[2023-06-05 07:01:18,815] [INFO] DFAST_QC pipeline started.
[2023-06-05 07:01:18,818] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 07:01:18,818] [INFO] DQC Reference Directory: /var/lib/cwl/stgf9f8226f-ba20-401b-ab7f-ba5e9e13659a/dqc_reference
[2023-06-05 07:01:21,160] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 07:01:21,161] [INFO] Task started: Prodigal
[2023-06-05 07:01:21,161] [INFO] Running command: gunzip -c /var/lib/cwl/stg402414c5-07b5-4115-8fc8-42810a3845f9/GCA_902758875.1_Rumen_uncultured_genome_RUG10409_genomic.fna.gz | prodigal -d GCA_902758875.1_Rumen_uncultured_genome_RUG10409_genomic.fna/cds.fna -a GCA_902758875.1_Rumen_uncultured_genome_RUG10409_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 07:01:26,278] [INFO] Task succeeded: Prodigal
[2023-06-05 07:01:26,279] [INFO] Task started: HMMsearch
[2023-06-05 07:01:26,279] [INFO] Running command: hmmsearch --tblout GCA_902758875.1_Rumen_uncultured_genome_RUG10409_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf9f8226f-ba20-401b-ab7f-ba5e9e13659a/dqc_reference/reference_markers.hmm GCA_902758875.1_Rumen_uncultured_genome_RUG10409_genomic.fna/protein.faa > /dev/null
[2023-06-05 07:01:26,533] [INFO] Task succeeded: HMMsearch
[2023-06-05 07:01:26,534] [INFO] Found 6/6 markers.
[2023-06-05 07:01:26,557] [INFO] Query marker FASTA was written to GCA_902758875.1_Rumen_uncultured_genome_RUG10409_genomic.fna/markers.fasta
[2023-06-05 07:01:26,558] [INFO] Task started: Blastn
[2023-06-05 07:01:26,558] [INFO] Running command: blastn -query GCA_902758875.1_Rumen_uncultured_genome_RUG10409_genomic.fna/markers.fasta -db /var/lib/cwl/stgf9f8226f-ba20-401b-ab7f-ba5e9e13659a/dqc_reference/reference_markers.fasta -out GCA_902758875.1_Rumen_uncultured_genome_RUG10409_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 07:01:27,221] [INFO] Task succeeded: Blastn
[2023-06-05 07:01:27,226] [INFO] Selected 21 target genomes.
[2023-06-05 07:01:27,226] [INFO] Target genome list was writen to GCA_902758875.1_Rumen_uncultured_genome_RUG10409_genomic.fna/target_genomes.txt
[2023-06-05 07:01:27,231] [INFO] Task started: fastANI
[2023-06-05 07:01:27,231] [INFO] Running command: fastANI --query /var/lib/cwl/stg402414c5-07b5-4115-8fc8-42810a3845f9/GCA_902758875.1_Rumen_uncultured_genome_RUG10409_genomic.fna.gz --refList GCA_902758875.1_Rumen_uncultured_genome_RUG10409_genomic.fna/target_genomes.txt --output GCA_902758875.1_Rumen_uncultured_genome_RUG10409_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 07:01:38,710] [INFO] Task succeeded: fastANI
[2023-06-05 07:01:38,711] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf9f8226f-ba20-401b-ab7f-ba5e9e13659a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 07:01:38,711] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf9f8226f-ba20-401b-ab7f-ba5e9e13659a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 07:01:38,713] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 07:01:38,713] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 07:01:38,714] [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
--------------------------------------------------------------------------------
[2023-06-05 07:01:38,716] [INFO] DFAST Taxonomy check result was written to GCA_902758875.1_Rumen_uncultured_genome_RUG10409_genomic.fna/tc_result.tsv
[2023-06-05 07:01:38,717] [INFO] ===== Taxonomy check completed =====
[2023-06-05 07:01:38,717] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 07:01:38,717] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf9f8226f-ba20-401b-ab7f-ba5e9e13659a/dqc_reference/checkm_data
[2023-06-05 07:01:38,721] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 07:01:38,755] [INFO] Task started: CheckM
[2023-06-05 07:01:38,755] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902758875.1_Rumen_uncultured_genome_RUG10409_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902758875.1_Rumen_uncultured_genome_RUG10409_genomic.fna/checkm_input GCA_902758875.1_Rumen_uncultured_genome_RUG10409_genomic.fna/checkm_result
