[2023-06-05 02:26:52,980] [INFO] DFAST_QC pipeline started.
[2023-06-05 02:26:52,983] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 02:26:52,983] [INFO] DQC Reference Directory: /var/lib/cwl/stg889d87c3-1396-4e3b-9f46-05334cf2cabb/dqc_reference
[2023-06-05 02:26:54,209] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 02:26:54,210] [INFO] Task started: Prodigal
[2023-06-05 02:26:54,210] [INFO] Running command: gunzip -c /var/lib/cwl/stg748a8508-7575-4454-a391-aa1c3e4fe5cf/GCA_902782945.1_Rumen_uncultured_genome_RUG12825_genomic.fna.gz | prodigal -d GCA_902782945.1_Rumen_uncultured_genome_RUG12825_genomic.fna/cds.fna -a GCA_902782945.1_Rumen_uncultured_genome_RUG12825_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 02:26:56,951] [INFO] Task succeeded: Prodigal
[2023-06-05 02:26:56,952] [INFO] Task started: HMMsearch
[2023-06-05 02:26:56,952] [INFO] Running command: hmmsearch --tblout GCA_902782945.1_Rumen_uncultured_genome_RUG12825_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg889d87c3-1396-4e3b-9f46-05334cf2cabb/dqc_reference/reference_markers.hmm GCA_902782945.1_Rumen_uncultured_genome_RUG12825_genomic.fna/protein.faa > /dev/null
[2023-06-05 02:26:57,245] [INFO] Task succeeded: HMMsearch
[2023-06-05 02:26:57,247] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg748a8508-7575-4454-a391-aa1c3e4fe5cf/GCA_902782945.1_Rumen_uncultured_genome_RUG12825_genomic.fna.gz]
[2023-06-05 02:26:57,277] [INFO] Query marker FASTA was written to GCA_902782945.1_Rumen_uncultured_genome_RUG12825_genomic.fna/markers.fasta
[2023-06-05 02:26:57,277] [INFO] Task started: Blastn
[2023-06-05 02:26:57,277] [INFO] Running command: blastn -query GCA_902782945.1_Rumen_uncultured_genome_RUG12825_genomic.fna/markers.fasta -db /var/lib/cwl/stg889d87c3-1396-4e3b-9f46-05334cf2cabb/dqc_reference/reference_markers.fasta -out GCA_902782945.1_Rumen_uncultured_genome_RUG12825_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:26:58,193] [INFO] Task succeeded: Blastn
[2023-06-05 02:26:58,202] [INFO] Selected 4 target genomes.
[2023-06-05 02:26:58,202] [INFO] Target genome list was writen to GCA_902782945.1_Rumen_uncultured_genome_RUG12825_genomic.fna/target_genomes.txt
[2023-06-05 02:26:58,227] [INFO] Task started: fastANI
[2023-06-05 02:26:58,227] [INFO] Running command: fastANI --query /var/lib/cwl/stg748a8508-7575-4454-a391-aa1c3e4fe5cf/GCA_902782945.1_Rumen_uncultured_genome_RUG12825_genomic.fna.gz --refList GCA_902782945.1_Rumen_uncultured_genome_RUG12825_genomic.fna/target_genomes.txt --output GCA_902782945.1_Rumen_uncultured_genome_RUG12825_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 02:26:59,784] [INFO] Task succeeded: fastANI
[2023-06-05 02:26:59,784] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg889d87c3-1396-4e3b-9f46-05334cf2cabb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 02:26:59,785] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg889d87c3-1396-4e3b-9f46-05334cf2cabb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 02:26:59,790] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 02:26:59,790] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 02:26:59,790] [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
Methanosphaera stadtmanae	strain=DSM 3091	GCA_000012545.1	2317	2317	type	True	80.0556	288	515	95	below_threshold
Methanosphaera cuniculi	strain=DSM 4103	GCA_003149675.1	1077256	1077256	type	True	78.7781	202	515	95	below_threshold
Methanosphaera cuniculi	strain=1R-7	GCA_002287195.1	1077256	1077256	type	True	78.7053	211	515	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 02:26:59,793] [INFO] DFAST Taxonomy check result was written to GCA_902782945.1_Rumen_uncultured_genome_RUG12825_genomic.fna/tc_result.tsv
