[2023-06-04 21:45:38,902] [INFO] DFAST_QC pipeline started.
[2023-06-04 21:45:38,904] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 21:45:38,904] [INFO] DQC Reference Directory: /var/lib/cwl/stg5b2ffecf-cb2f-4cd8-a563-f52690b51bdb/dqc_reference
[2023-06-04 21:45:40,188] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 21:45:40,189] [INFO] Task started: Prodigal
[2023-06-04 21:45:40,189] [INFO] Running command: gunzip -c /var/lib/cwl/stg0d1678d9-8122-4189-91b4-2a7de72c917e/GCA_902771795.1_Rumen_uncultured_genome_RUG11700_genomic.fna.gz | prodigal -d GCA_902771795.1_Rumen_uncultured_genome_RUG11700_genomic.fna/cds.fna -a GCA_902771795.1_Rumen_uncultured_genome_RUG11700_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 21:45:52,644] [INFO] Task succeeded: Prodigal
[2023-06-04 21:45:52,644] [INFO] Task started: HMMsearch
[2023-06-04 21:45:52,644] [INFO] Running command: hmmsearch --tblout GCA_902771795.1_Rumen_uncultured_genome_RUG11700_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5b2ffecf-cb2f-4cd8-a563-f52690b51bdb/dqc_reference/reference_markers.hmm GCA_902771795.1_Rumen_uncultured_genome_RUG11700_genomic.fna/protein.faa > /dev/null
[2023-06-04 21:45:52,874] [INFO] Task succeeded: HMMsearch
[2023-06-04 21:45:52,876] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg0d1678d9-8122-4189-91b4-2a7de72c917e/GCA_902771795.1_Rumen_uncultured_genome_RUG11700_genomic.fna.gz]
[2023-06-04 21:45:52,904] [INFO] Query marker FASTA was written to GCA_902771795.1_Rumen_uncultured_genome_RUG11700_genomic.fna/markers.fasta
[2023-06-04 21:45:52,905] [INFO] Task started: Blastn
[2023-06-04 21:45:52,905] [INFO] Running command: blastn -query GCA_902771795.1_Rumen_uncultured_genome_RUG11700_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b2ffecf-cb2f-4cd8-a563-f52690b51bdb/dqc_reference/reference_markers.fasta -out GCA_902771795.1_Rumen_uncultured_genome_RUG11700_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 21:45:53,554] [INFO] Task succeeded: Blastn
[2023-06-04 21:45:53,559] [INFO] Selected 23 target genomes.
[2023-06-04 21:45:53,559] [INFO] Target genome list was writen to GCA_902771795.1_Rumen_uncultured_genome_RUG11700_genomic.fna/target_genomes.txt
[2023-06-04 21:45:53,563] [INFO] Task started: fastANI
[2023-06-04 21:45:53,563] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d1678d9-8122-4189-91b4-2a7de72c917e/GCA_902771795.1_Rumen_uncultured_genome_RUG11700_genomic.fna.gz --refList GCA_902771795.1_Rumen_uncultured_genome_RUG11700_genomic.fna/target_genomes.txt --output GCA_902771795.1_Rumen_uncultured_genome_RUG11700_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 21:46:08,773] [INFO] Task succeeded: fastANI
[2023-06-04 21:46:08,774] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5b2ffecf-cb2f-4cd8-a563-f52690b51bdb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 21:46:08,775] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5b2ffecf-cb2f-4cd8-a563-f52690b51bdb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 21:46:08,777] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 21:46:08,777] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-04 21:46:08,777] [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 21:46:08,779] [INFO] DFAST Taxonomy check result was written to GCA_902771795.1_Rumen_uncultured_genome_RUG11700_genomic.fna/tc_result.tsv
[2023-06-04 21:46:08,780] [INFO] ===== Taxonomy check completed =====
[2023-06-04 21:46:08,781] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 21:46:08,781] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5b2ffecf-cb2f-4cd8-a563-f52690b51bdb/dqc_reference/checkm_data
[2023-06-04 21:46:08,785] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 21:46:08,811] [INFO] Task started: CheckM
[2023-06-04 21:46:08,811] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902771795.1_Rumen_uncultured_genome_RUG11700_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902771795.1_Rumen_uncultured_genome_RUG11700_genomic.fna/checkm_input GCA_902771795.1_Rumen_uncultured_genome_RUG11700_genomic.fna/checkm_result
[2023-06-04 21:46:46,439] [INFO] Task succeeded: CheckM
[2023-06-04 21:46:46,441] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 21:46:46,464] [INFO] ===== Completeness check finished =====
[2023-06-04 21:46:46,464] [INFO] ===== Start GTDB Search =====
[2023-06-04 21:46:46,465] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902771795.1_Rumen_uncultured_genome_RUG11700_genomic.fna/markers.fasta)
[2023-06-04 21:46:46,465] [INFO] Task started: Blastn
[2023-06-04 21:46:46,466] [INFO] Running command: blastn -query GCA_902771795.1_Rumen_uncultured_genome_RUG11700_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b2ffecf-cb2f-4cd8-a563-f52690b51bdb/dqc_reference/reference_markers_gtdb.fasta -out GCA_902771795.1_Rumen_uncultured_genome_RUG11700_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 21:46:47,440] [INFO] Task succeeded: Blastn
[2023-06-04 21:46:47,447] [INFO] Selected 15 target genomes.
