[2023-06-08 14:28:14,990] [INFO] DFAST_QC pipeline started.
[2023-06-08 14:28:14,992] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 14:28:14,993] [INFO] DQC Reference Directory: /var/lib/cwl/stg885a6908-593a-4237-9017-3536665e6ece/dqc_reference
[2023-06-08 14:28:18,280] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 14:28:18,282] [INFO] Task started: Prodigal
[2023-06-08 14:28:18,282] [INFO] Running command: gunzip -c /var/lib/cwl/stgc3ae5582-c3f6-4e63-b1f1-cb9a9dfda432/GCA_902765285.1_Rumen_uncultured_genome_RUG11049_genomic.fna.gz | prodigal -d GCA_902765285.1_Rumen_uncultured_genome_RUG11049_genomic.fna/cds.fna -a GCA_902765285.1_Rumen_uncultured_genome_RUG11049_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 14:28:22,655] [INFO] Task succeeded: Prodigal
[2023-06-08 14:28:22,656] [INFO] Task started: HMMsearch
[2023-06-08 14:28:22,656] [INFO] Running command: hmmsearch --tblout GCA_902765285.1_Rumen_uncultured_genome_RUG11049_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg885a6908-593a-4237-9017-3536665e6ece/dqc_reference/reference_markers.hmm GCA_902765285.1_Rumen_uncultured_genome_RUG11049_genomic.fna/protein.faa > /dev/null
[2023-06-08 14:28:23,002] [INFO] Task succeeded: HMMsearch
[2023-06-08 14:28:23,003] [INFO] Found 6/6 markers.
[2023-06-08 14:28:23,045] [INFO] Query marker FASTA was written to GCA_902765285.1_Rumen_uncultured_genome_RUG11049_genomic.fna/markers.fasta
[2023-06-08 14:28:23,045] [INFO] Task started: Blastn
[2023-06-08 14:28:23,045] [INFO] Running command: blastn -query GCA_902765285.1_Rumen_uncultured_genome_RUG11049_genomic.fna/markers.fasta -db /var/lib/cwl/stg885a6908-593a-4237-9017-3536665e6ece/dqc_reference/reference_markers.fasta -out GCA_902765285.1_Rumen_uncultured_genome_RUG11049_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 14:28:24,472] [INFO] Task succeeded: Blastn
[2023-06-08 14:28:24,482] [INFO] Selected 28 target genomes.
[2023-06-08 14:28:24,482] [INFO] Target genome list was writen to GCA_902765285.1_Rumen_uncultured_genome_RUG11049_genomic.fna/target_genomes.txt
[2023-06-08 14:28:24,491] [INFO] Task started: fastANI
[2023-06-08 14:28:24,492] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3ae5582-c3f6-4e63-b1f1-cb9a9dfda432/GCA_902765285.1_Rumen_uncultured_genome_RUG11049_genomic.fna.gz --refList GCA_902765285.1_Rumen_uncultured_genome_RUG11049_genomic.fna/target_genomes.txt --output GCA_902765285.1_Rumen_uncultured_genome_RUG11049_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 14:28:40,664] [INFO] Task succeeded: fastANI
[2023-06-08 14:28:40,665] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg885a6908-593a-4237-9017-3536665e6ece/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 14:28:40,666] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg885a6908-593a-4237-9017-3536665e6ece/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 14:28:40,667] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 14:28:40,668] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 14:28:40,668] [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
--------------------------------------------------------------------------------
[2023-06-08 14:28:40,670] [INFO] DFAST Taxonomy check result was written to GCA_902765285.1_Rumen_uncultured_genome_RUG11049_genomic.fna/tc_result.tsv
[2023-06-08 14:28:40,671] [INFO] ===== Taxonomy check completed =====
[2023-06-08 14:28:40,672] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 14:28:40,672] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg885a6908-593a-4237-9017-3536665e6ece/dqc_reference/checkm_data
[2023-06-08 14:28:40,681] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 14:28:40,709] [INFO] Task started: CheckM