[2023-06-05 02:26:59,794] [INFO] ===== Taxonomy check completed =====
[2023-06-05 02:26:59,794] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 02:26:59,795] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg889d87c3-1396-4e3b-9f46-05334cf2cabb/dqc_reference/checkm_data
[2023-06-05 02:26:59,797] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 02:26:59,820] [INFO] Task started: CheckM
[2023-06-05 02:26:59,821] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902782945.1_Rumen_uncultured_genome_RUG12825_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902782945.1_Rumen_uncultured_genome_RUG12825_genomic.fna/checkm_input GCA_902782945.1_Rumen_uncultured_genome_RUG12825_genomic.fna/checkm_result
[2023-06-05 02:27:17,968] [INFO] Task succeeded: CheckM
[2023-06-05 02:27:17,969] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.75%
Contamintation: 7.99%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-06-05 02:27:17,998] [INFO] ===== Completeness check finished =====
[2023-06-05 02:27:17,998] [INFO] ===== Start GTDB Search =====
[2023-06-05 02:27:17,999] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902782945.1_Rumen_uncultured_genome_RUG12825_genomic.fna/markers.fasta)
[2023-06-05 02:27:17,999] [INFO] Task started: Blastn
[2023-06-05 02:27:17,999] [INFO] Running command: blastn -query GCA_902782945.1_Rumen_uncultured_genome_RUG12825_genomic.fna/markers.fasta -db /var/lib/cwl/stg889d87c3-1396-4e3b-9f46-05334cf2cabb/dqc_reference/reference_markers_gtdb.fasta -out GCA_902782945.1_Rumen_uncultured_genome_RUG12825_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:27:18,535] [INFO] Task succeeded: Blastn
[2023-06-05 02:27:18,539] [INFO] Selected 5 target genomes.
[2023-06-05 02:27:18,539] [INFO] Target genome list was writen to GCA_902782945.1_Rumen_uncultured_genome_RUG12825_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 02:27:18,544] [INFO] Task started: fastANI
[2023-06-05 02:27:18,544] [INFO] Running command: fastANI --query /var/lib/cwl/stg748a8508-7575-4454-a391-aa1c3e4fe5cf/GCA_902782945.1_Rumen_uncultured_genome_RUG12825_genomic.fna.gz --refList GCA_902782945.1_Rumen_uncultured_genome_RUG12825_genomic.fna/target_genomes_gtdb.txt --output GCA_902782945.1_Rumen_uncultured_genome_RUG12825_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 02:27:20,750] [INFO] Task succeeded: fastANI
[2023-06-05 02:27:20,758] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 02:27:20,758] [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_902782945.1	s__Methanosphaera sp900322125	100.0	506	515	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanosphaera	95.0	97.80	97.01	0.80	0.75	4	conclusive
GCF_001729965.1	s__Methanosphaera sp001729965	80.7027	287	515	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanosphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000012545.1	s__Methanosphaera stadtmanae	80.0552	288	515	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanosphaera	95.0	99.82	99.70	0.99	0.98	6	-
GCF_003149675.1	s__Methanosphaera cuniculi	78.8001	201	515	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanosphaera	95.0	99.96	99.96	0.98	0.98	2	-
GCA_015062825.1	s__Methanosphaera stadtmanae_A	78.3144	199	515	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanosphaera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 02:27:20,761] [INFO] GTDB search result was written to GCA_902782945.1_Rumen_uncultured_genome_RUG12825_genomic.fna/result_gtdb.tsv
[2023-06-05 02:27:20,761] [INFO] ===== GTDB Search completed =====
[2023-06-05 02:27:20,765] [INFO] DFAST_QC result json was written to GCA_902782945.1_Rumen_uncultured_genome_RUG12825_genomic.fna/dqc_result.json
[2023-06-05 02:27:20,765] [INFO] DFAST_QC completed!
[2023-06-05 02:27:20,766] [INFO] Total running time: 0h0m28s