[2024-01-24 13:32:40,537] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:40,539] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:40,539] [INFO] DQC Reference Directory: /var/lib/cwl/stg3785026c-954e-460a-832c-d7a37509f073/dqc_reference
[2024-01-24 13:32:41,968] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:41,969] [INFO] Task started: Prodigal
[2024-01-24 13:32:41,969] [INFO] Running command: gunzip -c /var/lib/cwl/stg3a0c21be-8abb-4c0c-85f5-46e2a5c3af5d/GCF_900660745.1_57728_G01-3_genomic.fna.gz | prodigal -d GCF_900660745.1_57728_G01-3_genomic.fna/cds.fna -a GCF_900660745.1_57728_G01-3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:45,100] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:45,101] [INFO] Task started: HMMsearch
[2024-01-24 13:32:45,101] [INFO] Running command: hmmsearch --tblout GCF_900660745.1_57728_G01-3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3785026c-954e-460a-832c-d7a37509f073/dqc_reference/reference_markers.hmm GCF_900660745.1_57728_G01-3_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:45,314] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:45,316] [INFO] Found 6/6 markers.
[2024-01-24 13:32:45,336] [INFO] Query marker FASTA was written to GCF_900660745.1_57728_G01-3_genomic.fna/markers.fasta
[2024-01-24 13:32:45,336] [INFO] Task started: Blastn
[2024-01-24 13:32:45,337] [INFO] Running command: blastn -query GCF_900660745.1_57728_G01-3_genomic.fna/markers.fasta -db /var/lib/cwl/stg3785026c-954e-460a-832c-d7a37509f073/dqc_reference/reference_markers.fasta -out GCF_900660745.1_57728_G01-3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:46,016] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:46,020] [INFO] Selected 17 target genomes.
[2024-01-24 13:32:46,020] [INFO] Target genome list was writen to GCF_900660745.1_57728_G01-3_genomic.fna/target_genomes.txt
[2024-01-24 13:32:46,029] [INFO] Task started: fastANI
[2024-01-24 13:32:46,029] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a0c21be-8abb-4c0c-85f5-46e2a5c3af5d/GCF_900660745.1_57728_G01-3_genomic.fna.gz --refList GCF_900660745.1_57728_G01-3_genomic.fna/target_genomes.txt --output GCF_900660745.1_57728_G01-3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:52,633] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:52,633] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3785026c-954e-460a-832c-d7a37509f073/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:52,634] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3785026c-954e-460a-832c-d7a37509f073/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:52,642] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:32:52,643] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:52,643] [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
Haploplasma axanthum	strain=NCTC10138	GCA_900660745.1	29552	29552	type	True	100.0	625	627	95	conclusive
Haploplasma axanthum	strain=ATCC 25176	GCA_000428705.1	29552	29552	type	True	99.9186	569	627	95	conclusive
Haploplasma modicum	strain=ATCC 29102	GCA_000687835.1	2150	2150	type	True	78.1961	148	627	95	below_threshold
Mariniplasma anaerobium	strain=Mahy22	GCA_016865445.1	2735436	2735436	type	True	77.4751	81	627	95	below_threshold
Alteracholeplasma palmae	strain=J233	GCA_000968055.1	38986	38986	type	True	77.1304	86	627	95	below_threshold
Acholeplasma oculi	strain=NCTC10150	GCA_900444665.1	35623	35623	type	True	76.7078	61	627	95	below_threshold
Acholeplasma oculi	strain=ATCC 27350	GCA_900166985.1	35623	35623	type	True	76.5627	61	627	95	below_threshold
Acholeplasma equifetale	strain=ATCC 29724	GCA_000687735.1	264634	264634	type	True	76.4444	62	627	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:52,645] [INFO] DFAST Taxonomy check result was written to GCF_900660745.1_57728_G01-3_genomic.fna/tc_result.tsv
[2024-01-24 13:32:52,645] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:52,645] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:52,646] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3785026c-954e-460a-832c-d7a37509f073/dqc_reference/checkm_data
[2024-01-24 13:32:52,647] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:52,671] [INFO] Task started: CheckM
[2024-01-24 13:32:52,671] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900660745.1_57728_G01-3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900660745.1_57728_G01-3_genomic.fna/checkm_input GCF_900660745.1_57728_G01-3_genomic.fna/checkm_result
[2024-01-24 13:33:11,693] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:11,695] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:11,711] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:11,711] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:11,711] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900660745.1_57728_G01-3_genomic.fna/markers.fasta)
[2024-01-24 13:33:11,712] [INFO] Task started: Blastn
[2024-01-24 13:33:11,712] [INFO] Running command: blastn -query GCF_900660745.1_57728_G01-3_genomic.fna/markers.fasta -db /var/lib/cwl/stg3785026c-954e-460a-832c-d7a37509f073/dqc_reference/reference_markers_gtdb.fasta -out GCF_900660745.1_57728_G01-3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:12,764] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:12,767] [INFO] Selected 19 target genomes.
[2024-01-24 13:33:12,767] [INFO] Target genome list was writen to GCF_900660745.1_57728_G01-3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:12,783] [INFO] Task started: fastANI
[2024-01-24 13:33:12,783] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a0c21be-8abb-4c0c-85f5-46e2a5c3af5d/GCF_900660745.1_57728_G01-3_genomic.fna.gz --refList GCF_900660745.1_57728_G01-3_genomic.fna/target_genomes_gtdb.txt --output GCF_900660745.1_57728_G01-3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:18,345] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:18,354] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:18,354] [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_900660745.1	s__Acholeplasma_A axanthum	100.0	625	627	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__Acholeplasma_A	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_000687835.1	s__Acholeplasma_A modicum	78.1822	147	627	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__Acholeplasma_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012837395.1	s__Acholeplasma_A sp012837395	77.5221	76	627	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__Acholeplasma_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016865445.1	s__MZ-XQ sp016865445	77.4553	80	627	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__MZ-XQ	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002838205.1	s__MZ-XQ sp002838205	77.1947	78	627	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__MZ-XQ	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002838185.1	s__MZ-XQ sp002838185	77.0313	69	627	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__MZ-XQ	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018622495.1	s__WOFB19 sp018622495	76.9789	72	627	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__WOFB19	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000968055.1	s__Acholeplasma_D palmae	76.9608	83	627	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__Acholeplasma_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000687735.1	s__Acholeplasma equifetale	76.4444	62	627	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 13:33:18,356] [INFO] GTDB search result was written to GCF_900660745.1_57728_G01-3_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:18,357] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:18,360] [INFO] DFAST_QC result json was written to GCF_900660745.1_57728_G01-3_genomic.fna/dqc_result.json
[2024-01-24 13:33:18,360] [INFO] DFAST_QC completed!
[2024-01-24 13:33:18,360] [INFO] Total running time: 0h0m38s