[2024-01-24 14:06:29,879] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:29,888] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:29,888] [INFO] DQC Reference Directory: /var/lib/cwl/stg00967d7e-c6d4-4e29-bdec-bc1c5e3e3413/dqc_reference
[2024-01-24 14:06:31,155] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:31,156] [INFO] Task started: Prodigal
[2024-01-24 14:06:31,156] [INFO] Running command: gunzip -c /var/lib/cwl/stg369b0793-8857-4449-87fa-3d35ed6a8f3f/GCF_000423385.1_ASM42338v1_genomic.fna.gz | prodigal -d GCF_000423385.1_ASM42338v1_genomic.fna/cds.fna -a GCF_000423385.1_ASM42338v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:35,451] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:35,451] [INFO] Task started: HMMsearch
[2024-01-24 14:06:35,451] [INFO] Running command: hmmsearch --tblout GCF_000423385.1_ASM42338v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg00967d7e-c6d4-4e29-bdec-bc1c5e3e3413/dqc_reference/reference_markers.hmm GCF_000423385.1_ASM42338v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:35,656] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:35,658] [INFO] Found 6/6 markers.
[2024-01-24 14:06:35,681] [INFO] Query marker FASTA was written to GCF_000423385.1_ASM42338v1_genomic.fna/markers.fasta
[2024-01-24 14:06:35,681] [INFO] Task started: Blastn
[2024-01-24 14:06:35,681] [INFO] Running command: blastn -query GCF_000423385.1_ASM42338v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg00967d7e-c6d4-4e29-bdec-bc1c5e3e3413/dqc_reference/reference_markers.fasta -out GCF_000423385.1_ASM42338v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:36,297] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:36,301] [INFO] Selected 10 target genomes.
[2024-01-24 14:06:36,301] [INFO] Target genome list was writen to GCF_000423385.1_ASM42338v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:36,314] [INFO] Task started: fastANI
[2024-01-24 14:06:36,314] [INFO] Running command: fastANI --query /var/lib/cwl/stg369b0793-8857-4449-87fa-3d35ed6a8f3f/GCF_000423385.1_ASM42338v1_genomic.fna.gz --refList GCF_000423385.1_ASM42338v1_genomic.fna/target_genomes.txt --output GCF_000423385.1_ASM42338v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:41,174] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:41,174] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg00967d7e-c6d4-4e29-bdec-bc1c5e3e3413/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:41,175] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg00967d7e-c6d4-4e29-bdec-bc1c5e3e3413/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:41,179] [INFO] Found 4 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:06:41,180] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:41,180] [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
Megamonas hypermegale	strain=DSM 1672	GCA_000423385.1	158847	158847	type	True	100.0	690	693	95	conclusive
Megamonas hypermegale	strain=NCTC10570	GCA_900187035.1	158847	158847	type	True	99.9898	692	693	95	conclusive
Megamonas funiformis	strain=YIT 11815	GCA_000245775.1	437897	437897	type	True	81.5471	427	693	95	below_threshold
Megamonas funiformis	strain=JCM 14723	GCA_010669225.1	437897	437897	type	True	81.5193	440	693	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:41,182] [INFO] DFAST Taxonomy check result was written to GCF_000423385.1_ASM42338v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:41,182] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:41,182] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:41,182] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg00967d7e-c6d4-4e29-bdec-bc1c5e3e3413/dqc_reference/checkm_data
[2024-01-24 14:06:41,183] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:41,205] [INFO] Task started: CheckM
[2024-01-24 14:06:41,206] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000423385.1_ASM42338v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000423385.1_ASM42338v1_genomic.fna/checkm_input GCF_000423385.1_ASM42338v1_genomic.fna/checkm_result
[2024-01-24 14:07:00,142] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:00,143] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:00,168] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:00,169] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:00,169] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000423385.1_ASM42338v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:00,169] [INFO] Task started: Blastn
[2024-01-24 14:07:00,169] [INFO] Running command: blastn -query GCF_000423385.1_ASM42338v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg00967d7e-c6d4-4e29-bdec-bc1c5e3e3413/dqc_reference/reference_markers_gtdb.fasta -out GCF_000423385.1_ASM42338v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:01,180] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:01,183] [INFO] Selected 13 target genomes.
[2024-01-24 14:07:01,184] [INFO] Target genome list was writen to GCF_000423385.1_ASM42338v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:01,195] [INFO] Task started: fastANI
[2024-01-24 14:07:01,196] [INFO] Running command: fastANI --query /var/lib/cwl/stg369b0793-8857-4449-87fa-3d35ed6a8f3f/GCF_000423385.1_ASM42338v1_genomic.fna.gz --refList GCF_000423385.1_ASM42338v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000423385.1_ASM42338v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:06,283] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:06,290] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:06,290] [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_900187035.1	s__Megamonas hypermegale	99.9898	692	693	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Megamonas	95.0	98.37	97.31	0.90	0.84	6	conclusive
GCA_002314325.1	s__Megamonas hypermegale_A	81.7394	368	693	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Megamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010669225.1	s__Megamonas funiformis	81.5281	441	693	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Megamonas	95.0	97.89	97.23	0.89	0.80	26	-
GCA_900556715.1	s__Megamonas sp900556715	81.3184	194	693	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Megamonas	95.0	99.82	99.65	0.90	0.83	3	-
GCA_900554895.1	s__Megamonas gallistercoris	80.886	344	693	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Megamonas	95.0	98.29	98.29	0.76	0.76	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:06,291] [INFO] GTDB search result was written to GCF_000423385.1_ASM42338v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:06,292] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:06,294] [INFO] DFAST_QC result json was written to GCF_000423385.1_ASM42338v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:06,294] [INFO] DFAST_QC completed!
[2024-01-24 14:07:06,294] [INFO] Total running time: 0h0m36s