[2023-06-05 18:53:59,202] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:53:59,204] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:53:59,204] [INFO] DQC Reference Directory: /var/lib/cwl/stg38016b82-8aaa-4384-8e68-3185bd59bbb2/dqc_reference
[2023-06-05 18:54:00,301] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:54:00,302] [INFO] Task started: Prodigal
[2023-06-05 18:54:00,302] [INFO] Running command: gunzip -c /var/lib/cwl/stgd47afe7c-dc21-4740-8e0d-df228611de92/GCA_902771175.1_Rumen_uncultured_genome_RUG11646_genomic.fna.gz | prodigal -d GCA_902771175.1_Rumen_uncultured_genome_RUG11646_genomic.fna/cds.fna -a GCA_902771175.1_Rumen_uncultured_genome_RUG11646_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:54:10,307] [INFO] Task succeeded: Prodigal
[2023-06-05 18:54:10,307] [INFO] Task started: HMMsearch
[2023-06-05 18:54:10,307] [INFO] Running command: hmmsearch --tblout GCA_902771175.1_Rumen_uncultured_genome_RUG11646_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg38016b82-8aaa-4384-8e68-3185bd59bbb2/dqc_reference/reference_markers.hmm GCA_902771175.1_Rumen_uncultured_genome_RUG11646_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:54:10,495] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:54:10,496] [INFO] Found 6/6 markers.
[2023-06-05 18:54:10,525] [INFO] Query marker FASTA was written to GCA_902771175.1_Rumen_uncultured_genome_RUG11646_genomic.fna/markers.fasta
[2023-06-05 18:54:10,525] [INFO] Task started: Blastn
[2023-06-05 18:54:10,525] [INFO] Running command: blastn -query GCA_902771175.1_Rumen_uncultured_genome_RUG11646_genomic.fna/markers.fasta -db /var/lib/cwl/stg38016b82-8aaa-4384-8e68-3185bd59bbb2/dqc_reference/reference_markers.fasta -out GCA_902771175.1_Rumen_uncultured_genome_RUG11646_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:54:11,060] [INFO] Task succeeded: Blastn
[2023-06-05 18:54:11,065] [INFO] Selected 28 target genomes.
[2023-06-05 18:54:11,065] [INFO] Target genome list was writen to GCA_902771175.1_Rumen_uncultured_genome_RUG11646_genomic.fna/target_genomes.txt
[2023-06-05 18:54:11,070] [INFO] Task started: fastANI
[2023-06-05 18:54:11,070] [INFO] Running command: fastANI --query /var/lib/cwl/stgd47afe7c-dc21-4740-8e0d-df228611de92/GCA_902771175.1_Rumen_uncultured_genome_RUG11646_genomic.fna.gz --refList GCA_902771175.1_Rumen_uncultured_genome_RUG11646_genomic.fna/target_genomes.txt --output GCA_902771175.1_Rumen_uncultured_genome_RUG11646_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:54:39,359] [INFO] Task succeeded: fastANI
[2023-06-05 18:54:39,360] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg38016b82-8aaa-4384-8e68-3185bd59bbb2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:54:39,361] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg38016b82-8aaa-4384-8e68-3185bd59bbb2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:54:39,362] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:54:39,362] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 18:54:39,362] [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 18:54:39,364] [INFO] DFAST Taxonomy check result was written to GCA_902771175.1_Rumen_uncultured_genome_RUG11646_genomic.fna/tc_result.tsv
[2023-06-05 18:54:39,365] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:54:39,365] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:54:39,365] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg38016b82-8aaa-4384-8e68-3185bd59bbb2/dqc_reference/checkm_data
[2023-06-05 18:54:39,367] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:54:39,391] [INFO] Task started: CheckM
[2023-06-05 18:54:39,391] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902771175.1_Rumen_uncultured_genome_RUG11646_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902771175.1_Rumen_uncultured_genome_RUG11646_genomic.fna/checkm_input GCA_902771175.1_Rumen_uncultured_genome_RUG11646_genomic.fna/checkm_result
[2023-06-05 18:55:13,413] [INFO] Task succeeded: CheckM
[2023-06-05 18:55:13,414] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.88%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:55:13,435] [INFO] ===== Completeness check finished =====
[2023-06-05 18:55:13,435] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:55:13,436] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902771175.1_Rumen_uncultured_genome_RUG11646_genomic.fna/markers.fasta)
[2023-06-05 18:55:13,436] [INFO] Task started: Blastn
[2023-06-05 18:55:13,436] [INFO] Running command: blastn -query GCA_902771175.1_Rumen_uncultured_genome_RUG11646_genomic.fna/markers.fasta -db /var/lib/cwl/stg38016b82-8aaa-4384-8e68-3185bd59bbb2/dqc_reference/reference_markers_gtdb.fasta -out GCA_902771175.1_Rumen_uncultured_genome_RUG11646_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:55:14,386] [INFO] Task succeeded: Blastn
[2023-06-05 18:55:14,389] [INFO] Selected 19 target genomes.
