[2023-06-30 22:46:46,648] [INFO] DFAST_QC pipeline started.
[2023-06-30 22:46:46,650] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 22:46:46,650] [INFO] DQC Reference Directory: /var/lib/cwl/stgbd36a73d-3fb3-4633-905e-32e3f33a39ce/dqc_reference
[2023-06-30 22:46:47,831] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 22:46:47,832] [INFO] Task started: Prodigal
[2023-06-30 22:46:47,833] [INFO] Running command: gunzip -c /var/lib/cwl/stg06094249-3683-4b02-a757-5a5392204b78/GCA_016288855.1_ASM1628885v1_genomic.fna.gz | prodigal -d GCA_016288855.1_ASM1628885v1_genomic.fna/cds.fna -a GCA_016288855.1_ASM1628885v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 22:46:50,172] [INFO] Task succeeded: Prodigal
[2023-06-30 22:46:50,173] [INFO] Task started: HMMsearch
[2023-06-30 22:46:50,173] [INFO] Running command: hmmsearch --tblout GCA_016288855.1_ASM1628885v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbd36a73d-3fb3-4633-905e-32e3f33a39ce/dqc_reference/reference_markers.hmm GCA_016288855.1_ASM1628885v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 22:46:50,368] [INFO] Task succeeded: HMMsearch
[2023-06-30 22:46:50,369] [INFO] Found 6/6 markers.
[2023-06-30 22:46:50,388] [INFO] Query marker FASTA was written to GCA_016288855.1_ASM1628885v1_genomic.fna/markers.fasta
[2023-06-30 22:46:50,389] [INFO] Task started: Blastn
[2023-06-30 22:46:50,389] [INFO] Running command: blastn -query GCA_016288855.1_ASM1628885v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd36a73d-3fb3-4633-905e-32e3f33a39ce/dqc_reference/reference_markers.fasta -out GCA_016288855.1_ASM1628885v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 22:46:50,948] [INFO] Task succeeded: Blastn
[2023-06-30 22:46:50,951] [INFO] Selected 20 target genomes.
[2023-06-30 22:46:50,952] [INFO] Target genome list was writen to GCA_016288855.1_ASM1628885v1_genomic.fna/target_genomes.txt
[2023-06-30 22:46:50,955] [INFO] Task started: fastANI
[2023-06-30 22:46:50,955] [INFO] Running command: fastANI --query /var/lib/cwl/stg06094249-3683-4b02-a757-5a5392204b78/GCA_016288855.1_ASM1628885v1_genomic.fna.gz --refList GCA_016288855.1_ASM1628885v1_genomic.fna/target_genomes.txt --output GCA_016288855.1_ASM1628885v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 22:46:59,159] [INFO] Task succeeded: fastANI
[2023-06-30 22:46:59,160] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbd36a73d-3fb3-4633-905e-32e3f33a39ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 22:46:59,160] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbd36a73d-3fb3-4633-905e-32e3f33a39ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 22:46:59,164] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 22:46:59,164] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 22:46:59,164] [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
Anaeroplasma bactoclasticum	strain=ATCC 27112	GCA_003550015.1	2088	2088	type	True	77.7025	134	546	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 22:46:59,166] [INFO] DFAST Taxonomy check result was written to GCA_016288855.1_ASM1628885v1_genomic.fna/tc_result.tsv
[2023-06-30 22:46:59,167] [INFO] ===== Taxonomy check completed =====
[2023-06-30 22:46:59,167] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 22:46:59,167] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbd36a73d-3fb3-4633-905e-32e3f33a39ce/dqc_reference/checkm_data
[2023-06-30 22:46:59,168] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 22:46:59,187] [INFO] Task started: CheckM
[2023-06-30 22:46:59,188] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016288855.1_ASM1628885v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016288855.1_ASM1628885v1_genomic.fna/checkm_input GCA_016288855.1_ASM1628885v1_genomic.fna/checkm_result
[2023-06-30 22:47:13,886] [INFO] Task succeeded: CheckM
[2023-06-30 22:47:13,887] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 22:47:13,904] [INFO] ===== Completeness check finished =====
[2023-06-30 22:47:13,904] [INFO] ===== Start GTDB Search =====
[2023-06-30 22:47:13,905] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016288855.1_ASM1628885v1_genomic.fna/markers.fasta)
[2023-06-30 22:47:13,905] [INFO] Task started: Blastn
[2023-06-30 22:47:13,905] [INFO] Running command: blastn -query GCA_016288855.1_ASM1628885v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd36a73d-3fb3-4633-905e-32e3f33a39ce/dqc_reference/reference_markers_gtdb.fasta -out GCA_016288855.1_ASM1628885v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 22:47:14,657] [INFO] Task succeeded: Blastn
[2023-06-30 22:47:14,661] [INFO] Selected 16 target genomes.
