[2023-06-04 20:24:09,430] [INFO] DFAST_QC pipeline started.
[2023-06-04 20:24:09,433] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 20:24:09,434] [INFO] DQC Reference Directory: /var/lib/cwl/stgbef7d3ae-cf7c-4fef-b0a4-03d3f2465d7e/dqc_reference
[2023-06-04 20:24:11,089] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 20:24:11,089] [INFO] Task started: Prodigal
[2023-06-04 20:24:11,090] [INFO] Running command: gunzip -c /var/lib/cwl/stg4f3a3180-67be-498a-9e6c-bc6accffba37/GCA_902767155.1_Rumen_uncultured_genome_RUG11228_genomic.fna.gz | prodigal -d GCA_902767155.1_Rumen_uncultured_genome_RUG11228_genomic.fna/cds.fna -a GCA_902767155.1_Rumen_uncultured_genome_RUG11228_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 20:24:15,089] [INFO] Task succeeded: Prodigal
[2023-06-04 20:24:15,089] [INFO] Task started: HMMsearch
[2023-06-04 20:24:15,089] [INFO] Running command: hmmsearch --tblout GCA_902767155.1_Rumen_uncultured_genome_RUG11228_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbef7d3ae-cf7c-4fef-b0a4-03d3f2465d7e/dqc_reference/reference_markers.hmm GCA_902767155.1_Rumen_uncultured_genome_RUG11228_genomic.fna/protein.faa > /dev/null
[2023-06-04 20:24:15,360] [INFO] Task succeeded: HMMsearch
[2023-06-04 20:24:15,362] [INFO] Found 6/6 markers.
[2023-06-04 20:24:15,406] [INFO] Query marker FASTA was written to GCA_902767155.1_Rumen_uncultured_genome_RUG11228_genomic.fna/markers.fasta
[2023-06-04 20:24:15,406] [INFO] Task started: Blastn
[2023-06-04 20:24:15,407] [INFO] Running command: blastn -query GCA_902767155.1_Rumen_uncultured_genome_RUG11228_genomic.fna/markers.fasta -db /var/lib/cwl/stgbef7d3ae-cf7c-4fef-b0a4-03d3f2465d7e/dqc_reference/reference_markers.fasta -out GCA_902767155.1_Rumen_uncultured_genome_RUG11228_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 20:24:16,035] [INFO] Task succeeded: Blastn
[2023-06-04 20:24:16,039] [INFO] Selected 17 target genomes.
[2023-06-04 20:24:16,039] [INFO] Target genome list was writen to GCA_902767155.1_Rumen_uncultured_genome_RUG11228_genomic.fna/target_genomes.txt
[2023-06-04 20:24:16,045] [INFO] Task started: fastANI
[2023-06-04 20:24:16,045] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f3a3180-67be-498a-9e6c-bc6accffba37/GCA_902767155.1_Rumen_uncultured_genome_RUG11228_genomic.fna.gz --refList GCA_902767155.1_Rumen_uncultured_genome_RUG11228_genomic.fna/target_genomes.txt --output GCA_902767155.1_Rumen_uncultured_genome_RUG11228_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 20:24:21,840] [INFO] Task succeeded: fastANI
[2023-06-04 20:24:21,840] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbef7d3ae-cf7c-4fef-b0a4-03d3f2465d7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 20:24:21,840] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbef7d3ae-cf7c-4fef-b0a4-03d3f2465d7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 20:24:21,842] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 20:24:21,842] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-04 20:24:21,842] [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
--------------------------------------------------------------------------------
[2023-06-04 20:24:21,844] [INFO] DFAST Taxonomy check result was written to GCA_902767155.1_Rumen_uncultured_genome_RUG11228_genomic.fna/tc_result.tsv
[2023-06-04 20:24:21,845] [INFO] ===== Taxonomy check completed =====
[2023-06-04 20:24:21,845] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 20:24:21,845] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbef7d3ae-cf7c-4fef-b0a4-03d3f2465d7e/dqc_reference/checkm_data
[2023-06-04 20:24:21,848] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 20:24:21,875] [INFO] Task started: CheckM
[2023-06-04 20:24:21,876] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902767155.1_Rumen_uncultured_genome_RUG11228_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902767155.1_Rumen_uncultured_genome_RUG11228_genomic.fna/checkm_input GCA_902767155.1_Rumen_uncultured_genome_RUG11228_genomic.fna/checkm_result
[2023-06-04 20:24:41,618] [INFO] Task succeeded: CheckM
