[2023-06-08 12:26:25,392] [INFO] DFAST_QC pipeline started.
[2023-06-08 12:26:25,396] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 12:26:25,396] [INFO] DQC Reference Directory: /var/lib/cwl/stg1891320b-4824-430a-8b7e-be7abbe79b6a/dqc_reference
[2023-06-08 12:26:26,657] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 12:26:26,658] [INFO] Task started: Prodigal
[2023-06-08 12:26:26,658] [INFO] Running command: gunzip -c /var/lib/cwl/stgd5e05fa6-f7e5-469d-900c-fba1e80b5b97/GCA_902778355.1_Rumen_uncultured_genome_RUG12363_genomic.fna.gz | prodigal -d GCA_902778355.1_Rumen_uncultured_genome_RUG12363_genomic.fna/cds.fna -a GCA_902778355.1_Rumen_uncultured_genome_RUG12363_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 12:26:49,556] [INFO] Task succeeded: Prodigal
[2023-06-08 12:26:49,556] [INFO] Task started: HMMsearch
[2023-06-08 12:26:49,556] [INFO] Running command: hmmsearch --tblout GCA_902778355.1_Rumen_uncultured_genome_RUG12363_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1891320b-4824-430a-8b7e-be7abbe79b6a/dqc_reference/reference_markers.hmm GCA_902778355.1_Rumen_uncultured_genome_RUG12363_genomic.fna/protein.faa > /dev/null
[2023-06-08 12:26:49,827] [INFO] Task succeeded: HMMsearch
[2023-06-08 12:26:49,829] [INFO] Found 6/6 markers.
[2023-06-08 12:26:49,862] [INFO] Query marker FASTA was written to GCA_902778355.1_Rumen_uncultured_genome_RUG12363_genomic.fna/markers.fasta
[2023-06-08 12:26:49,863] [INFO] Task started: Blastn
[2023-06-08 12:26:49,863] [INFO] Running command: blastn -query GCA_902778355.1_Rumen_uncultured_genome_RUG12363_genomic.fna/markers.fasta -db /var/lib/cwl/stg1891320b-4824-430a-8b7e-be7abbe79b6a/dqc_reference/reference_markers.fasta -out GCA_902778355.1_Rumen_uncultured_genome_RUG12363_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:26:50,492] [INFO] Task succeeded: Blastn
[2023-06-08 12:26:50,496] [INFO] Selected 28 target genomes.
[2023-06-08 12:26:50,497] [INFO] Target genome list was writen to GCA_902778355.1_Rumen_uncultured_genome_RUG12363_genomic.fna/target_genomes.txt
[2023-06-08 12:26:50,502] [INFO] Task started: fastANI
[2023-06-08 12:26:50,502] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5e05fa6-f7e5-469d-900c-fba1e80b5b97/GCA_902778355.1_Rumen_uncultured_genome_RUG12363_genomic.fna.gz --refList GCA_902778355.1_Rumen_uncultured_genome_RUG12363_genomic.fna/target_genomes.txt --output GCA_902778355.1_Rumen_uncultured_genome_RUG12363_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 12:27:06,153] [INFO] Task succeeded: fastANI
[2023-06-08 12:27:06,153] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1891320b-4824-430a-8b7e-be7abbe79b6a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 12:27:06,154] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1891320b-4824-430a-8b7e-be7abbe79b6a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 12:27:06,160] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 12:27:06,161] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 12:27:06,161] [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
Sodaliphilus pleomorphus	strain=Oil-RF-744-WCA-WT-10	GCA_009676955.1	2606626	2606626	type	True	75.9869	56	1157	95	below_threshold
Sodaliphilus pleomorphus	strain=Oil-RF-744-WCA-WT-10	GCA_009696565.1	2606626	2606626	type	True	75.9439	56	1157	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	75.8721	69	1157	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 12:27:06,163] [INFO] DFAST Taxonomy check result was written to GCA_902778355.1_Rumen_uncultured_genome_RUG12363_genomic.fna/tc_result.tsv
[2023-06-08 12:27:06,163] [INFO] ===== Taxonomy check completed =====
[2023-06-08 12:27:06,164] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 12:27:06,164] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1891320b-4824-430a-8b7e-be7abbe79b6a/dqc_reference/checkm_data
[2023-06-08 12:27:06,165] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 12:27:06,207] [INFO] Task started: CheckM
[2023-06-08 12:27:06,207] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902778355.1_Rumen_uncultured_genome_RUG12363_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902778355.1_Rumen_uncultured_genome_RUG12363_genomic.fna/checkm_input GCA_902778355.1_Rumen_uncultured_genome_RUG12363_genomic.fna/checkm_result
[2023-06-08 12:28:10,536] [INFO] Task succeeded: CheckM
[2023-06-08 12:28:10,538] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 12:28:10,558] [INFO] ===== Completeness check finished =====
[2023-06-08 12:28:10,559] [INFO] ===== Start GTDB Search =====
[2023-06-08 12:28:10,560] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902778355.1_Rumen_uncultured_genome_RUG12363_genomic.fna/markers.fasta)
[2023-06-08 12:28:10,561] [INFO] Task started: Blastn
[2023-06-08 12:28:10,561] [INFO] Running command: blastn -query GCA_902778355.1_Rumen_uncultured_genome_RUG12363_genomic.fna/markers.fasta -db /var/lib/cwl/stg1891320b-4824-430a-8b7e-be7abbe79b6a/dqc_reference/reference_markers_gtdb.fasta -out GCA_902778355.1_Rumen_uncultured_genome_RUG12363_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:28:11,459] [INFO] Task succeeded: Blastn
[2023-06-08 12:28:11,464] [INFO] Selected 18 target genomes.
