[2023-06-05 12:22:31,979] [INFO] DFAST_QC pipeline started.
[2023-06-05 12:22:31,982] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 12:22:31,982] [INFO] DQC Reference Directory: /var/lib/cwl/stg2007cb0b-58fd-484f-b063-9701b2c3e182/dqc_reference
[2023-06-05 12:22:33,473] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 12:22:33,474] [INFO] Task started: Prodigal
[2023-06-05 12:22:33,474] [INFO] Running command: gunzip -c /var/lib/cwl/stg7259ade0-f95b-43ec-ad14-9a9d160dce54/GCA_902798705.1_Rumen_uncultured_genome_RUG14395_genomic.fna.gz | prodigal -d GCA_902798705.1_Rumen_uncultured_genome_RUG14395_genomic.fna/cds.fna -a GCA_902798705.1_Rumen_uncultured_genome_RUG14395_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 12:22:53,313] [INFO] Task succeeded: Prodigal
[2023-06-05 12:22:53,314] [INFO] Task started: HMMsearch
[2023-06-05 12:22:53,314] [INFO] Running command: hmmsearch --tblout GCA_902798705.1_Rumen_uncultured_genome_RUG14395_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2007cb0b-58fd-484f-b063-9701b2c3e182/dqc_reference/reference_markers.hmm GCA_902798705.1_Rumen_uncultured_genome_RUG14395_genomic.fna/protein.faa > /dev/null
[2023-06-05 12:22:53,537] [INFO] Task succeeded: HMMsearch
[2023-06-05 12:22:53,538] [INFO] Found 6/6 markers.
[2023-06-05 12:22:53,570] [INFO] Query marker FASTA was written to GCA_902798705.1_Rumen_uncultured_genome_RUG14395_genomic.fna/markers.fasta
[2023-06-05 12:22:53,571] [INFO] Task started: Blastn
[2023-06-05 12:22:53,571] [INFO] Running command: blastn -query GCA_902798705.1_Rumen_uncultured_genome_RUG14395_genomic.fna/markers.fasta -db /var/lib/cwl/stg2007cb0b-58fd-484f-b063-9701b2c3e182/dqc_reference/reference_markers.fasta -out GCA_902798705.1_Rumen_uncultured_genome_RUG14395_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 12:22:54,197] [INFO] Task succeeded: Blastn
[2023-06-05 12:22:54,201] [INFO] Selected 34 target genomes.
[2023-06-05 12:22:54,201] [INFO] Target genome list was writen to GCA_902798705.1_Rumen_uncultured_genome_RUG14395_genomic.fna/target_genomes.txt
[2023-06-05 12:22:54,205] [INFO] Task started: fastANI
[2023-06-05 12:22:54,205] [INFO] Running command: fastANI --query /var/lib/cwl/stg7259ade0-f95b-43ec-ad14-9a9d160dce54/GCA_902798705.1_Rumen_uncultured_genome_RUG14395_genomic.fna.gz --refList GCA_902798705.1_Rumen_uncultured_genome_RUG14395_genomic.fna/target_genomes.txt --output GCA_902798705.1_Rumen_uncultured_genome_RUG14395_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 12:23:11,572] [INFO] Task succeeded: fastANI
[2023-06-05 12:23:11,572] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2007cb0b-58fd-484f-b063-9701b2c3e182/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 12:23:11,572] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2007cb0b-58fd-484f-b063-9701b2c3e182/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 12:23:11,574] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 12:23:11,574] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 12:23:11,575] [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 12:23:11,588] [INFO] DFAST Taxonomy check result was written to GCA_902798705.1_Rumen_uncultured_genome_RUG14395_genomic.fna/tc_result.tsv
[2023-06-05 12:23:11,588] [INFO] ===== Taxonomy check completed =====
[2023-06-05 12:23:11,589] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 12:23:11,589] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2007cb0b-58fd-484f-b063-9701b2c3e182/dqc_reference/checkm_data
[2023-06-05 12:23:11,591] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 12:23:11,625] [INFO] Task started: CheckM
[2023-06-05 12:23:11,625] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902798705.1_Rumen_uncultured_genome_RUG14395_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902798705.1_Rumen_uncultured_genome_RUG14395_genomic.fna/checkm_input GCA_902798705.1_Rumen_uncultured_genome_RUG14395_genomic.fna/checkm_result
[2023-06-05 12:24:07,978] [INFO] Task succeeded: CheckM
[2023-06-05 12:24:07,980] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 12:24:07,997] [INFO] ===== Completeness check finished =====
[2023-06-05 12:24:07,997] [INFO] ===== Start GTDB Search =====
[2023-06-05 12:24:07,997] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902798705.1_Rumen_uncultured_genome_RUG14395_genomic.fna/markers.fasta)
[2023-06-05 12:24:07,998] [INFO] Task started: Blastn
[2023-06-05 12:24:07,998] [INFO] Running command: blastn -query GCA_902798705.1_Rumen_uncultured_genome_RUG14395_genomic.fna/markers.fasta -db /var/lib/cwl/stg2007cb0b-58fd-484f-b063-9701b2c3e182/dqc_reference/reference_markers_gtdb.fasta -out GCA_902798705.1_Rumen_uncultured_genome_RUG14395_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 12:24:08,790] [INFO] Task succeeded: Blastn
[2023-06-05 12:24:08,794] [INFO] Selected 19 target genomes.