[2023-06-05 18:55:14,389] [INFO] Target genome list was writen to GCA_902771175.1_Rumen_uncultured_genome_RUG11646_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:55:14,405] [INFO] Task started: fastANI
[2023-06-05 18:55:14,405] [INFO] Running command: fastANI --query /var/lib/cwl/stgd47afe7c-dc21-4740-8e0d-df228611de92/GCA_902771175.1_Rumen_uncultured_genome_RUG11646_genomic.fna.gz --refList GCA_902771175.1_Rumen_uncultured_genome_RUG11646_genomic.fna/target_genomes_gtdb.txt --output GCA_902771175.1_Rumen_uncultured_genome_RUG11646_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:55:22,927] [INFO] Task succeeded: fastANI
[2023-06-05 18:55:22,938] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 18:55:22,939] [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_902778935.1	s__RF16 sp902778935	97.0443	573	672	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	96.50	96.20	0.85	0.83	6	conclusive
GCA_900317345.1	s__RF16 sp900317345	82.5364	358	672	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	98.36	96.72	0.91	0.83	3	-
GCA_900317885.1	s__RF16 sp900317885	79.7944	283	672	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	97.25	96.25	0.86	0.83	5	-
GCA_902762355.1	s__RF16 sp902762355	79.6694	251	672	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902798015.1	s__RF16 sp902798015	79.6577	219	672	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900319105.1	s__RF16 sp900319105	79.579	277	672	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	97.16	95.90	0.87	0.77	5	-
GCA_905233255.1	s__RF16 sp905233255	79.4354	271	672	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900321005.1	s__RF16 sp900321005	79.3898	251	672	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	97.51	96.64	0.88	0.83	5	-
GCA_902798385.1	s__RF16 sp902798385	79.2796	252	672	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017507715.1	s__RF16 sp017507715	79.1046	230	672	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902792535.1	s__RF16 sp902792535	79.0483	263	672	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902799185.1	s__RF16 sp902799185	79.0247	263	672	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902769535.1	s__RF16 sp902769535	79.019	244	672	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902785605.1	s__RF16 sp902785605	79.0152	256	672	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	96.88	96.82	0.84	0.82	4	-
GCA_902774995.1	s__RF16 sp902774995	78.9621	233	672	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	95.68	95.65	0.72	0.66	3	-
GCA_902799875.1	s__RF16 sp902799875	78.9426	260	672	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017649925.1	s__RF16 sp017649925	78.5749	196	672	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905233375.1	s__RF16 sp905233375	78.4859	221	672	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017423085.1	s__RF16 sp017423085	78.2339	179	672	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	98.54	98.52	0.72	0.68	3	-
--------------------------------------------------------------------------------
[2023-06-05 18:55:22,940] [INFO] GTDB search result was written to GCA_902771175.1_Rumen_uncultured_genome_RUG11646_genomic.fna/result_gtdb.tsv
[2023-06-05 18:55:22,941] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:55:22,944] [INFO] DFAST_QC result json was written to GCA_902771175.1_Rumen_uncultured_genome_RUG11646_genomic.fna/dqc_result.json
[2023-06-05 18:55:22,944] [INFO] DFAST_QC completed!
[2023-06-05 18:55:22,944] [INFO] Total running time: 0h1m24s