[2023-06-08 12:28:11,464] [INFO] Target genome list was writen to GCA_902778355.1_Rumen_uncultured_genome_RUG12363_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 12:28:11,468] [INFO] Task started: fastANI
[2023-06-08 12:28:11,469] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5e05fa6-f7e5-469d-900c-fba1e80b5b97/GCA_902778355.1_Rumen_uncultured_genome_RUG12363_genomic.fna.gz --refList GCA_902778355.1_Rumen_uncultured_genome_RUG12363_genomic.fna/target_genomes_gtdb.txt --output GCA_902778355.1_Rumen_uncultured_genome_RUG12363_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 12:28:21,360] [INFO] Task succeeded: fastANI
[2023-06-08 12:28:21,379] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 12:28:21,379] [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_902788315.1	s__UBA4372 sp902788315	97.8419	992	1157	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	98.21	97.94	0.89	0.88	4	conclusive
GCA_002394305.1	s__UBA4372 sp002394305	78.4557	231	1157	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	97.13	97.13	0.80	0.80	2	-
GCA_905235575.1	s__UBA4372 sp905235575	78.4195	322	1157	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902787575.1	s__UBA4372 sp900320715	78.322	295	1157	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	98.55	98.27	0.96	0.94	8	-
GCA_902799985.1	s__UBA4372 sp902799985	78.2592	241	1157	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	97.87	97.87	0.82	0.82	2	-
GCA_017483665.1	s__UBA4372 sp017483665	78.0155	246	1157	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017444005.1	s__UBA4372 sp017444005	77.9036	173	1157	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002395775.1	s__UBA4372 sp002395775	77.5947	166	1157	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	96.87	96.87	0.81	0.81	2	-
GCA_900320565.1	s__UBA4372 sp900320565	77.3577	135	1157	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	96.88	95.84	0.86	0.80	13	-
GCA_900313705.1	s__UBA4372 sp900313705	77.3488	181	1157	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	97.31	96.93	0.85	0.79	9	-
GCA_017935785.1	s__UBA4372 sp017935785	77.2657	108	1157	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	97.67	97.67	0.84	0.84	2	-
GCA_017541265.1	s__UBA4372 sp017541265	77.1376	184	1157	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905235285.1	s__UBA4372 sp905235285	77.0755	115	1157	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017379075.1	s__UBA4372 sp017379075	76.9261	137	1157	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	95.81	95.71	0.83	0.83	3	-
GCA_017559845.1	s__UBA4372 sp017559845	76.5772	135	1157	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900315455.1	s__Prevotella sp900315455	76.453	79	1157	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.41	96.59	0.90	0.86	13	-
GCA_019118325.1	s__Bacteroides intestinavium	76.365	68	1157	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019116285.1	s__Bacteroides merdigallinarum	76.0531	79	1157	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 12:28:21,381] [INFO] GTDB search result was written to GCA_902778355.1_Rumen_uncultured_genome_RUG12363_genomic.fna/result_gtdb.tsv
[2023-06-08 12:28:21,382] [INFO] ===== GTDB Search completed =====
[2023-06-08 12:28:21,385] [INFO] DFAST_QC result json was written to GCA_902778355.1_Rumen_uncultured_genome_RUG12363_genomic.fna/dqc_result.json
[2023-06-08 12:28:21,385] [INFO] DFAST_QC completed!
[2023-06-08 12:28:21,385] [INFO] Total running time: 0h1m56s