[2023-06-30 22:47:14,661] [INFO] Target genome list was writen to GCA_016288855.1_ASM1628885v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 22:47:14,667] [INFO] Task started: fastANI
[2023-06-30 22:47:14,667] [INFO] Running command: fastANI --query /var/lib/cwl/stg06094249-3683-4b02-a757-5a5392204b78/GCA_016288855.1_ASM1628885v1_genomic.fna.gz --refList GCA_016288855.1_ASM1628885v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016288855.1_ASM1628885v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 22:47:19,440] [INFO] Task succeeded: fastANI
[2023-06-30 22:47:19,451] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 22:47:19,451] [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
GCA_016288855.1	s__Anaeroplasma sp016288855	100.0	536	546	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Anaeroplasmataceae;g__Anaeroplasma	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902783745.1	s__Anaeroplasma sp902783745	84.5728	289	546	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Anaeroplasmataceae;g__Anaeroplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017441525.1	s__Anaeroplasma sp017441525	78.5272	167	546	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Anaeroplasmataceae;g__Anaeroplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017449215.1	s__Anaeroplasma sp017449215	78.1765	192	546	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Anaeroplasmataceae;g__Anaeroplasma	95.0	95.35	95.35	0.87	0.87	2	-
GCA_017444645.1	s__Anaeroplasma sp017444645	78.1308	174	546	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Anaeroplasmataceae;g__Anaeroplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002449755.1	s__Anaeroplasma sp002449755	78.013	164	546	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Anaeroplasmataceae;g__Anaeroplasma	95.0	98.36	98.36	0.87	0.87	2	-
GCF_003550015.1	s__Anaeroplasma bactoclasticum	77.7657	130	546	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Anaeroplasmataceae;g__Anaeroplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017524905.1	s__Anaeroplasma sp017524905	77.4667	155	546	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Anaeroplasmataceae;g__Anaeroplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017462645.1	s__Anaeroplasma sp017462645	77.4152	72	546	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Anaeroplasmataceae;g__Anaeroplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902796895.1	s__Anaeroplasma sp902796895	77.384	121	546	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Anaeroplasmataceae;g__Anaeroplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900767915.1	s__Anaeroplasma sp900767915	77.2198	120	546	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Anaeroplasmataceae;g__Anaeroplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900770055.1	s__Anaeroplasma sp900770055	77.1184	94	546	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Anaeroplasmataceae;g__Anaeroplasma	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 22:47:19,453] [INFO] GTDB search result was written to GCA_016288855.1_ASM1628885v1_genomic.fna/result_gtdb.tsv
[2023-06-30 22:47:19,454] [INFO] ===== GTDB Search completed =====
[2023-06-30 22:47:19,457] [INFO] DFAST_QC result json was written to GCA_016288855.1_ASM1628885v1_genomic.fna/dqc_result.json
[2023-06-30 22:47:19,457] [INFO] DFAST_QC completed!
[2023-06-30 22:47:19,457] [INFO] Total running time: 0h0m33s