[2024-01-24 14:19:59,647] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:59,649] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:59,650] [INFO] DQC Reference Directory: /var/lib/cwl/stgd88eccbb-9e4f-4ea1-a6fd-9b19d62596e2/dqc_reference
[2024-01-24 14:20:01,007] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:20:01,008] [INFO] Task started: Prodigal
[2024-01-24 14:20:01,008] [INFO] Running command: gunzip -c /var/lib/cwl/stg6b840e49-435b-434d-b683-a03b99b94b56/GCF_900660435.1_50465_D02-3_genomic.fna.gz | prodigal -d GCF_900660435.1_50465_D02-3_genomic.fna/cds.fna -a GCF_900660435.1_50465_D02-3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:20:02,293] [INFO] Task succeeded: Prodigal
[2024-01-24 14:20:02,294] [INFO] Task started: HMMsearch
[2024-01-24 14:20:02,294] [INFO] Running command: hmmsearch --tblout GCF_900660435.1_50465_D02-3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd88eccbb-9e4f-4ea1-a6fd-9b19d62596e2/dqc_reference/reference_markers.hmm GCF_900660435.1_50465_D02-3_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:20:02,456] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:20:02,458] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg6b840e49-435b-434d-b683-a03b99b94b56/GCF_900660435.1_50465_D02-3_genomic.fna.gz]
[2024-01-24 14:20:02,475] [INFO] Query marker FASTA was written to GCF_900660435.1_50465_D02-3_genomic.fna/markers.fasta
[2024-01-24 14:20:02,476] [INFO] Task started: Blastn
[2024-01-24 14:20:02,476] [INFO] Running command: blastn -query GCF_900660435.1_50465_D02-3_genomic.fna/markers.fasta -db /var/lib/cwl/stgd88eccbb-9e4f-4ea1-a6fd-9b19d62596e2/dqc_reference/reference_markers.fasta -out GCF_900660435.1_50465_D02-3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:03,003] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:03,006] [INFO] Selected 17 target genomes.
[2024-01-24 14:20:03,007] [INFO] Target genome list was writen to GCF_900660435.1_50465_D02-3_genomic.fna/target_genomes.txt
[2024-01-24 14:20:03,017] [INFO] Task started: fastANI
[2024-01-24 14:20:03,017] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b840e49-435b-434d-b683-a03b99b94b56/GCF_900660435.1_50465_D02-3_genomic.fna.gz --refList GCF_900660435.1_50465_D02-3_genomic.fna/target_genomes.txt --output GCF_900660435.1_50465_D02-3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:07,908] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:07,908] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd88eccbb-9e4f-4ea1-a6fd-9b19d62596e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:07,908] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd88eccbb-9e4f-4ea1-a6fd-9b19d62596e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:07,916] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:20:07,916] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:07,916] [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 orale	strain=NCTC10112	GCA_900660435.1	2121	2121	type	True	100.0	263	266	95	conclusive
Metamycoplasma orale	strain=ATCC 23714	GCA_000420105.1	2121	2121	type	True	99.9348	225	266	95	conclusive
Metamycoplasma salivarium	strain=ATCC 23064	GCA_000485555.1	2124	2124	type	True	78.4281	71	266	95	below_threshold
Metamycoplasma salivarium	strain=NCTC10113	GCA_900660445.2	2124	2124	type	True	78.1391	79	266	95	below_threshold
Metamycoplasma hyosynoviae	strain=ATCC 25591	GCA_004365165.1	29559	29559	type	True	78.0727	64	266	95	below_threshold
Mycoplasma struthionis	strain=237IA	GCA_003855455.1	538220	538220	type	True	78.0699	68	266	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:07,918] [INFO] DFAST Taxonomy check result was written to GCF_900660435.1_50465_D02-3_genomic.fna/tc_result.tsv
[2024-01-24 14:20:07,918] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:07,918] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:07,919] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd88eccbb-9e4f-4ea1-a6fd-9b19d62596e2/dqc_reference/checkm_data
[2024-01-24 14:20:07,920] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:07,935] [INFO] Task started: CheckM
[2024-01-24 14:20:07,935] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900660435.1_50465_D02-3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900660435.1_50465_D02-3_genomic.fna/checkm_input GCF_900660435.1_50465_D02-3_genomic.fna/checkm_result
[2024-01-24 14:20:21,536] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:21,537] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:21,557] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:21,558] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:21,558] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900660435.1_50465_D02-3_genomic.fna/markers.fasta)
[2024-01-24 14:20:21,559] [INFO] Task started: Blastn
[2024-01-24 14:20:21,559] [INFO] Running command: blastn -query GCF_900660435.1_50465_D02-3_genomic.fna/markers.fasta -db /var/lib/cwl/stgd88eccbb-9e4f-4ea1-a6fd-9b19d62596e2/dqc_reference/reference_markers_gtdb.fasta -out GCF_900660435.1_50465_D02-3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:22,041] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:22,045] [INFO] Selected 18 target genomes.
[2024-01-24 14:20:22,045] [INFO] Target genome list was writen to GCF_900660435.1_50465_D02-3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:22,060] [INFO] Task started: fastANI
[2024-01-24 14:20:22,061] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b840e49-435b-434d-b683-a03b99b94b56/GCF_900660435.1_50465_D02-3_genomic.fna.gz --refList GCF_900660435.1_50465_D02-3_genomic.fna/target_genomes_gtdb.txt --output GCF_900660435.1_50465_D02-3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:27,119] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:27,128] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:20:27,129] [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_000420105.1	s__Metamycoplasma orale	99.9348	225	266	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_000702805.1	s__Metamycoplasma anseris	78.2672	59	266	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900660445.2	s__Metamycoplasma salivarium	78.1391	79	266	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003855455.1	s__Metamycoplasma struthionis	78.0699	68	266	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	98.82	98.82	0.96	0.96	2	-
GCF_004365165.1	s__Metamycoplasma hyosynoviae	78.0175	65	266	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	98.38	98.29	0.94	0.91	9	-
GCF_006385185.1	s__Metamycoplasma equirhinis	77.5362	57	266	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 14:20:27,136] [INFO] GTDB search result was written to GCF_900660435.1_50465_D02-3_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:27,137] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:27,139] [INFO] DFAST_QC result json was written to GCF_900660435.1_50465_D02-3_genomic.fna/dqc_result.json
[2024-01-24 14:20:27,139] [INFO] DFAST_QC completed!
[2024-01-24 14:20:27,140] [INFO] Total running time: 0h0m27s