronis	77.7958	72	225	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:30:57,573] [INFO] GTDB search result was written to GCF_006385185.1_ASM638518v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:30:57,574] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:30:57,576] [INFO] DFAST_QC result json was written to GCF_006385185.1_ASM638518v1_genomic.fna/dqc_result.json
[2024-01-24 14:30:57,576] [INFO] DFAST_QC completed!
[2024-01-24 14:30:57,577] [INFO] Total running time: 0h0m24s