[2023-06-05 02:27:21,204] [INFO] DFAST_QC pipeline started.
[2023-06-05 02:27:21,211] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 02:27:21,212] [INFO] DQC Reference Directory: /var/lib/cwl/stg95cd9aa6-c7a4-4d51-b5bd-55749a5a0d87/dqc_reference
[2023-06-05 02:27:22,557] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 02:27:22,558] [INFO] Task started: Prodigal
[2023-06-05 02:27:22,558] [INFO] Running command: gunzip -c /var/lib/cwl/stgcb464ff5-f349-456e-943f-4cda885f37b6/GCA_902756005.1_Rumen_uncultured_genome_RUG10118_genomic.fna.gz | prodigal -d GCA_902756005.1_Rumen_uncultured_genome_RUG10118_genomic.fna/cds.fna -a GCA_902756005.1_Rumen_uncultured_genome_RUG10118_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 02:27:29,070] [INFO] Task succeeded: Prodigal
[2023-06-05 02:27:29,070] [INFO] Task started: HMMsearch
[2023-06-05 02:27:29,070] [INFO] Running command: hmmsearch --tblout GCA_902756005.1_Rumen_uncultured_genome_RUG10118_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg95cd9aa6-c7a4-4d51-b5bd-55749a5a0d87/dqc_reference/reference_markers.hmm GCA_902756005.1_Rumen_uncultured_genome_RUG10118_genomic.fna/protein.faa > /dev/null
[2023-06-05 02:27:29,351] [INFO] Task succeeded: HMMsearch
[2023-06-05 02:27:29,353] [INFO] Found 6/6 markers.
[2023-06-05 02:27:29,384] [INFO] Query marker FASTA was written to GCA_902756005.1_Rumen_uncultured_genome_RUG10118_genomic.fna/markers.fasta
[2023-06-05 02:27:29,385] [INFO] Task started: Blastn
[2023-06-05 02:27:29,385] [INFO] Running command: blastn -query GCA_902756005.1_Rumen_uncultured_genome_RUG10118_genomic.fna/markers.fasta -db /var/lib/cwl/stg95cd9aa6-c7a4-4d51-b5bd-55749a5a0d87/dqc_reference/reference_markers.fasta -out GCA_902756005.1_Rumen_uncultured_genome_RUG10118_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:27:29,988] [INFO] Task succeeded: Blastn
[2023-06-05 02:27:29,992] [INFO] Selected 29 target genomes.
[2023-06-05 02:27:29,992] [INFO] Target genome list was writen to GCA_902756005.1_Rumen_uncultured_genome_RUG10118_genomic.fna/target_genomes.txt
[2023-06-05 02:27:30,014] [INFO] Task started: fastANI
[2023-06-05 02:27:30,014] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb464ff5-f349-456e-943f-4cda885f37b6/GCA_902756005.1_Rumen_uncultured_genome_RUG10118_genomic.fna.gz --refList GCA_902756005.1_Rumen_uncultured_genome_RUG10118_genomic.fna/target_genomes.txt --output GCA_902756005.1_Rumen_uncultured_genome_RUG10118_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 02:27:46,139] [INFO] Task succeeded: fastANI
[2023-06-05 02:27:46,140] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg95cd9aa6-c7a4-4d51-b5bd-55749a5a0d87/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 02:27:46,141] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg95cd9aa6-c7a4-4d51-b5bd-55749a5a0d87/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 02:27:46,143] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 02:27:46,144] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 02:27:46,144] [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 02:27:46,146] [INFO] DFAST Taxonomy check result was written to GCA_902756005.1_Rumen_uncultured_genome_RUG10118_genomic.fna/tc_result.tsv
[2023-06-05 02:27:46,147] [INFO] ===== Taxonomy check completed =====
[2023-06-05 02:27:46,148] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 02:27:46,148] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg95cd9aa6-c7a4-4d51-b5bd-55749a5a0d87/dqc_reference/checkm_data
[2023-06-05 02:27:46,152] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 02:27:46,185] [INFO] Task started: CheckM
[2023-06-05 02:27:46,185] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902756005.1_Rumen_uncultured_genome_RUG10118_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902756005.1_Rumen_uncultured_genome_RUG10118_genomic.fna/checkm_input GCA_902756005.1_Rumen_uncultured_genome_RUG10118_genomic.fna/checkm_result
