[2024-01-24 15:27:01,885] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:27:01,887] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:27:01,887] [INFO] DQC Reference Directory: /var/lib/cwl/stg67d99e75-9a7d-4d17-b1d9-6660b861c7f4/dqc_reference
[2024-01-24 15:27:03,190] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:27:03,191] [INFO] Task started: Prodigal
[2024-01-24 15:27:03,191] [INFO] Running command: gunzip -c /var/lib/cwl/stgc5c0fd5d-37d9-4d84-b365-15acbb679106/GCF_002441935.1_ASM244193v1_genomic.fna.gz | prodigal -d GCF_002441935.1_ASM244193v1_genomic.fna/cds.fna -a GCF_002441935.1_ASM244193v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:04,615] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:04,616] [INFO] Task started: HMMsearch
[2024-01-24 15:27:04,616] [INFO] Running command: hmmsearch --tblout GCF_002441935.1_ASM244193v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg67d99e75-9a7d-4d17-b1d9-6660b861c7f4/dqc_reference/reference_markers.hmm GCF_002441935.1_ASM244193v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:04,783] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:04,785] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc5c0fd5d-37d9-4d84-b365-15acbb679106/GCF_002441935.1_ASM244193v1_genomic.fna.gz]
[2024-01-24 15:27:04,799] [INFO] Query marker FASTA was written to GCF_002441935.1_ASM244193v1_genomic.fna/markers.fasta
[2024-01-24 15:27:04,799] [INFO] Task started: Blastn
[2024-01-24 15:27:04,799] [INFO] Running command: blastn -query GCF_002441935.1_ASM244193v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg67d99e75-9a7d-4d17-b1d9-6660b861c7f4/dqc_reference/reference_markers.fasta -out GCF_002441935.1_ASM244193v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:05,378] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:05,384] [INFO] Selected 14 target genomes.
[2024-01-24 15:27:05,384] [INFO] Target genome list was writen to GCF_002441935.1_ASM244193v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:05,390] [INFO] Task started: fastANI
[2024-01-24 15:27:05,391] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5c0fd5d-37d9-4d84-b365-15acbb679106/GCF_002441935.1_ASM244193v1_genomic.fna.gz --refList GCF_002441935.1_ASM244193v1_genomic.fna/target_genomes.txt --output GCF_002441935.1_ASM244193v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:08,111] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:08,111] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg67d99e75-9a7d-4d17-b1d9-6660b861c7f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:08,112] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg67d99e75-9a7d-4d17-b1d9-6660b861c7f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:08,122] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 15:27:08,122] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:08,122] [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
Mesoplasma lactucae	strain=831-C4	GCA_002441935.1	138853	138853	type	True	100.0	278	279	95	conclusive
Mesoplasma lactucae	strain=831-C4	GCA_002804225.1	138853	138853	type	True	99.9984	276	279	95	conclusive
Mesoplasma lactucae	strain=ATCC 49193	GCA_023566395.1	138853	138853	type	True	99.9982	271	279	95	conclusive
Mycoplasma cottewii	strain=VIS	GCA_024918975.1	51364	51364	type	True	78.1904	59	279	95	below_threshold
Williamsoniiplasma somnilux	strain=PYAN-1	GCA_002804005.1	215578	215578	type	True	78.0574	51	279	95	below_threshold
Mesoplasma chauliocola	strain=CHPA-2	GCA_002290085.1	216427	216427	type	True	77.5447	56	279	95	below_threshold
Mesoplasma chauliocola	strain=ATCC 49578	GCA_000518825.1	216427	216427	type	True	77.5135	52	279	95	below_threshold
Williamsoniiplasma luminosum	strain=ATCC 49195	GCA_000526855.1	214888	214888	type	True	77.4034	59	279	95	below_threshold
Williamsoniiplasma luminosum	strain=PIMN-1	GCA_002803985.1	214888	214888	type	True	77.3649	60	279	95	below_threshold
Mycoplasma mycoides subsp. capri	strain=PG3	GCA_000590435.1	40477	2102	type	True	77.1017	52	279	95	below_threshold
Mycoplasma mycoides subsp. capri	strain=PG3	GCA_000339035.1	40477	2102	type	True	76.9105	50	279	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:08,249] [INFO] DFAST Taxonomy check result was written to GCF_002441935.1_ASM244193v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:08,250] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:08,250] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:08,250] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg67d99e75-9a7d-4d17-b1d9-6660b861c7f4/dqc_reference/checkm_data
[2024-01-24 15:27:08,251] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:08,263] [INFO] Task started: CheckM
[2024-01-24 15:27:08,263] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002441935.1_ASM244193v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002441935.1_ASM244193v1_genomic.fna/checkm_input GCF_002441935.1_ASM244193v1_genomic.fna/checkm_result
[2024-01-24 15:27:21,589] [INFO] Task succeeded: CheckM
[2024-01-24 15:27:21,590] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:27:21,607] [INFO] ===== Completeness check finished =====
[2024-01-24 15:27:21,608] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:27:21,608] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002441935.1_ASM244193v1_genomic.fna/markers.fasta)
[2024-01-24 15:27:21,609] [INFO] Task started: Blastn
[2024-01-24 15:27:21,609] [INFO] Running command: blastn -query GCF_002441935.1_ASM244193v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg67d99e75-9a7d-4d17-b1d9-6660b861c7f4/dqc_reference/reference_markers_gtdb.fasta -out GCF_002441935.1_ASM244193v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:22,409] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:22,413] [INFO] Selected 24 target genomes.
[2024-01-24 15:27:22,413] [INFO] Target genome list was writen to GCF_002441935.1_ASM244193v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:27:22,430] [INFO] Task started: fastANI
[2024-01-24 15:27:22,430] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5c0fd5d-37d9-4d84-b365-15acbb679106/GCF_002441935.1_ASM244193v1_genomic.fna.gz --refList GCF_002441935.1_ASM244193v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002441935.1_ASM244193v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:27:28,083] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:28,089] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:27:28,089] [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_002441935.1	s__Edwardiiplasma lactucae	100.0	278	279	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Edwardiiplasma	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_002804025.1	s__Mesoplasma tabanidae	78.2566	51	279	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mesoplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002804005.1	s__Williamsoniiplasma somnilux	78.0574	51	279	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Williamsoniiplasma	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002290085.1	s__Mesoplasma chauliocola	77.8021	57	279	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mesoplasma	95.0	99.98	99.98	0.99	0.99	2	-
GCF_900489555.1	s__Mycoplasma capri	77.0767	55	279	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mycoplasma	95.6652	99.61	97.30	0.99	0.89	26	-
--------------------------------------------------------------------------------
[2024-01-24 15:27:28,091] [INFO] GTDB search result was written to GCF_002441935.1_ASM244193v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:27:28,091] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:27:28,095] [INFO] DFAST_QC result json was written to GCF_002441935.1_ASM244193v1_genomic.fna/dqc_result.json
[2024-01-24 15:27:28,095] [INFO] DFAST_QC completed!
[2024-01-24 15:27:28,095] [INFO] Total running time: 0h0m26s