[2024-01-24 13:49:11,451] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:11,453] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:11,453] [INFO] DQC Reference Directory: /var/lib/cwl/stgf009f693-69a5-499c-b4d2-61e1e68120f2/dqc_reference
[2024-01-24 13:49:12,737] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:12,738] [INFO] Task started: Prodigal
[2024-01-24 13:49:12,738] [INFO] Running command: gunzip -c /var/lib/cwl/stg2235a2c3-9dd8-4d96-8077-44b9409b85e3/GCF_003855455.1_ASM385545v1_genomic.fna.gz | prodigal -d GCF_003855455.1_ASM385545v1_genomic.fna/cds.fna -a GCF_003855455.1_ASM385545v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:13,808] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:13,808] [INFO] Task started: HMMsearch
[2024-01-24 13:49:13,808] [INFO] Running command: hmmsearch --tblout GCF_003855455.1_ASM385545v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf009f693-69a5-499c-b4d2-61e1e68120f2/dqc_reference/reference_markers.hmm GCF_003855455.1_ASM385545v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:13,951] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:13,952] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg2235a2c3-9dd8-4d96-8077-44b9409b85e3/GCF_003855455.1_ASM385545v1_genomic.fna.gz]
[2024-01-24 13:49:13,968] [INFO] Query marker FASTA was written to GCF_003855455.1_ASM385545v1_genomic.fna/markers.fasta
[2024-01-24 13:49:13,968] [INFO] Task started: Blastn
[2024-01-24 13:49:13,969] [INFO] Running command: blastn -query GCF_003855455.1_ASM385545v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf009f693-69a5-499c-b4d2-61e1e68120f2/dqc_reference/reference_markers.fasta -out GCF_003855455.1_ASM385545v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:14,528] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:14,531] [INFO] Selected 14 target genomes.
[2024-01-24 13:49:14,532] [INFO] Target genome list was writen to GCF_003855455.1_ASM385545v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:14,556] [INFO] Task started: fastANI
[2024-01-24 13:49:14,556] [INFO] Running command: fastANI --query /var/lib/cwl/stg2235a2c3-9dd8-4d96-8077-44b9409b85e3/GCF_003855455.1_ASM385545v1_genomic.fna.gz --refList GCF_003855455.1_ASM385545v1_genomic.fna/target_genomes.txt --output GCF_003855455.1_ASM385545v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:19,697] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:19,697] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf009f693-69a5-499c-b4d2-61e1e68120f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:19,698] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf009f693-69a5-499c-b4d2-61e1e68120f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:19,704] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:19,704] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:19,704] [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
Mycoplasma struthionis	strain=237IA	GCA_003855455.1	538220	538220	type	True	100.0	241	245	95	conclusive
Metamycoplasma anseris	strain=ATCC 49234	GCA_003285045.1	92400	92400	type	True	79.1116	72	245	95	below_threshold
Metamycoplasma anseris	strain=ATCC 49234	GCA_000702805.1	92400	92400	type	True	78.8162	71	245	95	below_threshold
Metamycoplasma orale	strain=NCTC10112	GCA_900660435.1	2121	2121	type	True	77.8622	64	245	95	below_threshold
Metamycoplasma orale	strain=ATCC 23714	GCA_000420105.1	2121	2121	type	True	77.6398	67	245	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:19,705] [INFO] DFAST Taxonomy check result was written to GCF_003855455.1_ASM385545v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:19,706] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:19,706] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:19,706] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf009f693-69a5-499c-b4d2-61e1e68120f2/dqc_reference/checkm_data
[2024-01-24 13:49:19,707] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:19,718] [INFO] Task started: CheckM
[2024-01-24 13:49:19,718] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003855455.1_ASM385545v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003855455.1_ASM385545v1_genomic.fna/checkm_input GCF_003855455.1_ASM385545v1_genomic.fna/checkm_result
[2024-01-24 13:49:32,474] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:32,475] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:32,492] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:32,493] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:32,493] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003855455.1_ASM385545v1_genomic.fna/markers.fasta)
[2024-01-24 13:49:32,493] [INFO] Task started: Blastn
[2024-01-24 13:49:32,493] [INFO] Running command: blastn -query GCF_003855455.1_ASM385545v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf009f693-69a5-499c-b4d2-61e1e68120f2/dqc_reference/reference_markers_gtdb.fasta -out GCF_003855455.1_ASM385545v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:33,029] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:33,032] [INFO] Selected 18 target genomes.
[2024-01-24 13:49:33,033] [INFO] Target genome list was writen to GCF_003855455.1_ASM385545v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:33,049] [INFO] Task started: fastANI
[2024-01-24 13:49:33,050] [INFO] Running command: fastANI --query /var/lib/cwl/stg2235a2c3-9dd8-4d96-8077-44b9409b85e3/GCF_003855455.1_ASM385545v1_genomic.fna.gz --refList GCF_003855455.1_ASM385545v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003855455.1_ASM385545v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:49:37,482] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:37,491] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:49:37,491] [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_003855455.1	s__Metamycoplasma struthionis	100.0	244	245	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	98.82	98.82	0.96	0.96	2	conclusive
GCF_000620005.1	s__Metamycoplasma spumans	79.0584	86	245	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	78.9881	72	245	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	78.8162	71	245	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900476125.1	s__Metamycoplasma alkalescens	78.783	76	245	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	99.14	98.30	0.97	0.94	3	-
GCF_006385795.1	s__Metamycoplasma falconis	78.6315	81	245	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003332325.1	s__Metamycoplasma phocidae	78.5439	73	245	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900660445.2	s__Metamycoplasma salivarium	78.3145	56	245	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000420105.1	s__Metamycoplasma orale	77.6883	66	245	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 13:49:37,493] [INFO] GTDB search result was written to GCF_003855455.1_ASM385545v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:49:37,493] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:49:37,496] [INFO] DFAST_QC result json was written to GCF_003855455.1_ASM385545v1_genomic.fna/dqc_result.json
[2024-01-24 13:49:37,496] [INFO] DFAST_QC completed!
[2024-01-24 13:49:37,496] [INFO] Total running time: 0h0m26s