[2023-06-05 02:28:10,973] [INFO] Task succeeded: CheckM
[2023-06-05 02:28:10,974] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.75%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 02:28:10,994] [INFO] ===== Completeness check finished =====
[2023-06-05 02:28:10,994] [INFO] ===== Start GTDB Search =====
[2023-06-05 02:28:10,995] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902756005.1_Rumen_uncultured_genome_RUG10118_genomic.fna/markers.fasta)
[2023-06-05 02:28:10,995] [INFO] Task started: Blastn
[2023-06-05 02:28:10,995] [INFO] Running command: blastn -query GCA_902756005.1_Rumen_uncultured_genome_RUG10118_genomic.fna/markers.fasta -db /var/lib/cwl/stg95cd9aa6-c7a4-4d51-b5bd-55749a5a0d87/dqc_reference/reference_markers_gtdb.fasta -out GCA_902756005.1_Rumen_uncultured_genome_RUG10118_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:28:11,866] [INFO] Task succeeded: Blastn
[2023-06-05 02:28:11,872] [INFO] Selected 10 target genomes.
[2023-06-05 02:28:11,872] [INFO] Target genome list was writen to GCA_902756005.1_Rumen_uncultured_genome_RUG10118_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 02:28:11,985] [INFO] Task started: fastANI
[2023-06-05 02:28:11,986] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb464ff5-f349-456e-943f-4cda885f37b6/GCA_902756005.1_Rumen_uncultured_genome_RUG10118_genomic.fna.gz --refList GCA_902756005.1_Rumen_uncultured_genome_RUG10118_genomic.fna/target_genomes_gtdb.txt --output GCA_902756005.1_Rumen_uncultured_genome_RUG10118_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 02:28:16,963] [INFO] Task succeeded: fastANI
[2023-06-05 02:28:16,982] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 02:28:16,982] [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_900316415.1	s__RUG740 sp900316415	100.0	819	821	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__RUG740	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_017469265.1	s__RUG740 sp017469265	81.4654	390	821	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__RUG740	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902778055.1	s__RUG740 sp902778055	81.4005	414	821	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__RUG740	95.0	97.78	97.78	0.89	0.89	2	-
GCA_017464305.1	s__RUG740 sp017464305	80.9047	253	821	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__RUG740	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017470145.1	s__RUG740 sp017470145	80.8966	332	821	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__RUG740	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017412715.1	s__RUG740 sp017412715	80.8602	244	821	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__RUG740	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900321945.1	s__RUG740 sp900321945	79.6596	206	821	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__RUG740	95.0	100.00	100.00	0.98	0.98	2	-
GCA_017433675.1	s__RUG740 sp017433675	79.6478	222	821	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__RUG740	95.0	97.89	97.89	0.67	0.67	2	-
GCA_017509255.1	s__RGIG5966 sp017509255	79.0414	213	821	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__RGIG5966	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015056415.1	s__UBA11524 sp015056415	77.1759	127	821	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 02:28:16,985] [INFO] GTDB search result was written to GCA_902756005.1_Rumen_uncultured_genome_RUG10118_genomic.fna/result_gtdb.tsv
[2023-06-05 02:28:16,985] [INFO] ===== GTDB Search completed =====
[2023-06-05 02:28:16,989] [INFO] DFAST_QC result json was written to GCA_902756005.1_Rumen_uncultured_genome_RUG10118_genomic.fna/dqc_result.json
[2023-06-05 02:28:16,990] [INFO] DFAST_QC completed!
[2023-06-05 02:28:16,990] [INFO] Total running time: 0h0m56s