[2023-06-08 19:51:42,703] [INFO] DFAST_QC pipeline started.
[2023-06-08 19:51:42,706] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 19:51:42,706] [INFO] DQC Reference Directory: /var/lib/cwl/stg61ea5971-30c5-45a3-b704-5cdc1e1c55cf/dqc_reference
[2023-06-08 19:51:43,959] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 19:51:43,960] [INFO] Task started: Prodigal
[2023-06-08 19:51:43,961] [INFO] Running command: gunzip -c /var/lib/cwl/stge06cf9c7-7543-4eec-9d69-4173ee0de23e/GCA_902795285.1_Rumen_uncultured_genome_RUG14051_genomic.fna.gz | prodigal -d GCA_902795285.1_Rumen_uncultured_genome_RUG14051_genomic.fna/cds.fna -a GCA_902795285.1_Rumen_uncultured_genome_RUG14051_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 19:51:56,369] [INFO] Task succeeded: Prodigal
[2023-06-08 19:51:56,370] [INFO] Task started: HMMsearch
[2023-06-08 19:51:56,370] [INFO] Running command: hmmsearch --tblout GCA_902795285.1_Rumen_uncultured_genome_RUG14051_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg61ea5971-30c5-45a3-b704-5cdc1e1c55cf/dqc_reference/reference_markers.hmm GCA_902795285.1_Rumen_uncultured_genome_RUG14051_genomic.fna/protein.faa > /dev/null
[2023-06-08 19:51:56,601] [INFO] Task succeeded: HMMsearch
[2023-06-08 19:51:56,603] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge06cf9c7-7543-4eec-9d69-4173ee0de23e/GCA_902795285.1_Rumen_uncultured_genome_RUG14051_genomic.fna.gz]
[2023-06-08 19:51:56,631] [INFO] Query marker FASTA was written to GCA_902795285.1_Rumen_uncultured_genome_RUG14051_genomic.fna/markers.fasta
[2023-06-08 19:51:56,631] [INFO] Task started: Blastn
[2023-06-08 19:51:56,631] [INFO] Running command: blastn -query GCA_902795285.1_Rumen_uncultured_genome_RUG14051_genomic.fna/markers.fasta -db /var/lib/cwl/stg61ea5971-30c5-45a3-b704-5cdc1e1c55cf/dqc_reference/reference_markers.fasta -out GCA_902795285.1_Rumen_uncultured_genome_RUG14051_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 19:51:57,239] [INFO] Task succeeded: Blastn
[2023-06-08 19:51:57,243] [INFO] Selected 21 target genomes.
[2023-06-08 19:51:57,243] [INFO] Target genome list was writen to GCA_902795285.1_Rumen_uncultured_genome_RUG14051_genomic.fna/target_genomes.txt
[2023-06-08 19:51:57,244] [INFO] Task started: fastANI
[2023-06-08 19:51:57,245] [INFO] Running command: fastANI --query /var/lib/cwl/stge06cf9c7-7543-4eec-9d69-4173ee0de23e/GCA_902795285.1_Rumen_uncultured_genome_RUG14051_genomic.fna.gz --refList GCA_902795285.1_Rumen_uncultured_genome_RUG14051_genomic.fna/target_genomes.txt --output GCA_902795285.1_Rumen_uncultured_genome_RUG14051_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 19:52:06,977] [INFO] Task succeeded: fastANI
[2023-06-08 19:52:06,978] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg61ea5971-30c5-45a3-b704-5cdc1e1c55cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 19:52:06,979] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg61ea5971-30c5-45a3-b704-5cdc1e1c55cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 19:52:06,991] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 19:52:06,991] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 19:52:06,991] [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
Prevotella ruminicola	strain=Bryant 23	GCA_000025925.1	839	839	type	True	77.6577	50	663	95	below_threshold
Prevotella ruminicola	strain=ATCC 19189	GCA_900108375.1	839	839	type	True	77.366	50	663	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_000157935.1	165179	165179	suspected-type	True	77.0972	61	663	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_025151535.1	165179	165179	suspected-type	True	77.0477	62	663	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	76.9039	61	663	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	76.3936	52	663	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 19:52:06,993] [INFO] DFAST Taxonomy check result was written to GCA_902795285.1_Rumen_uncultured_genome_RUG14051_genomic.fna/tc_result.tsv