[2023-06-04 21:46:47,448] [INFO] Target genome list was writen to GCA_902771795.1_Rumen_uncultured_genome_RUG11700_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 21:46:47,455] [INFO] Task started: fastANI
[2023-06-04 21:46:47,456] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d1678d9-8122-4189-91b4-2a7de72c917e/GCA_902771795.1_Rumen_uncultured_genome_RUG11700_genomic.fna.gz --refList GCA_902771795.1_Rumen_uncultured_genome_RUG11700_genomic.fna/target_genomes_gtdb.txt --output GCA_902771795.1_Rumen_uncultured_genome_RUG11700_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 21:46:53,668] [INFO] Task succeeded: fastANI
[2023-06-04 21:46:53,688] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 21:46:53,688] [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_900317925.1	s__Cryptobacteroides sp900317925	97.866	557	650	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.64	96.11	0.85	0.74	52	conclusive
GCA_902799895.1	s__Cryptobacteroides sp902799895	91.5566	452	650	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.23	98.23	0.80	0.80	2	-
GCA_902762435.1	s__Cryptobacteroides sp902762435	77.9083	134	650	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.59	98.59	0.91	0.91	2	-
GCA_017483985.1	s__Cryptobacteroides sp017483985	77.7952	152	650	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016287075.1	s__Cryptobacteroides sp016287075	77.7288	157	650	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902779765.1	s__Cryptobacteroides sp902779765	77.4974	90	650	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.01	96.70	0.92	0.90	3	-
GCA_017471045.1	s__Cryptobacteroides sp017471045	77.4751	126	650	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017535125.1	s__Cryptobacteroides sp017535125	77.3764	115	650	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016283985.1	s__Cryptobacteroides sp016283985	77.1777	89	650	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900320185.1	s__Cryptobacteroides sp900320185	77.1548	77	650	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.66	98.37	0.88	0.82	11	-
GCA_902798975.1	s__Cryptobacteroides sp902798975	77.122	123	650	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900319185.1	s__Cryptobacteroides sp900319185	77.1218	92	650	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.95	98.63	0.93	0.89	6	-
GCA_902803715.1	s__Cryptobacteroides sp902803715	76.9605	124	650	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.42	97.90	0.88	0.86	3	-
GCA_902766985.1	s__Cryptobacteroides sp902766985	76.8732	62	650	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.09	97.97	0.82	0.68	3	-
GCA_902780935.1	s__Cryptobacteroides sp902780935	76.703	87	650	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.52	97.52	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2023-06-04 21:46:53,690] [INFO] GTDB search result was written to GCA_902771795.1_Rumen_uncultured_genome_RUG11700_genomic.fna/result_gtdb.tsv
[2023-06-04 21:46:53,691] [INFO] ===== GTDB Search completed =====
[2023-06-04 21:46:53,694] [INFO] DFAST_QC result json was written to GCA_902771795.1_Rumen_uncultured_genome_RUG11700_genomic.fna/dqc_result.json
[2023-06-04 21:46:53,695] [INFO] DFAST_QC completed!
[2023-06-04 21:46:53,695] [INFO] Total running time: 0h1m15s