[2024-01-24 13:40:28,248] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:28,251] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:28,251] [INFO] DQC Reference Directory: /var/lib/cwl/stg4e407c68-8025-4821-9d9b-ff2d69a6a83a/dqc_reference
[2024-01-24 13:40:29,673] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:29,675] [INFO] Task started: Prodigal
[2024-01-24 13:40:29,675] [INFO] Running command: gunzip -c /var/lib/cwl/stg3c0da28a-ca25-4670-8fe3-a40f4e15d1e3/GCF_017052655.1_ASM1705265v1_genomic.fna.gz | prodigal -d GCF_017052655.1_ASM1705265v1_genomic.fna/cds.fna -a GCF_017052655.1_ASM1705265v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:32,357] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:32,358] [INFO] Task started: HMMsearch
[2024-01-24 13:40:32,358] [INFO] Running command: hmmsearch --tblout GCF_017052655.1_ASM1705265v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4e407c68-8025-4821-9d9b-ff2d69a6a83a/dqc_reference/reference_markers.hmm GCF_017052655.1_ASM1705265v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:32,564] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:32,565] [INFO] Found 6/6 markers.
[2024-01-24 13:40:32,582] [INFO] Query marker FASTA was written to GCF_017052655.1_ASM1705265v1_genomic.fna/markers.fasta
[2024-01-24 13:40:32,582] [INFO] Task started: Blastn
[2024-01-24 13:40:32,582] [INFO] Running command: blastn -query GCF_017052655.1_ASM1705265v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e407c68-8025-4821-9d9b-ff2d69a6a83a/dqc_reference/reference_markers.fasta -out GCF_017052655.1_ASM1705265v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:33,163] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:33,167] [INFO] Selected 16 target genomes.
[2024-01-24 13:40:33,167] [INFO] Target genome list was writen to GCF_017052655.1_ASM1705265v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:33,187] [INFO] Task started: fastANI
[2024-01-24 13:40:33,187] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c0da28a-ca25-4670-8fe3-a40f4e15d1e3/GCF_017052655.1_ASM1705265v1_genomic.fna.gz --refList GCF_017052655.1_ASM1705265v1_genomic.fna/target_genomes.txt --output GCF_017052655.1_ASM1705265v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:38,602] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:38,603] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4e407c68-8025-4821-9d9b-ff2d69a6a83a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:38,603] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4e407c68-8025-4821-9d9b-ff2d69a6a83a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:38,614] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:40:38,615] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:40:38,615] [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
Acholeplasma equirhinis	strain=N93	GCA_017052655.1	555393	555393	type	True	100.0	479	479	95	conclusive
Acholeplasma hippikon	strain=NCTC10172	GCA_900660755.1	264636	264636	type	True	78.9315	152	479	95	below_threshold
Acholeplasma hippikon	strain=ATCC 29725	GCA_000702765.1	264636	264636	type	True	78.8475	146	479	95	below_threshold
Acholeplasma equifetale	strain=ATCC 29724	GCA_000687735.1	264634	264634	type	True	78.126	123	479	95	below_threshold
Acholeplasma oculi	strain=ATCC 27350	GCA_900166985.1	35623	35623	type	True	78.0316	126	479	95	below_threshold
Acholeplasma laidlawii	strain=PG-8A	GCA_000018785.1	2148	2148	type	True	77.5807	122	479	95	below_threshold
Acholeplasma laidlawii	strain=NCTC10116	GCA_900476025.1	2148	2148	type	True	77.5232	119	479	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:38,616] [INFO] DFAST Taxonomy check result was written to GCF_017052655.1_ASM1705265v1_genomic.fna/tc_result.tsv
[2024-01-24 13:40:38,617] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:38,617] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:38,617] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4e407c68-8025-4821-9d9b-ff2d69a6a83a/dqc_reference/checkm_data
[2024-01-24 13:40:38,619] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:38,637] [INFO] Task started: CheckM
[2024-01-24 13:40:38,637] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017052655.1_ASM1705265v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017052655.1_ASM1705265v1_genomic.fna/checkm_input GCF_017052655.1_ASM1705265v1_genomic.fna/checkm_result
[2024-01-24 13:40:55,513] [INFO] Task succeeded: CheckM
[2024-01-24 13:40:55,514] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:40:55,539] [INFO] ===== Completeness check finished =====
[2024-01-24 13:40:55,539] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:40:55,539] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017052655.1_ASM1705265v1_genomic.fna/markers.fasta)
[2024-01-24 13:40:55,540] [INFO] Task started: Blastn
[2024-01-24 13:40:55,540] [INFO] Running command: blastn -query GCF_017052655.1_ASM1705265v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e407c68-8025-4821-9d9b-ff2d69a6a83a/dqc_reference/reference_markers_gtdb.fasta -out GCF_017052655.1_ASM1705265v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:56,363] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:56,366] [INFO] Selected 10 target genomes.
[2024-01-24 13:40:56,366] [INFO] Target genome list was writen to GCF_017052655.1_ASM1705265v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:40:56,374] [INFO] Task started: fastANI
[2024-01-24 13:40:56,374] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c0da28a-ca25-4670-8fe3-a40f4e15d1e3/GCF_017052655.1_ASM1705265v1_genomic.fna.gz --refList GCF_017052655.1_ASM1705265v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017052655.1_ASM1705265v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:40:59,227] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:59,234] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:40:59,234] [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_017052655.1	s__Acholeplasma equirhinis	100.0	479	479	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__Acholeplasma	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900660755.1	s__Acholeplasma hippikon	78.9459	151	479	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__Acholeplasma	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000687735.1	s__Acholeplasma equifetale	78.126	123	479	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__Acholeplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900166985.1	s__Acholeplasma oculi	78.0049	127	479	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__Acholeplasma	95.0	99.99	99.99	0.99	0.99	3	-
GCA_002399815.1	s__Acholeplasma sp002399815	77.9886	138	479	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__Acholeplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015709225.1	s__Acholeplasma laidlawii_A	77.6559	120	479	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__Acholeplasma	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:40:59,236] [INFO] GTDB search result was written to GCF_017052655.1_ASM1705265v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:40:59,237] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:40:59,241] [INFO] DFAST_QC result json was written to GCF_017052655.1_ASM1705265v1_genomic.fna/dqc_result.json
[2024-01-24 13:40:59,241] [INFO] DFAST_QC completed!
[2024-01-24 13:40:59,241] [INFO] Total running time: 0h0m31s