[2024-01-25 18:55:35,768] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:55:35,770] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:55:35,770] [INFO] DQC Reference Directory: /var/lib/cwl/stgfe2f3f4e-6ccb-4c77-8735-d3f57db5636b/dqc_reference
[2024-01-25 18:55:36,899] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:55:36,899] [INFO] Task started: Prodigal
[2024-01-25 18:55:36,899] [INFO] Running command: gunzip -c /var/lib/cwl/stge89da6e7-bd7a-4340-806c-6018151a9277/GCF_003583385.1_ASM358338v1_genomic.fna.gz | prodigal -d GCF_003583385.1_ASM358338v1_genomic.fna/cds.fna -a GCF_003583385.1_ASM358338v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:55:37,875] [INFO] Task succeeded: Prodigal
[2024-01-25 18:55:37,876] [INFO] Task started: HMMsearch
[2024-01-25 18:55:37,876] [INFO] Running command: hmmsearch --tblout GCF_003583385.1_ASM358338v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfe2f3f4e-6ccb-4c77-8735-d3f57db5636b/dqc_reference/reference_markers.hmm GCF_003583385.1_ASM358338v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:55:38,064] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:55:38,065] [WARNING] Found 4/6 markers. [/var/lib/cwl/stge89da6e7-bd7a-4340-806c-6018151a9277/GCF_003583385.1_ASM358338v1_genomic.fna.gz]
[2024-01-25 18:55:38,076] [INFO] Query marker FASTA was written to GCF_003583385.1_ASM358338v1_genomic.fna/markers.fasta
[2024-01-25 18:55:38,076] [INFO] Task started: Blastn
[2024-01-25 18:55:38,076] [INFO] Running command: blastn -query GCF_003583385.1_ASM358338v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfe2f3f4e-6ccb-4c77-8735-d3f57db5636b/dqc_reference/reference_markers.fasta -out GCF_003583385.1_ASM358338v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:55:38,587] [INFO] Task succeeded: Blastn
[2024-01-25 18:55:38,590] [INFO] Selected 9 target genomes.
[2024-01-25 18:55:38,590] [INFO] Target genome list was writen to GCF_003583385.1_ASM358338v1_genomic.fna/target_genomes.txt
[2024-01-25 18:55:38,598] [INFO] Task started: fastANI
[2024-01-25 18:55:38,598] [INFO] Running command: fastANI --query /var/lib/cwl/stge89da6e7-bd7a-4340-806c-6018151a9277/GCF_003583385.1_ASM358338v1_genomic.fna.gz --refList GCF_003583385.1_ASM358338v1_genomic.fna/target_genomes.txt --output GCF_003583385.1_ASM358338v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:55:40,638] [INFO] Task succeeded: fastANI
[2024-01-25 18:55:40,638] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfe2f3f4e-6ccb-4c77-8735-d3f57db5636b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:55:40,639] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfe2f3f4e-6ccb-4c77-8735-d3f57db5636b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:55:40,644] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:55:40,644] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:55:40,645] [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 gallopavonis	strain=WR1	GCA_003583385.1	76629	76629	type	True	100.0	219	222	95	conclusive
Mycoplasmopsis gallopavonis	strain=NCTC10186	GCA_900660635.1	76629	76629	type	True	99.9694	222	222	95	conclusive
Mycoplasmopsis glycophila	strain=NCTC10194	GCA_900660605.1	171285	171285	type	True	80.1812	110	222	95	below_threshold
Mycoplasmopsis glycophila	strain=ATCC 35277	GCA_000687855.1	171285	171285	type	True	79.9648	104	222	95	below_threshold
Mycoplasmopsis columboralis	strain=ATCC 29258	GCA_000701845.1	171282	171282	type	True	78.6367	51	222	95	below_threshold
Mycoplasma leonicaptivi	strain=ATCC 49890	GCA_000622205.1	36742	36742	type	True	78.0713	52	222	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:55:40,646] [INFO] DFAST Taxonomy check result was written to GCF_003583385.1_ASM358338v1_genomic.fna/tc_result.tsv
[2024-01-25 18:55:40,647] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:55:40,648] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:55:40,648] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfe2f3f4e-6ccb-4c77-8735-d3f57db5636b/dqc_reference/checkm_data
[2024-01-25 18:55:40,649] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:55:40,660] [INFO] Task started: CheckM
[2024-01-25 18:55:40,660] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003583385.1_ASM358338v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003583385.1_ASM358338v1_genomic.fna/checkm_input GCF_003583385.1_ASM358338v1_genomic.fna/checkm_result
[2024-01-25 18:55:51,321] [INFO] Task succeeded: CheckM
[2024-01-25 18:55:51,322] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:55:51,342] [INFO] ===== Completeness check finished =====
[2024-01-25 18:55:51,342] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:55:51,342] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003583385.1_ASM358338v1_genomic.fna/markers.fasta)
[2024-01-25 18:55:51,342] [INFO] Task started: Blastn
[2024-01-25 18:55:51,342] [INFO] Running command: blastn -query GCF_003583385.1_ASM358338v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfe2f3f4e-6ccb-4c77-8735-d3f57db5636b/dqc_reference/reference_markers_gtdb.fasta -out GCF_003583385.1_ASM358338v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:55:52,059] [INFO] Task succeeded: Blastn
[2024-01-25 18:55:52,062] [INFO] Selected 18 target genomes.
[2024-01-25 18:55:52,062] [INFO] Target genome list was writen to GCF_003583385.1_ASM358338v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:55:52,080] [INFO] Task started: fastANI
[2024-01-25 18:55:52,081] [INFO] Running command: fastANI --query /var/lib/cwl/stge89da6e7-bd7a-4340-806c-6018151a9277/GCF_003583385.1_ASM358338v1_genomic.fna.gz --refList GCF_003583385.1_ASM358338v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003583385.1_ASM358338v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:55:56,409] [INFO] Task succeeded: fastANI
[2024-01-25 18:55:56,415] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:55:56,415] [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_900660635.1	s__Mycoplasmopsis_A gallopavonis	99.9694	222	222	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis_A	95.0	99.97	99.97	1.00	1.00	2	conclusive
GCF_900660605.1	s__Mycoplasmopsis_A glycophilum	80.3415	110	222	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000733865.1	s__Mycoplasmopsis_A buteonis	79.4534	108	222	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900660675.1	s__Mycoplasmopsis_A columborale	78.801	51	222	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis_A	95.0	99.98	99.98	0.99	0.99	2	-
GCF_013348745.1	s__Mycoplasmopsis_A sp013348745	78.6908	51	222	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001553195.1	s__Mycoplasmopsis_A canis	78.2719	50	222	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis_A	95.0	98.31	97.62	0.97	0.93	8	-
GCF_000622205.1	s__Mycoplasmopsis_A leonicaptivi	78.0713	52	222	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:55:56,417] [INFO] GTDB search result was written to GCF_003583385.1_ASM358338v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:55:56,417] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:55:56,420] [INFO] DFAST_QC result json was written to GCF_003583385.1_ASM358338v1_genomic.fna/dqc_result.json
[2024-01-25 18:55:56,420] [INFO] DFAST_QC completed!
[2024-01-25 18:55:56,420] [INFO] Total running time: 0h0m21s