[2023-06-08 14:28:40,709] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902765285.1_Rumen_uncultured_genome_RUG11049_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902765285.1_Rumen_uncultured_genome_RUG11049_genomic.fna/checkm_input GCA_902765285.1_Rumen_uncultured_genome_RUG11049_genomic.fna/checkm_result
[2023-06-08 14:29:01,755] [INFO] Task succeeded: CheckM
[2023-06-08 14:29:01,757] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.22%
Contamintation: 6.25%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-08 14:29:01,780] [INFO] ===== Completeness check finished =====
[2023-06-08 14:29:01,781] [INFO] ===== Start GTDB Search =====
[2023-06-08 14:29:01,781] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902765285.1_Rumen_uncultured_genome_RUG11049_genomic.fna/markers.fasta)
[2023-06-08 14:29:01,781] [INFO] Task started: Blastn
[2023-06-08 14:29:01,782] [INFO] Running command: blastn -query GCA_902765285.1_Rumen_uncultured_genome_RUG11049_genomic.fna/markers.fasta -db /var/lib/cwl/stg885a6908-593a-4237-9017-3536665e6ece/dqc_reference/reference_markers_gtdb.fasta -out GCA_902765285.1_Rumen_uncultured_genome_RUG11049_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 14:29:02,923] [INFO] Task succeeded: Blastn
[2023-06-08 14:29:02,927] [INFO] Selected 11 target genomes.
[2023-06-08 14:29:02,927] [INFO] Target genome list was writen to GCA_902765285.1_Rumen_uncultured_genome_RUG11049_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 14:29:02,933] [INFO] Task started: fastANI
[2023-06-08 14:29:02,933] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3ae5582-c3f6-4e63-b1f1-cb9a9dfda432/GCA_902765285.1_Rumen_uncultured_genome_RUG11049_genomic.fna.gz --refList GCA_902765285.1_Rumen_uncultured_genome_RUG11049_genomic.fna/target_genomes_gtdb.txt --output GCA_902765285.1_Rumen_uncultured_genome_RUG11049_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 14:29:07,540] [INFO] Task succeeded: fastANI
[2023-06-08 14:29:07,550] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 14:29:07,551] [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_900100595.1	s__Ruminococcus_E sp900100595	98.5962	468	523	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	98.87	97.87	0.91	0.78	34	conclusive
GCF_016680995.1	s__Ruminococcus_E sp016680995	84.1431	201	523	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900320415.1	s__Ruminococcus_E sp900320415	82.822	256	523	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	99.69	99.69	0.84	0.84	2	-
GCA_900316555.1	s__Ruminococcus_E sp900316555	82.5538	298	523	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	98.80	96.62	0.88	0.77	62	-
GCF_018918205.1	s__Ruminococcus_E sp018918205	81.39	232	523	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902765625.1	s__Ruminococcus_E sp902765625	80.848	287	523	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	99.31	99.27	0.90	0.89	5	-
GCA_902761375.1	s__Ruminococcus_E sp902761375	80.016	199	523	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902784855.1	s__Ruminococcus_E sp902784855	80.0001	251	523	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900316815.1	s__Ruminococcus_E sp900316815	79.9409	204	523	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	99.08	98.49	0.85	0.78	7	-
GCA_900317595.1	s__Ruminococcus_E sp900317595	79.1395	189	523	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	99.55	99.10	0.91	0.83	3	-
GCA_902764715.1	s__Ruminococcus_E sp902764715	77.9017	84	523	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 14:29:07,553] [INFO] GTDB search result was written to GCA_902765285.1_Rumen_uncultured_genome_RUG11049_genomic.fna/result_gtdb.tsv
[2023-06-08 14:29:07,553] [INFO] ===== GTDB Search completed =====
[2023-06-08 14:29:07,556] [INFO] DFAST_QC result json was written to GCA_902765285.1_Rumen_uncultured_genome_RUG11049_genomic.fna/dqc_result.json
[2023-06-08 14:29:07,556] [INFO] DFAST_QC completed!
[2023-06-08 14:29:07,557] [INFO] Total running time: 0h0m53s