[2023-06-05 12:24:08,794] [INFO] Target genome list was writen to GCA_902798705.1_Rumen_uncultured_genome_RUG14395_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 12:24:08,836] [INFO] Task started: fastANI
[2023-06-05 12:24:08,837] [INFO] Running command: fastANI --query /var/lib/cwl/stg7259ade0-f95b-43ec-ad14-9a9d160dce54/GCA_902798705.1_Rumen_uncultured_genome_RUG14395_genomic.fna.gz --refList GCA_902798705.1_Rumen_uncultured_genome_RUG14395_genomic.fna/target_genomes_gtdb.txt --output GCA_902798705.1_Rumen_uncultured_genome_RUG14395_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 12:24:18,797] [INFO] Task succeeded: fastANI
[2023-06-05 12:24:18,808] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 12:24:18,808] [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_902798705.1	s__UBA3839 sp902798705	100.0	989	999	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA3839	95.0	96.86	96.85	0.82	0.82	3	conclusive
GCA_900313845.1	s__UBA3839 sp900313845	86.3603	451	999	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA3839	95.0	96.94	95.74	0.85	0.70	7	-
GCA_002393575.1	s__UBA3839 sp002393575	85.6757	682	999	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA3839	95.0	96.72	96.72	0.83	0.83	2	-
GCA_900318775.1	s__UBA4334 sp900318775	78.2251	99	999	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	98.63	98.03	0.91	0.87	6	-
GCA_900319385.1	s__UBA3839 sp900319385	77.4388	121	999	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA3839	95.0	99.85	99.85	0.97	0.97	2	-
GCA_900321835.1	s__UBA3839 sp900321835	77.4104	110	999	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA3839	95.0	98.37	97.84	0.86	0.77	6	-
GCA_017614895.1	s__UBA4334 sp017614895	77.3909	109	999	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017483605.1	s__UBA4334 sp017483605	77.3774	118	999	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	96.79	96.79	0.77	0.77	2	-
GCA_905234555.1	s__UBA3839 sp905234555	77.3281	130	999	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA3839	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902785075.1	s__UBA1786 sp902785075	77.0437	70	999	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1786	95.0	97.36	97.36	0.82	0.82	2	-
GCA_002393555.1	s__UBA4334 sp002393555	77.0367	131	999	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	97.14	96.87	0.79	0.76	3	-
GCA_017615245.1	s__UBA1786 sp017615245	76.6767	66	999	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1786	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900317305.1	s__Prevotella sp900317305	76.3937	63	999	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.38	97.82	0.87	0.83	11	-
--------------------------------------------------------------------------------
[2023-06-05 12:24:18,810] [INFO] GTDB search result was written to GCA_902798705.1_Rumen_uncultured_genome_RUG14395_genomic.fna/result_gtdb.tsv
[2023-06-05 12:24:18,811] [INFO] ===== GTDB Search completed =====
[2023-06-05 12:24:18,813] [INFO] DFAST_QC result json was written to GCA_902798705.1_Rumen_uncultured_genome_RUG14395_genomic.fna/dqc_result.json
[2023-06-05 12:24:18,814] [INFO] DFAST_QC completed!
[2023-06-05 12:24:18,814] [INFO] Total running time: 0h1m47s