[2023-06-04 18:46:22,874] [INFO] DFAST_QC pipeline started.
[2023-06-04 18:46:22,876] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 18:46:22,876] [INFO] DQC Reference Directory: /var/lib/cwl/stg58fb5a3f-4d04-44f4-9a83-dbe22a4c17da/dqc_reference
[2023-06-04 18:46:24,756] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 18:46:24,757] [INFO] Task started: Prodigal
[2023-06-04 18:46:24,757] [INFO] Running command: gunzip -c /var/lib/cwl/stgb4dd46f7-ad21-4660-a393-6de1706e9902/GCA_902771015.1_Rumen_uncultured_genome_RUG11621_genomic.fna.gz | prodigal -d GCA_902771015.1_Rumen_uncultured_genome_RUG11621_genomic.fna/cds.fna -a GCA_902771015.1_Rumen_uncultured_genome_RUG11621_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 18:46:30,904] [INFO] Task succeeded: Prodigal
[2023-06-04 18:46:30,905] [INFO] Task started: HMMsearch
[2023-06-04 18:46:30,905] [INFO] Running command: hmmsearch --tblout GCA_902771015.1_Rumen_uncultured_genome_RUG11621_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg58fb5a3f-4d04-44f4-9a83-dbe22a4c17da/dqc_reference/reference_markers.hmm GCA_902771015.1_Rumen_uncultured_genome_RUG11621_genomic.fna/protein.faa > /dev/null
[2023-06-04 18:46:31,180] [INFO] Task succeeded: HMMsearch
[2023-06-04 18:46:31,182] [INFO] Found 6/6 markers.
[2023-06-04 18:46:31,212] [INFO] Query marker FASTA was written to GCA_902771015.1_Rumen_uncultured_genome_RUG11621_genomic.fna/markers.fasta
[2023-06-04 18:46:31,213] [INFO] Task started: Blastn
[2023-06-04 18:46:31,213] [INFO] Running command: blastn -query GCA_902771015.1_Rumen_uncultured_genome_RUG11621_genomic.fna/markers.fasta -db /var/lib/cwl/stg58fb5a3f-4d04-44f4-9a83-dbe22a4c17da/dqc_reference/reference_markers.fasta -out GCA_902771015.1_Rumen_uncultured_genome_RUG11621_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 18:46:31,850] [INFO] Task succeeded: Blastn
[2023-06-04 18:46:31,856] [INFO] Selected 32 target genomes.
[2023-06-04 18:46:31,857] [INFO] Target genome list was writen to GCA_902771015.1_Rumen_uncultured_genome_RUG11621_genomic.fna/target_genomes.txt
[2023-06-04 18:46:31,873] [INFO] Task started: fastANI
[2023-06-04 18:46:31,873] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4dd46f7-ad21-4660-a393-6de1706e9902/GCA_902771015.1_Rumen_uncultured_genome_RUG11621_genomic.fna.gz --refList GCA_902771015.1_Rumen_uncultured_genome_RUG11621_genomic.fna/target_genomes.txt --output GCA_902771015.1_Rumen_uncultured_genome_RUG11621_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 18:46:48,243] [INFO] Task succeeded: fastANI
[2023-06-04 18:46:48,244] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg58fb5a3f-4d04-44f4-9a83-dbe22a4c17da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 18:46:48,244] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg58fb5a3f-4d04-44f4-9a83-dbe22a4c17da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 18:46:48,249] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 18:46:48,249] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-04 18:46:48,250] [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
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	77.4292	57	737	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	77.0311	52	737	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	76.8497	54	737	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 18:46:48,252] [INFO] DFAST Taxonomy check result was written to GCA_902771015.1_Rumen_uncultured_genome_RUG11621_genomic.fna/tc_result.tsv
[2023-06-04 18:46:48,252] [INFO] ===== Taxonomy check completed =====
[2023-06-04 18:46:48,252] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 18:46:48,253] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg58fb5a3f-4d04-44f4-9a83-dbe22a4c17da/dqc_reference/checkm_data
[2023-06-04 18:46:48,253] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 18:46:48,286] [INFO] Task started: CheckM
[2023-06-04 18:46:48,286] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902771015.1_Rumen_uncultured_genome_RUG11621_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902771015.1_Rumen_uncultured_genome_RUG11621_genomic.fna/checkm_input GCA_902771015.1_Rumen_uncultured_genome_RUG11621_genomic.fna/checkm_result
[2023-06-04 18:47:13,551] [INFO] Task succeeded: CheckM
[2023-06-04 18:47:13,552] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 8.29%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-04 18:47:13,580] [INFO] ===== Completeness check finished =====
[2023-06-04 18:47:13,580] [INFO] ===== Start GTDB Search =====
[2023-06-04 18:47:13,581] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902771015.1_Rumen_uncultured_genome_RUG11621_genomic.fna/markers.fasta)
[2023-06-04 18:47:13,581] [INFO] Task started: Blastn
[2023-06-04 18:47:13,581] [INFO] Running command: blastn -query GCA_902771015.1_Rumen_uncultured_genome_RUG11621_genomic.fna/markers.fasta -db /var/lib/cwl/stg58fb5a3f-4d04-44f4-9a83-dbe22a4c17da/dqc_reference/reference_markers_gtdb.fasta -out GCA_902771015.1_Rumen_uncultured_genome_RUG11621_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 18:47:14,525] [INFO] Task succeeded: Blastn
[2023-06-04 18:47:14,529] [INFO] Selected 20 target genomes.
