[2024-01-24 14:04:44,466] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:04:44,468] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:04:44,469] [INFO] DQC Reference Directory: /var/lib/cwl/stg8795df70-de9e-47ac-81e8-6301f3e875cf/dqc_reference
[2024-01-24 14:04:45,651] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:04:45,651] [INFO] Task started: Prodigal
[2024-01-24 14:04:45,652] [INFO] Running command: gunzip -c /var/lib/cwl/stg89acd2b1-1b4b-43e1-97af-a9a97803cc89/GCF_003285045.1_ASM328504v1_genomic.fna.gz | prodigal -d GCF_003285045.1_ASM328504v1_genomic.fna/cds.fna -a GCF_003285045.1_ASM328504v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:04:46,852] [INFO] Task succeeded: Prodigal
[2024-01-24 14:04:46,852] [INFO] Task started: HMMsearch
[2024-01-24 14:04:46,853] [INFO] Running command: hmmsearch --tblout GCF_003285045.1_ASM328504v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8795df70-de9e-47ac-81e8-6301f3e875cf/dqc_reference/reference_markers.hmm GCF_003285045.1_ASM328504v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:04:47,020] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:04:47,022] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg89acd2b1-1b4b-43e1-97af-a9a97803cc89/GCF_003285045.1_ASM328504v1_genomic.fna.gz]
[2024-01-24 14:04:47,034] [INFO] Query marker FASTA was written to GCF_003285045.1_ASM328504v1_genomic.fna/markers.fasta
[2024-01-24 14:04:47,035] [INFO] Task started: Blastn
[2024-01-24 14:04:47,035] [INFO] Running command: blastn -query GCF_003285045.1_ASM328504v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8795df70-de9e-47ac-81e8-6301f3e875cf/dqc_reference/reference_markers.fasta -out GCF_003285045.1_ASM328504v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:04:47,517] [INFO] Task succeeded: Blastn
[2024-01-24 14:04:47,522] [INFO] Selected 15 target genomes.
[2024-01-24 14:04:47,522] [INFO] Target genome list was writen to GCF_003285045.1_ASM328504v1_genomic.fna/target_genomes.txt
[2024-01-24 14:04:47,637] [INFO] Task started: fastANI
[2024-01-24 14:04:47,638] [INFO] Running command: fastANI --query /var/lib/cwl/stg89acd2b1-1b4b-43e1-97af-a9a97803cc89/GCF_003285045.1_ASM328504v1_genomic.fna.gz --refList GCF_003285045.1_ASM328504v1_genomic.fna/target_genomes.txt --output GCF_003285045.1_ASM328504v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:04:51,437] [INFO] Task succeeded: fastANI
[2024-01-24 14:04:51,438] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8795df70-de9e-47ac-81e8-6301f3e875cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:04:51,439] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8795df70-de9e-47ac-81e8-6301f3e875cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:04:51,448] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:04:51,449] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:04:51,449] [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 anseris	strain=ATCC 49234	GCA_003285045.1	92400	92400	type	True	100.0	248	250	95	conclusive
Metamycoplasma anseris	strain=ATCC 49234	GCA_000702805.1	92400	92400	type	True	99.9659	231	250	95	conclusive
Metamycoplasma cloacale	strain=NCTC 10199	GCA_003269445.1	92401	92401	type	True	80.1417	106	250	95	below_threshold
Metamycoplasma cloacale	strain=NCTC10199	GCA_900660735.1	92401	92401	type	True	80.1301	108	250	95	below_threshold
Metamycoplasma cloacale	strain=ATCC 35276	GCA_000702745.1	92401	92401	type	True	79.8562	105	250	95	below_threshold
Mycoplasma struthionis	strain=237IA	GCA_003855455.1	538220	538220	type	True	78.9674	73	250	95	below_threshold
Metamycoplasma auris	strain=ATCC 51348	GCA_003253435.1	51363	51363	type	True	78.6249	56	250	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:04:51,450] [INFO] DFAST Taxonomy check result was written to GCF_003285045.1_ASM328504v1_genomic.fna/tc_result.tsv
[2024-01-24 14:04:51,451] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:04:51,451] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:04:51,451] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8795df70-de9e-47ac-81e8-6301f3e875cf/dqc_reference/checkm_data
[2024-01-24 14:04:51,453] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:04:51,468] [INFO] Task started: CheckM
[2024-01-24 14:04:51,468] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003285045.1_ASM328504v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003285045.1_ASM328504v1_genomic.fna/checkm_input GCF_003285045.1_ASM328504v1_genomic.fna/checkm_result
[2024-01-24 14:05:03,636] [INFO] Task succeeded: CheckM
[2024-01-24 14:05:03,638] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:05:03,654] [INFO] ===== Completeness check finished =====
[2024-01-24 14:05:03,654] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:05:03,655] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003285045.1_ASM328504v1_genomic.fna/markers.fasta)
[2024-01-24 14:05:03,655] [INFO] Task started: Blastn
[2024-01-24 14:05:03,655] [INFO] Running command: blastn -query GCF_003285045.1_ASM328504v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8795df70-de9e-47ac-81e8-6301f3e875cf/dqc_reference/reference_markers_gtdb.fasta -out GCF_003285045.1_ASM328504v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:04,086] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:04,089] [INFO] Selected 16 target genomes.
[2024-01-24 14:05:04,089] [INFO] Target genome list was writen to GCF_003285045.1_ASM328504v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:05:04,139] [INFO] Task started: fastANI
[2024-01-24 14:05:04,140] [INFO] Running command: fastANI --query /var/lib/cwl/stg89acd2b1-1b4b-43e1-97af-a9a97803cc89/GCF_003285045.1_ASM328504v1_genomic.fna.gz --refList GCF_003285045.1_ASM328504v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003285045.1_ASM328504v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:05:06,814] [INFO] Task succeeded: fastANI
[2024-01-24 14:05:06,826] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:05:06,826] [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_000702805.1	s__Metamycoplasma anseris	99.9659	231	250	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_900660735.1	s__Metamycoplasma cloacale	80.1301	108	250	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	100.00	100.00	1.00	1.00	3	-
GCF_003855455.1	s__Metamycoplasma struthionis	78.9537	72	250	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	98.82	98.82	0.96	0.96	2	-
GCF_012934885.1	s__Metamycoplasma sp012934885	78.7994	55	250	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	98.25	98.25	0.95	0.95	2	-
GCF_900660445.2	s__Metamycoplasma salivarium	78.661	66	250	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003253435.1	s__Metamycoplasma auris	78.6249	56	250	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000420105.1	s__Metamycoplasma orale	78.0417	62	250	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006385185.1	s__Metamycoplasma equirhinis	77.946	61	250	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 14:05:06,828] [INFO] GTDB search result was written to GCF_003285045.1_ASM328504v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:05:06,828] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:05:06,831] [INFO] DFAST_QC result json was written to GCF_003285045.1_ASM328504v1_genomic.fna/dqc_result.json
[2024-01-24 14:05:06,831] [INFO] DFAST_QC completed!
[2024-01-24 14:05:06,831] [INFO] Total running time: 0h0m22s