[2024-01-24 11:12:27,064] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:27,066] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:27,067] [INFO] DQC Reference Directory: /var/lib/cwl/stgca625030-e71c-46d0-b7e1-2bc0555df923/dqc_reference
[2024-01-24 11:12:28,400] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:28,401] [INFO] Task started: Prodigal
[2024-01-24 11:12:28,401] [INFO] Running command: gunzip -c /var/lib/cwl/stg8ceb7147-ac67-43f9-936c-dc97354c02e3/GCF_024498235.1_ASM2449823v1_genomic.fna.gz | prodigal -d GCF_024498235.1_ASM2449823v1_genomic.fna/cds.fna -a GCF_024498235.1_ASM2449823v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:30,368] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:30,368] [INFO] Task started: HMMsearch
[2024-01-24 11:12:30,369] [INFO] Running command: hmmsearch --tblout GCF_024498235.1_ASM2449823v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgca625030-e71c-46d0-b7e1-2bc0555df923/dqc_reference/reference_markers.hmm GCF_024498235.1_ASM2449823v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:30,604] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:30,605] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg8ceb7147-ac67-43f9-936c-dc97354c02e3/GCF_024498235.1_ASM2449823v1_genomic.fna.gz]
[2024-01-24 11:12:30,619] [INFO] Query marker FASTA was written to GCF_024498235.1_ASM2449823v1_genomic.fna/markers.fasta
[2024-01-24 11:12:30,636] [INFO] Task started: Blastn
[2024-01-24 11:12:30,637] [INFO] Running command: blastn -query GCF_024498235.1_ASM2449823v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca625030-e71c-46d0-b7e1-2bc0555df923/dqc_reference/reference_markers.fasta -out GCF_024498235.1_ASM2449823v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:33,424] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:33,428] [INFO] Selected 10 target genomes.
[2024-01-24 11:12:33,428] [INFO] Target genome list was writen to GCF_024498235.1_ASM2449823v1_genomic.fna/target_genomes.txt
[2024-01-24 11:12:33,444] [INFO] Task started: fastANI
[2024-01-24 11:12:33,444] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ceb7147-ac67-43f9-936c-dc97354c02e3/GCF_024498235.1_ASM2449823v1_genomic.fna.gz --refList GCF_024498235.1_ASM2449823v1_genomic.fna/target_genomes.txt --output GCF_024498235.1_ASM2449823v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:12:36,271] [INFO] Task succeeded: fastANI
[2024-01-24 11:12:36,271] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgca625030-e71c-46d0-b7e1-2bc0555df923/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:12:36,272] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgca625030-e71c-46d0-b7e1-2bc0555df923/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:12:36,283] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:12:36,283] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:12:36,283] [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 citelli	strain=RG-2C	GCA_024498235.1	171281	171281	type	True	100.0	409	409	95	conclusive
Mycoplasmopsis citelli	strain=NCTC10181	GCA_900660645.1	171281	171281	type	True	98.6774	375	409	95	conclusive
Mycoplasmopsis columboralis	strain=NCTC10179	GCA_900660675.1	171282	171282	type	True	79.6928	153	409	95	below_threshold
Mycoplasmopsis columboralis	strain=ATCC 29258	GCA_000701845.1	171282	171282	type	True	79.5181	144	409	95	below_threshold
Mycoplasmopsis glycophila	strain=NCTC10194	GCA_900660605.1	171285	171285	type	True	78.4796	60	409	95	below_threshold
Mycoplasmopsis cricetuli	strain=ATCC 35279	GCA_000526955.1	171283	171283	type	True	78.408	103	409	95	below_threshold
Mycoplasmopsis gallopavonis	strain=NCTC10186	GCA_900660635.1	76629	76629	type	True	78.2959	58	409	95	below_threshold
Mycoplasmopsis gallopavonis	strain=WR1	GCA_003583385.1	76629	76629	type	True	77.6973	50	409	95	below_threshold
Mycoplasmopsis verecunda	strain=ATCC 27862	GCA_900167035.1	171291	171291	type	True	76.682	53	409	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:12:36,285] [INFO] DFAST Taxonomy check result was written to GCF_024498235.1_ASM2449823v1_genomic.fna/tc_result.tsv
[2024-01-24 11:12:36,286] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:12:36,286] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:12:36,286] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgca625030-e71c-46d0-b7e1-2bc0555df923/dqc_reference/checkm_data
[2024-01-24 11:12:36,287] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:12:36,300] [INFO] Task started: CheckM
[2024-01-24 11:12:36,301] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024498235.1_ASM2449823v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024498235.1_ASM2449823v1_genomic.fna/checkm_input GCF_024498235.1_ASM2449823v1_genomic.fna/checkm_result
[2024-01-24 11:12:52,597] [INFO] Task succeeded: CheckM
[2024-01-24 11:12:52,598] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:12:52,632] [INFO] ===== Completeness check finished =====
[2024-01-24 11:12:52,632] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:12:52,632] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024498235.1_ASM2449823v1_genomic.fna/markers.fasta)
[2024-01-24 11:12:52,632] [INFO] Task started: Blastn
[2024-01-24 11:12:52,633] [INFO] Running command: blastn -query GCF_024498235.1_ASM2449823v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca625030-e71c-46d0-b7e1-2bc0555df923/dqc_reference/reference_markers_gtdb.fasta -out GCF_024498235.1_ASM2449823v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:53,883] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:53,887] [INFO] Selected 15 target genomes.
[2024-01-24 11:12:53,888] [INFO] Target genome list was writen to GCF_024498235.1_ASM2449823v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:12:53,898] [INFO] Task started: fastANI
[2024-01-24 11:12:53,898] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ceb7147-ac67-43f9-936c-dc97354c02e3/GCF_024498235.1_ASM2449823v1_genomic.fna.gz --refList GCF_024498235.1_ASM2449823v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024498235.1_ASM2449823v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:12:57,719] [INFO] Task succeeded: fastANI
[2024-01-24 11:12:57,727] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:12:57,728] [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_900660645.1	s__Mycoplasmopsis_A citelli	98.6774	375	409	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900660675.1	s__Mycoplasmopsis_A columborale	79.6585	154	409	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_900660635.1	s__Mycoplasmopsis_A gallopavonis	78.7068	57	409	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis_A	95.0	99.97	99.97	1.00	1.00	2	-
GCF_900660605.1	s__Mycoplasmopsis_A glycophilum	78.5266	60	409	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_000526955.1	s__Mycoplasmopsis_A cricetuli	78.4437	102	409	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_009792315.1	s__Mycoplasmopsis_A sp009792315	78.1674	74	409	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_900660495.1	s__Mycoplasmopsis_A gallinaceum	77.6629	73	409	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis_A	95.0	96.30	96.30	0.91	0.91	2	-
GCF_000178375.1	s__Mycoplasmopsis_A alligatoris	77.0775	56	409	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_900167035.1	s__Mycoplasmopsis_A verecundum	76.5747	52	409	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:12:57,729] [INFO] GTDB search result was written to GCF_024498235.1_ASM2449823v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:12:57,730] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:12:57,740] [INFO] DFAST_QC result json was written to GCF_024498235.1_ASM2449823v1_genomic.fna/dqc_result.json
[2024-01-24 11:12:57,741] [INFO] DFAST_QC completed!
[2024-01-24 11:12:57,741] [INFO] Total running time: 0h0m31s