[2023-06-04 20:24:41,619] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.16%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 20:24:41,642] [INFO] ===== Completeness check finished =====
[2023-06-04 20:24:41,642] [INFO] ===== Start GTDB Search =====
[2023-06-04 20:24:41,642] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902767155.1_Rumen_uncultured_genome_RUG11228_genomic.fna/markers.fasta)
[2023-06-04 20:24:41,643] [INFO] Task started: Blastn
[2023-06-04 20:24:41,643] [INFO] Running command: blastn -query GCA_902767155.1_Rumen_uncultured_genome_RUG11228_genomic.fna/markers.fasta -db /var/lib/cwl/stgbef7d3ae-cf7c-4fef-b0a4-03d3f2465d7e/dqc_reference/reference_markers_gtdb.fasta -out GCA_902767155.1_Rumen_uncultured_genome_RUG11228_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 20:24:42,629] [INFO] Task succeeded: Blastn
[2023-06-04 20:24:42,635] [INFO] Selected 20 target genomes.
[2023-06-04 20:24:42,635] [INFO] Target genome list was writen to GCA_902767155.1_Rumen_uncultured_genome_RUG11228_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 20:24:42,684] [INFO] Task started: fastANI
[2023-06-04 20:24:42,684] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f3a3180-67be-498a-9e6c-bc6accffba37/GCA_902767155.1_Rumen_uncultured_genome_RUG11228_genomic.fna.gz --refList GCA_902767155.1_Rumen_uncultured_genome_RUG11228_genomic.fna/target_genomes_gtdb.txt --output GCA_902767155.1_Rumen_uncultured_genome_RUG11228_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 20:24:49,873] [INFO] Task succeeded: fastANI
[2023-06-04 20:24:49,891] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 20:24:49,892] [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_902767155.1	s__UBA1213 sp902767155	100.0	568	579	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1213	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900315465.1	s__UBA1213 sp900315465	77.6315	141	579	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1213	95.0	99.88	99.88	0.90	0.90	2	-
GCA_902778175.1	s__UBA1213 sp902778175	77.4417	128	579	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1213	95.0	98.60	98.60	0.84	0.84	2	-
GCA_900317395.1	s__UBA1213 sp900317395	77.2699	85	579	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1213	95.0	99.75	99.75	0.88	0.88	2	-
GCA_902764235.1	s__UBA1213 sp902764235	77.2323	116	579	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1213	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902801055.1	s__UBA1213 sp902801055	77.193	109	579	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1213	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902763365.1	s__UBA1213 sp902763365	77.1145	124	579	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1213	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017475765.1	s__UBA1213 sp017475765	77.1094	111	579	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1213	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900320235.1	s__UBA1213 sp900320235	77.007	90	579	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1213	95.0	99.73	99.73	0.83	0.83	2	-
GCA_902773065.1	s__UBA1213 sp902773065	76.7868	65	579	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1213	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902802985.1	s__UBA1213 sp902802985	76.257	71	579	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1213	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902783065.1	s__UBA1213 sp902783065	76.12	73	579	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1213	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902766305.1	s__UBA1213 sp902766305	76.1032	76	579	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1213	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 20:24:49,894] [INFO] GTDB search result was written to GCA_902767155.1_Rumen_uncultured_genome_RUG11228_genomic.fna/result_gtdb.tsv
[2023-06-04 20:24:49,894] [INFO] ===== GTDB Search completed =====
[2023-06-04 20:24:49,897] [INFO] DFAST_QC result json was written to GCA_902767155.1_Rumen_uncultured_genome_RUG11228_genomic.fna/dqc_result.json
[2023-06-04 20:24:49,898] [INFO] DFAST_QC completed!
[2023-06-04 20:24:49,898] [INFO] Total running time: 0h0m40s