[2024-01-24 13:09:49,374] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:49,376] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:49,376] [INFO] DQC Reference Directory: /var/lib/cwl/stg51b3b287-9bb4-4a5a-b2d1-3efb7e899106/dqc_reference
[2024-01-24 13:09:50,728] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:50,729] [INFO] Task started: Prodigal
[2024-01-24 13:09:50,729] [INFO] Running command: gunzip -c /var/lib/cwl/stga4298970-d583-44e5-9119-ccd36c9d9840/GCF_006385795.1_ASM638579v1_genomic.fna.gz | prodigal -d GCF_006385795.1_ASM638579v1_genomic.fna/cds.fna -a GCF_006385795.1_ASM638579v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:51,658] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:51,659] [INFO] Task started: HMMsearch
[2024-01-24 13:09:51,659] [INFO] Running command: hmmsearch --tblout GCF_006385795.1_ASM638579v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg51b3b287-9bb4-4a5a-b2d1-3efb7e899106/dqc_reference/reference_markers.hmm GCF_006385795.1_ASM638579v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:51,841] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:51,842] [WARNING] Found 3/6 markers. [/var/lib/cwl/stga4298970-d583-44e5-9119-ccd36c9d9840/GCF_006385795.1_ASM638579v1_genomic.fna.gz]
[2024-01-24 13:09:51,855] [INFO] Query marker FASTA was written to GCF_006385795.1_ASM638579v1_genomic.fna/markers.fasta
[2024-01-24 13:09:51,855] [INFO] Task started: Blastn
[2024-01-24 13:09:51,856] [INFO] Running command: blastn -query GCF_006385795.1_ASM638579v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg51b3b287-9bb4-4a5a-b2d1-3efb7e899106/dqc_reference/reference_markers.fasta -out GCF_006385795.1_ASM638579v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:52,415] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:52,419] [INFO] Selected 12 target genomes.
[2024-01-24 13:09:52,419] [INFO] Target genome list was writen to GCF_006385795.1_ASM638579v1_genomic.fna/target_genomes.txt
[2024-01-24 13:09:52,530] [INFO] Task started: fastANI
[2024-01-24 13:09:52,530] [INFO] Running command: fastANI --query /var/lib/cwl/stga4298970-d583-44e5-9119-ccd36c9d9840/GCF_006385795.1_ASM638579v1_genomic.fna.gz --refList GCF_006385795.1_ASM638579v1_genomic.fna/target_genomes.txt --output GCF_006385795.1_ASM638579v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:09:54,536] [INFO] Task succeeded: fastANI
[2024-01-24 13:09:54,536] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg51b3b287-9bb4-4a5a-b2d1-3efb7e899106/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:09:54,537] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg51b3b287-9bb4-4a5a-b2d1-3efb7e899106/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:09:54,544] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:09:54,544] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:09:54,544] [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 falconis	strain=ATCC 51372	GCA_006385795.1	92403	92403	type	True	100.0	208	209	95	conclusive
Mycoplasma struthionis	strain=237IA	GCA_003855455.1	538220	538220	type	True	78.786	81	209	95	below_threshold
Metamycoplasma cloacale	strain=ATCC 35276	GCA_000702745.1	92401	92401	type	True	78.4422	55	209	95	below_threshold
Metamycoplasma cloacale	strain=NCTC 10199	GCA_003269445.1	92401	92401	type	True	78.4005	54	209	95	below_threshold
Metamycoplasma cloacale	strain=NCTC10199	GCA_900660735.1	92401	92401	type	True	78.2208	55	209	95	below_threshold
Metamycoplasma anseris	strain=ATCC 49234	GCA_000702805.1	92400	92400	type	True	78.0708	67	209	95	below_threshold
Metamycoplasma anseris	strain=ATCC 49234	GCA_003285045.1	92400	92400	type	True	77.9333	70	209	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:09:54,546] [INFO] DFAST Taxonomy check result was written to GCF_006385795.1_ASM638579v1_genomic.fna/tc_result.tsv
[2024-01-24 13:09:54,547] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:09:54,547] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:09:54,547] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg51b3b287-9bb4-4a5a-b2d1-3efb7e899106/dqc_reference/checkm_data
[2024-01-24 13:09:54,548] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:09:54,557] [INFO] Task started: CheckM
[2024-01-24 13:09:54,558] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006385795.1_ASM638579v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006385795.1_ASM638579v1_genomic.fna/checkm_input GCF_006385795.1_ASM638579v1_genomic.fna/checkm_result
[2024-01-24 13:10:06,368] [INFO] Task succeeded: CheckM
[2024-01-24 13:10:06,369] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:10:06,385] [INFO] ===== Completeness check finished =====
[2024-01-24 13:10:06,385] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:10:06,386] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006385795.1_ASM638579v1_genomic.fna/markers.fasta)
[2024-01-24 13:10:06,386] [INFO] Task started: Blastn
[2024-01-24 13:10:06,386] [INFO] Running command: blastn -query GCF_006385795.1_ASM638579v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg51b3b287-9bb4-4a5a-b2d1-3efb7e899106/dqc_reference/reference_markers_gtdb.fasta -out GCF_006385795.1_ASM638579v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:07,093] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:07,097] [INFO] Selected 11 target genomes.
[2024-01-24 13:10:07,097] [INFO] Target genome list was writen to GCF_006385795.1_ASM638579v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:10:07,150] [INFO] Task started: fastANI
[2024-01-24 13:10:07,150] [INFO] Running command: fastANI --query /var/lib/cwl/stga4298970-d583-44e5-9119-ccd36c9d9840/GCF_006385795.1_ASM638579v1_genomic.fna.gz --refList GCF_006385795.1_ASM638579v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006385795.1_ASM638579v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:10:08,762] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:08,778] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:10:08,779] [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_006385795.1	s__Metamycoplasma falconis	100.0	208	209	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_003855455.1	s__Metamycoplasma struthionis	78.786	81	209	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	98.82	98.82	0.96	0.96	2	-
GCF_900660725.1	s__Metamycoplasma arginini	78.6681	76	209	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	98.27	98.11	0.94	0.92	6	-
GCF_006385185.1	s__Metamycoplasma equirhinis	78.4566	63	209	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900660735.1	s__Metamycoplasma cloacale	78.1522	56	209	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	100.00	100.00	1.00	1.00	3	-
GCF_000702805.1	s__Metamycoplasma anseris	78.0664	67	209	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000367765.1	s__Metamycoplasma auris_A	77.5557	55	209	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900660445.2	s__Metamycoplasma salivarium	77.2579	50	209	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:10:08,781] [INFO] GTDB search result was written to GCF_006385795.1_ASM638579v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:10:08,782] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:10:08,786] [INFO] DFAST_QC result json was written to GCF_006385795.1_ASM638579v1_genomic.fna/dqc_result.json
[2024-01-24 13:10:08,787] [INFO] DFAST_QC completed!
[2024-01-24 13:10:08,787] [INFO] Total running time: 0h0m19s