[2023-06-05 07:02:00,086] [INFO] Task succeeded: CheckM
[2023-06-05 07:02:00,087] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 07:02:00,112] [INFO] ===== Completeness check finished =====
[2023-06-05 07:02:00,112] [INFO] ===== Start GTDB Search =====
[2023-06-05 07:02:00,113] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902758875.1_Rumen_uncultured_genome_RUG10409_genomic.fna/markers.fasta)
[2023-06-05 07:02:00,113] [INFO] Task started: Blastn
[2023-06-05 07:02:00,113] [INFO] Running command: blastn -query GCA_902758875.1_Rumen_uncultured_genome_RUG10409_genomic.fna/markers.fasta -db /var/lib/cwl/stgf9f8226f-ba20-401b-ab7f-ba5e9e13659a/dqc_reference/reference_markers_gtdb.fasta -out GCA_902758875.1_Rumen_uncultured_genome_RUG10409_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 07:02:01,248] [INFO] Task succeeded: Blastn
[2023-06-05 07:02:01,255] [INFO] Selected 10 target genomes.
[2023-06-05 07:02:01,256] [INFO] Target genome list was writen to GCA_902758875.1_Rumen_uncultured_genome_RUG10409_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 07:02:01,261] [INFO] Task started: fastANI
[2023-06-05 07:02:01,261] [INFO] Running command: fastANI --query /var/lib/cwl/stg402414c5-07b5-4115-8fc8-42810a3845f9/GCA_902758875.1_Rumen_uncultured_genome_RUG10409_genomic.fna.gz --refList GCA_902758875.1_Rumen_uncultured_genome_RUG10409_genomic.fna/target_genomes_gtdb.txt --output GCA_902758875.1_Rumen_uncultured_genome_RUG10409_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 07:02:06,397] [INFO] Task succeeded: fastANI
[2023-06-05 07:02:06,408] [INFO] Found 10 fastANI hits (2 hits with ANI > circumscription radius)
[2023-06-05 07:02:06,409] [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_902768995.1	s__RUG472 sp902768995	98.4179	380	542	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__RUG472	95.0	98.42	98.10	0.83	0.75	15	inconclusive
GCA_900319345.1	s__RUG472 sp900319345	95.1613	455	542	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__RUG472	95.0	98.47	97.84	0.91	0.80	6	inconclusive
GCA_902786465.1	s__RUG472 sp902786465	93.8266	444	542	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__RUG472	95.0	96.79	96.79	0.84	0.84	2	-
GCA_902761365.1	s__RUG472 sp902761365	87.6443	407	542	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__RUG472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902802805.1	s__RUG472 sp902802805	87.5246	403	542	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__RUG472	95.0	97.22	97.22	0.86	0.86	2	-
GCA_902801845.1	s__RUG472 sp902801845	87.3343	447	542	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__RUG472	95.0	96.79	96.35	0.92	0.91	4	-
GCA_902802575.1	s__RUG472 sp902802575	86.9871	408	542	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__RUG472	95.0	95.40	95.40	0.82	0.82	2	-
GCA_017545535.1	s__RUG472 sp017545535	86.745	431	542	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__RUG472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902798825.1	s__RUG472 sp902798825	86.5262	421	542	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__RUG472	95.0	97.85	97.83	0.89	0.89	3	-
GCA_902765005.1	s__RUG472 sp902765005	85.5167	432	542	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__RUG472	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 07:02:06,411] [INFO] GTDB search result was written to GCA_902758875.1_Rumen_uncultured_genome_RUG10409_genomic.fna/result_gtdb.tsv
[2023-06-05 07:02:06,411] [INFO] ===== GTDB Search completed =====
[2023-06-05 07:02:06,415] [INFO] DFAST_QC result json was written to GCA_902758875.1_Rumen_uncultured_genome_RUG10409_genomic.fna/dqc_result.json
[2023-06-05 07:02:06,415] [INFO] DFAST_QC completed!
[2023-06-05 07:02:06,415] [INFO] Total running time: 0h0m48s