[2024-01-24 13:33:40,968] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:33:40,970] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:33:40,970] [INFO] DQC Reference Directory: /var/lib/cwl/stg9cc6c617-bc95-4b42-b3aa-8c5d7ead436d/dqc_reference
[2024-01-24 13:33:42,197] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:33:42,198] [INFO] Task started: Prodigal
[2024-01-24 13:33:42,198] [INFO] Running command: gunzip -c /var/lib/cwl/stgcc1b4e31-52b3-4edf-9287-a95b838b7623/GCF_900660695.1_57612_E01-3_genomic.fna.gz | prodigal -d GCF_900660695.1_57612_E01-3_genomic.fna/cds.fna -a GCF_900660695.1_57612_E01-3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:33:43,177] [INFO] Task succeeded: Prodigal
[2024-01-24 13:33:43,177] [INFO] Task started: HMMsearch
[2024-01-24 13:33:43,177] [INFO] Running command: hmmsearch --tblout GCF_900660695.1_57612_E01-3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9cc6c617-bc95-4b42-b3aa-8c5d7ead436d/dqc_reference/reference_markers.hmm GCF_900660695.1_57612_E01-3_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:33:43,347] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:33:43,349] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgcc1b4e31-52b3-4edf-9287-a95b838b7623/GCF_900660695.1_57612_E01-3_genomic.fna.gz]
[2024-01-24 13:33:43,360] [INFO] Query marker FASTA was written to GCF_900660695.1_57612_E01-3_genomic.fna/markers.fasta
[2024-01-24 13:33:43,360] [INFO] Task started: Blastn
[2024-01-24 13:33:43,360] [INFO] Running command: blastn -query GCF_900660695.1_57612_E01-3_genomic.fna/markers.fasta -db /var/lib/cwl/stg9cc6c617-bc95-4b42-b3aa-8c5d7ead436d/dqc_reference/reference_markers.fasta -out GCF_900660695.1_57612_E01-3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:43,848] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:43,853] [INFO] Selected 10 target genomes.
[2024-01-24 13:33:43,854] [INFO] Target genome list was writen to GCF_900660695.1_57612_E01-3_genomic.fna/target_genomes.txt
[2024-01-24 13:33:43,937] [INFO] Task started: fastANI
[2024-01-24 13:33:43,937] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc1b4e31-52b3-4edf-9287-a95b838b7623/GCF_900660695.1_57612_E01-3_genomic.fna.gz --refList GCF_900660695.1_57612_E01-3_genomic.fna/target_genomes.txt --output GCF_900660695.1_57612_E01-3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:46,608] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:46,608] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9cc6c617-bc95-4b42-b3aa-8c5d7ead436d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:46,609] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9cc6c617-bc95-4b42-b3aa-8c5d7ead436d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:46,620] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:33:46,620] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:46,620] [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 meleagridis	strain=NCTC10153	GCA_900660695.1	29561	29561	type	True	100.0	214	214	95	conclusive
Mycoplasmopsis meleagridis	strain=ATCC 25294	GCA_000969625.1	29561	29561	type	True	99.964	203	214	95	conclusive
Mycoplasmopsis iners	strain=ATCC 19705	GCA_000701805.1	76630	76630	type	True	78.554	69	214	95	below_threshold
Mycoplasmopsis columbina	strain=NCTC10178	GCA_900660685.1	114881	114881	type	True	78.094	74	214	95	below_threshold
Mycoplasmopsis columbina	strain=ATCC 29257	GCA_000712175.1	114881	114881	type	True	77.639	75	214	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:46,622] [INFO] DFAST Taxonomy check result was written to GCF_900660695.1_57612_E01-3_genomic.fna/tc_result.tsv
[2024-01-24 13:33:46,630] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:46,630] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:46,630] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9cc6c617-bc95-4b42-b3aa-8c5d7ead436d/dqc_reference/checkm_data
[2024-01-24 13:33:46,632] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:46,648] [INFO] Task started: CheckM
[2024-01-24 13:33:46,649] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900660695.1_57612_E01-3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900660695.1_57612_E01-3_genomic.fna/checkm_input GCF_900660695.1_57612_E01-3_genomic.fna/checkm_result
[2024-01-24 13:33:58,382] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:58,383] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:58,400] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:58,400] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:58,401] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900660695.1_57612_E01-3_genomic.fna/markers.fasta)
[2024-01-24 13:33:58,401] [INFO] Task started: Blastn
[2024-01-24 13:33:58,401] [INFO] Running command: blastn -query GCF_900660695.1_57612_E01-3_genomic.fna/markers.fasta -db /var/lib/cwl/stg9cc6c617-bc95-4b42-b3aa-8c5d7ead436d/dqc_reference/reference_markers_gtdb.fasta -out GCF_900660695.1_57612_E01-3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:58,846] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:58,850] [INFO] Selected 16 target genomes.
[2024-01-24 13:33:58,850] [INFO] Target genome list was writen to GCF_900660695.1_57612_E01-3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:58,918] [INFO] Task started: fastANI
[2024-01-24 13:33:58,918] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc1b4e31-52b3-4edf-9287-a95b838b7623/GCF_900660695.1_57612_E01-3_genomic.fna.gz --refList GCF_900660695.1_57612_E01-3_genomic.fna/target_genomes_gtdb.txt --output GCF_900660695.1_57612_E01-3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:01,523] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:01,530] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:01,531] [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_900660695.1	s__Mycoplasmopsis meleagridis	100.0	214	214	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis	95.0	99.56	98.69	0.99	0.98	4	conclusive
GCF_000701805.1	s__Mycoplasmopsis iners	78.554	69	214	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900660685.1	s__Mycoplasmopsis columbina	78.094	74	214	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis	95.0	99.36	98.73	0.99	0.99	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:01,533] [INFO] GTDB search result was written to GCF_900660695.1_57612_E01-3_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:01,534] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:01,536] [INFO] DFAST_QC result json was written to GCF_900660695.1_57612_E01-3_genomic.fna/dqc_result.json
[2024-01-24 13:34:01,536] [INFO] DFAST_QC completed!
[2024-01-24 13:34:01,536] [INFO] Total running time: 0h0m21s