[2023-06-04 18:47:14,529] [INFO] Target genome list was writen to GCA_902771015.1_Rumen_uncultured_genome_RUG11621_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 18:47:14,544] [INFO] Task started: fastANI
[2023-06-04 18:47:14,545] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4dd46f7-ad21-4660-a393-6de1706e9902/GCA_902771015.1_Rumen_uncultured_genome_RUG11621_genomic.fna.gz --refList GCA_902771015.1_Rumen_uncultured_genome_RUG11621_genomic.fna/target_genomes_gtdb.txt --output GCA_902771015.1_Rumen_uncultured_genome_RUG11621_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 18:47:25,199] [INFO] Task succeeded: fastANI
[2023-06-04 18:47:25,216] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 18:47:25,217] [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_900317375.1	s__Limivicinus sp900317375	97.9865	634	737	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	98.11	95.61	0.84	0.72	56	conclusive
GCA_017538965.1	s__Limivicinus sp017538965	82.7264	422	737	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017458335.1	s__Limivicinus sp017458335	80.5127	236	737	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017627975.1	s__Limivicinus sp017627975	80.0886	211	737	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017458065.1	s__Limivicinus sp017458065	79.977	277	737	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902798545.1	s__Limivicinus sp902798545	79.6036	204	737	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017430985.1	s__Limivicinus sp017430985	79.3268	147	737	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902778285.1	s__Limivicinus sp902778285	79.2309	201	737	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	98.33	98.33	0.79	0.79	2	-
GCA_900319465.1	s__Limivicinus sp900319465	79.2052	179	737	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	99.77	99.67	0.93	0.92	4	-
GCA_902778275.1	s__Limivicinus sp902778275	79.0253	170	737	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900319635.1	s__Limivicinus sp900319635	78.9809	153	737	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	97.84	96.83	0.85	0.76	6	-
GCA_902779945.1	s__Limivicinus sp902779945	78.8751	186	737	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902761635.1	s__Limivicinus sp902761635	78.7662	199	737	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902775355.1	s__Limivicinus sp902775355	78.7016	168	737	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017545165.1	s__Limivicinus sp017545165	78.65	127	737	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017395085.1	s__Limivicinus sp017395085	78.4585	162	737	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	97.30	96.83	0.71	0.71	3	-
GCA_905234575.1	s__CAJOIG01 sp905234575	77.5137	71	737	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAJOIG01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 18:47:25,219] [INFO] GTDB search result was written to GCA_902771015.1_Rumen_uncultured_genome_RUG11621_genomic.fna/result_gtdb.tsv
[2023-06-04 18:47:25,220] [INFO] ===== GTDB Search completed =====
[2023-06-04 18:47:25,223] [INFO] DFAST_QC result json was written to GCA_902771015.1_Rumen_uncultured_genome_RUG11621_genomic.fna/dqc_result.json
[2023-06-04 18:47:25,224] [INFO] DFAST_QC completed!
[2023-06-04 18:47:25,224] [INFO] Total running time: 0h1m2s