[2024-01-24 13:31:57,791] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:57,793] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:57,793] [INFO] DQC Reference Directory: /var/lib/cwl/stgf00633b5-f7a4-4964-8649-be53a0618118/dqc_reference
[2024-01-24 13:31:59,101] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:59,102] [INFO] Task started: Prodigal
[2024-01-24 13:31:59,102] [INFO] Running command: gunzip -c /var/lib/cwl/stgf89f291f-7fe6-47f1-b520-c63c8be07227/GCF_002749675.1_ASM274967v1_genomic.fna.gz | prodigal -d GCF_002749675.1_ASM274967v1_genomic.fna/cds.fna -a GCF_002749675.1_ASM274967v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:00,502] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:00,502] [INFO] Task started: HMMsearch
[2024-01-24 13:32:00,503] [INFO] Running command: hmmsearch --tblout GCF_002749675.1_ASM274967v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf00633b5-f7a4-4964-8649-be53a0618118/dqc_reference/reference_markers.hmm GCF_002749675.1_ASM274967v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:00,635] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:00,636] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgf89f291f-7fe6-47f1-b520-c63c8be07227/GCF_002749675.1_ASM274967v1_genomic.fna.gz]
[2024-01-24 13:32:00,650] [INFO] Query marker FASTA was written to GCF_002749675.1_ASM274967v1_genomic.fna/markers.fasta
[2024-01-24 13:32:00,650] [INFO] Task started: Blastn
[2024-01-24 13:32:00,650] [INFO] Running command: blastn -query GCF_002749675.1_ASM274967v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf00633b5-f7a4-4964-8649-be53a0618118/dqc_reference/reference_markers.fasta -out GCF_002749675.1_ASM274967v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:01,127] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:01,130] [INFO] Selected 15 target genomes.
[2024-01-24 13:32:01,131] [INFO] Target genome list was writen to GCF_002749675.1_ASM274967v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:01,192] [INFO] Task started: fastANI
[2024-01-24 13:32:01,192] [INFO] Running command: fastANI --query /var/lib/cwl/stgf89f291f-7fe6-47f1-b520-c63c8be07227/GCF_002749675.1_ASM274967v1_genomic.fna.gz --refList GCF_002749675.1_ASM274967v1_genomic.fna/target_genomes.txt --output GCF_002749675.1_ASM274967v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:04,352] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:04,352] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf00633b5-f7a4-4964-8649-be53a0618118/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:04,353] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf00633b5-f7a4-4964-8649-be53a0618118/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:04,361] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:32:04,361] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:04,361] [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 entomophilum	strain=TAC	GCA_002749675.1	2149	2149	type	True	100.0	281	282	95	conclusive
Mesoplasma entomophilum	strain=TAC	GCA_002804125.1	2149	2149	type	True	99.9954	282	282	95	conclusive
Mesoplasma coleopterae	strain=BARC 779	GCA_002804245.1	324078	324078	type	True	94.1859	236	282	95	below_threshold
Mesoplasma florum	strain=L1; ATCC 33453	GCA_000008305.1	2151	2151	type	True	88.3511	226	282	95	below_threshold
Mesoplasma grammopterae	strain=ATCC 49580	GCA_000701525.1	217215	217215	type	True	87.9064	227	282	95	below_threshold
Mesoplasma tabanidae	strain=BARC 857	GCA_002804025.1	219745	219745	type	True	87.8361	229	282	95	below_threshold
Entomoplasma melaleucae	strain=ATCC 49191	GCA_000685885.1	81459	81459	type	True	84.9378	195	282	95	below_threshold
Entomoplasma melaleucae	strain=M1	GCA_002804105.1	81459	81459	type	True	84.8633	207	282	95	below_threshold
Mesoplasma chauliocola	strain=CHPA-2	GCA_002290085.1	216427	216427	type	True	84.0596	208	282	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:04,368] [INFO] DFAST Taxonomy check result was written to GCF_002749675.1_ASM274967v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:04,368] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:04,368] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:04,369] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf00633b5-f7a4-4964-8649-be53a0618118/dqc_reference/checkm_data
[2024-01-24 13:32:04,370] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:04,384] [INFO] Task started: CheckM
[2024-01-24 13:32:04,384] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002749675.1_ASM274967v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002749675.1_ASM274967v1_genomic.fna/checkm_input GCF_002749675.1_ASM274967v1_genomic.fna/checkm_result
[2024-01-24 13:32:16,731] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:16,732] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:16,749] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:16,749] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:16,750] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002749675.1_ASM274967v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:16,750] [INFO] Task started: Blastn
[2024-01-24 13:32:16,750] [INFO] Running command: blastn -query GCF_002749675.1_ASM274967v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf00633b5-f7a4-4964-8649-be53a0618118/dqc_reference/reference_markers_gtdb.fasta -out GCF_002749675.1_ASM274967v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:17,166] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:17,173] [INFO] Selected 7 target genomes.
[2024-01-24 13:32:17,173] [INFO] Target genome list was writen to GCF_002749675.1_ASM274967v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:17,178] [INFO] Task started: fastANI
[2024-01-24 13:32:17,178] [INFO] Running command: fastANI --query /var/lib/cwl/stgf89f291f-7fe6-47f1-b520-c63c8be07227/GCF_002749675.1_ASM274967v1_genomic.fna.gz --refList GCF_002749675.1_ASM274967v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002749675.1_ASM274967v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:32:18,576] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:18,582] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:32:18,582] [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_002804125.1	s__Mesoplasma entomophilum	99.9954	281	282	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mesoplasma	95.0	99.01	98.03	0.96	0.92	3	conclusive
GCF_002804245.1	s__Mesoplasma coleopterae	94.1859	236	282	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mesoplasma	95.0	98.88	98.62	0.96	0.96	3	-
GCF_000008305.1	s__Mesoplasma florum	88.3513	226	282	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mesoplasma	95.9326	98.30	97.69	0.92	0.91	10	-
GCF_000701525.1	s__Mesoplasma grammopterae	87.9064	227	282	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mesoplasma	95.9326	98.59	97.19	0.95	0.91	3	-
GCF_002804025.1	s__Mesoplasma tabanidae	87.8947	228	282	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mesoplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002804105.1	s__Mesoplasma melaleucae	84.8633	207	282	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mesoplasma	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002290085.1	s__Mesoplasma chauliocola	84.0951	207	282	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mesoplasma	95.0	99.98	99.98	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:32:18,584] [INFO] GTDB search result was written to GCF_002749675.1_ASM274967v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:32:18,585] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:32:18,587] [INFO] DFAST_QC result json was written to GCF_002749675.1_ASM274967v1_genomic.fna/dqc_result.json
[2024-01-24 13:32:18,588] [INFO] DFAST_QC completed!
[2024-01-24 13:32:18,588] [INFO] Total running time: 0h0m21s