[2023-06-08 19:52:06,994] [INFO] ===== Taxonomy check completed =====
[2023-06-08 19:52:06,994] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 19:52:06,994] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg61ea5971-30c5-45a3-b704-5cdc1e1c55cf/dqc_reference/checkm_data
[2023-06-08 19:52:06,995] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 19:52:07,028] [INFO] Task started: CheckM
[2023-06-08 19:52:07,028] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902795285.1_Rumen_uncultured_genome_RUG14051_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902795285.1_Rumen_uncultured_genome_RUG14051_genomic.fna/checkm_input GCA_902795285.1_Rumen_uncultured_genome_RUG14051_genomic.fna/checkm_result
[2023-06-08 19:52:46,267] [INFO] Task succeeded: CheckM
[2023-06-08 19:52:46,268] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 19:52:46,290] [INFO] ===== Completeness check finished =====
[2023-06-08 19:52:46,290] [INFO] ===== Start GTDB Search =====
[2023-06-08 19:52:46,291] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902795285.1_Rumen_uncultured_genome_RUG14051_genomic.fna/markers.fasta)
[2023-06-08 19:52:46,291] [INFO] Task started: Blastn
[2023-06-08 19:52:46,291] [INFO] Running command: blastn -query GCA_902795285.1_Rumen_uncultured_genome_RUG14051_genomic.fna/markers.fasta -db /var/lib/cwl/stg61ea5971-30c5-45a3-b704-5cdc1e1c55cf/dqc_reference/reference_markers_gtdb.fasta -out GCA_902795285.1_Rumen_uncultured_genome_RUG14051_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 19:52:47,134] [INFO] Task succeeded: Blastn
[2023-06-08 19:52:47,138] [INFO] Selected 19 target genomes.
[2023-06-08 19:52:47,139] [INFO] Target genome list was writen to GCA_902795285.1_Rumen_uncultured_genome_RUG14051_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 19:52:47,142] [INFO] Task started: fastANI
[2023-06-08 19:52:47,142] [INFO] Running command: fastANI --query /var/lib/cwl/stge06cf9c7-7543-4eec-9d69-4173ee0de23e/GCA_902795285.1_Rumen_uncultured_genome_RUG14051_genomic.fna.gz --refList GCA_902795285.1_Rumen_uncultured_genome_RUG14051_genomic.fna/target_genomes_gtdb.txt --output GCA_902795285.1_Rumen_uncultured_genome_RUG14051_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 19:52:57,860] [INFO] Task succeeded: fastANI
[2023-06-08 19:52:57,872] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 19:52:57,872] [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_900102385.1	s__Ga6A1 sp900102385	97.1921	631	663	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Ga6A1	95.0	97.13	96.74	0.91	0.83	31	conclusive
GCA_017617315.1	s__Ga6A1 sp017617315	91.4753	613	663	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Ga6A1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017617575.1	s__UBA4334 sp017617575	77.4478	66	663	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019052365.1	s__Prevotella sp000434975	77.0143	54	663	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.22	96.59	0.82	0.74	11	-
GCF_001275135.1	s__Prevotella rara	76.9253	52	663	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.17	97.70	0.90	0.86	7	-
GCA_000436695.1	s__Prevotella sp000436695	76.6182	50	663	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.96	98.24	0.85	0.83	3	-
--------------------------------------------------------------------------------
[2023-06-08 19:52:57,874] [INFO] GTDB search result was written to GCA_902795285.1_Rumen_uncultured_genome_RUG14051_genomic.fna/result_gtdb.tsv
[2023-06-08 19:52:57,874] [INFO] ===== GTDB Search completed =====
[2023-06-08 19:52:57,877] [INFO] DFAST_QC result json was written to GCA_902795285.1_Rumen_uncultured_genome_RUG14051_genomic.fna/dqc_result.json
[2023-06-08 19:52:57,877] [INFO] DFAST_QC completed!
[2023-06-08 19:52:57,878] [INFO] Total running time: 0h1m15s