[2023-06-08 04:43:03,144] [INFO] DFAST_QC pipeline started.
[2023-06-08 04:43:03,147] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 04:43:03,147] [INFO] DQC Reference Directory: /var/lib/cwl/stg9ed75e93-167f-4b7f-b419-333b6361ba27/dqc_reference
[2023-06-08 04:43:04,415] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 04:43:04,417] [INFO] Task started: Prodigal
[2023-06-08 04:43:04,417] [INFO] Running command: gunzip -c /var/lib/cwl/stg70ebc356-c9fd-42ac-aa9a-25b665f71947/GCA_902800305.1_Rumen_uncultured_genome_RUG14560_genomic.fna.gz | prodigal -d GCA_902800305.1_Rumen_uncultured_genome_RUG14560_genomic.fna/cds.fna -a GCA_902800305.1_Rumen_uncultured_genome_RUG14560_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 04:43:28,483] [INFO] Task succeeded: Prodigal
[2023-06-08 04:43:28,483] [INFO] Task started: HMMsearch
[2023-06-08 04:43:28,483] [INFO] Running command: hmmsearch --tblout GCA_902800305.1_Rumen_uncultured_genome_RUG14560_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9ed75e93-167f-4b7f-b419-333b6361ba27/dqc_reference/reference_markers.hmm GCA_902800305.1_Rumen_uncultured_genome_RUG14560_genomic.fna/protein.faa > /dev/null
[2023-06-08 04:43:28,780] [INFO] Task succeeded: HMMsearch
[2023-06-08 04:43:28,782] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg70ebc356-c9fd-42ac-aa9a-25b665f71947/GCA_902800305.1_Rumen_uncultured_genome_RUG14560_genomic.fna.gz]
[2023-06-08 04:43:28,820] [INFO] Query marker FASTA was written to GCA_902800305.1_Rumen_uncultured_genome_RUG14560_genomic.fna/markers.fasta
[2023-06-08 04:43:28,821] [INFO] Task started: Blastn
[2023-06-08 04:43:28,821] [INFO] Running command: blastn -query GCA_902800305.1_Rumen_uncultured_genome_RUG14560_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ed75e93-167f-4b7f-b419-333b6361ba27/dqc_reference/reference_markers.fasta -out GCA_902800305.1_Rumen_uncultured_genome_RUG14560_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 04:43:29,494] [INFO] Task succeeded: Blastn
[2023-06-08 04:43:29,498] [INFO] Selected 27 target genomes.
[2023-06-08 04:43:29,499] [INFO] Target genome list was writen to GCA_902800305.1_Rumen_uncultured_genome_RUG14560_genomic.fna/target_genomes.txt
[2023-06-08 04:43:29,501] [INFO] Task started: fastANI
[2023-06-08 04:43:29,501] [INFO] Running command: fastANI --query /var/lib/cwl/stg70ebc356-c9fd-42ac-aa9a-25b665f71947/GCA_902800305.1_Rumen_uncultured_genome_RUG14560_genomic.fna.gz --refList GCA_902800305.1_Rumen_uncultured_genome_RUG14560_genomic.fna/target_genomes.txt --output GCA_902800305.1_Rumen_uncultured_genome_RUG14560_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 04:43:44,102] [INFO] Task succeeded: fastANI
[2023-06-08 04:43:44,102] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9ed75e93-167f-4b7f-b419-333b6361ba27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 04:43:44,103] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9ed75e93-167f-4b7f-b419-333b6361ba27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 04:43:44,110] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 04:43:44,110] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 04:43:44,111] [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
Prevotella brevis	strain=ATCC 19188	GCA_000621725.1	83231	83231	type	True	75.9807	67	1190	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 04:43:44,113] [INFO] DFAST Taxonomy check result was written to GCA_902800305.1_Rumen_uncultured_genome_RUG14560_genomic.fna/tc_result.tsv
[2023-06-08 04:43:44,113] [INFO] ===== Taxonomy check completed =====
[2023-06-08 04:43:44,114] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 04:43:44,114] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9ed75e93-167f-4b7f-b419-333b6361ba27/dqc_reference/checkm_data
[2023-06-08 04:43:44,116] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 04:43:44,154] [INFO] Task started: CheckM
[2023-06-08 04:43:44,154] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902800305.1_Rumen_uncultured_genome_RUG14560_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902800305.1_Rumen_uncultured_genome_RUG14560_genomic.fna/checkm_input GCA_902800305.1_Rumen_uncultured_genome_RUG14560_genomic.fna/checkm_result
[2023-06-08 04:44:51,484] [INFO] Task succeeded: CheckM
[2023-06-08 04:44:51,485] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 04:44:51,504] [INFO] ===== Completeness check finished =====
[2023-06-08 04:44:51,504] [INFO] ===== Start GTDB Search =====
[2023-06-08 04:44:51,505] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902800305.1_Rumen_uncultured_genome_RUG14560_genomic.fna/markers.fasta)
[2023-06-08 04:44:51,505] [INFO] Task started: Blastn
[2023-06-08 04:44:51,505] [INFO] Running command: blastn -query GCA_902800305.1_Rumen_uncultured_genome_RUG14560_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ed75e93-167f-4b7f-b419-333b6361ba27/dqc_reference/reference_markers_gtdb.fasta -out GCA_902800305.1_Rumen_uncultured_genome_RUG14560_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 04:44:52,519] [INFO] Task succeeded: Blastn
[2023-06-08 04:44:52,524] [INFO] Selected 20 target genomes.
[2023-06-08 04:44:52,524] [INFO] Target genome list was writen to GCA_902800305.1_Rumen_uncultured_genome_RUG14560_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 04:44:52,527] [INFO] Task started: fastANI
[2023-06-08 04:44:52,527] [INFO] Running command: fastANI --query /var/lib/cwl/stg70ebc356-c9fd-42ac-aa9a-25b665f71947/GCA_902800305.1_Rumen_uncultured_genome_RUG14560_genomic.fna.gz --refList GCA_902800305.1_Rumen_uncultured_genome_RUG14560_genomic.fna/target_genomes_gtdb.txt --output GCA_902800305.1_Rumen_uncultured_genome_RUG14560_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 04:45:04,352] [INFO] Task succeeded: fastANI
[2023-06-08 04:45:04,375] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 04:45:04,375] [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_902800305.1	s__UBA4334 sp902800305	100.0	1186	1190	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	97.11	97.11	0.80	0.80	2	conclusive
GCA_902801475.1	s__UBA4334 sp902801475	80.5218	406	1190	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	97.71	97.36	0.83	0.79	15	-
GCA_017448965.1	s__UBA4334 sp017448965	80.1314	422	1190	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002393555.1	s__UBA4334 sp002393555	80.1133	404	1190	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	97.14	96.87	0.79	0.76	3	-
GCA_017483605.1	s__UBA4334 sp017483605	79.9118	461	1190	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	96.79	96.79	0.77	0.77	2	-
GCA_017448825.1	s__UBA4334 sp017448825	79.9021	467	1190	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016280445.1	s__UBA4334 sp016280445	79.8991	442	1190	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017470525.1	s__UBA4334 sp017470525	79.8717	433	1190	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905234125.1	s__UBA4334 sp905234125	79.7954	420	1190	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	98.16	98.16	0.81	0.81	2	-
GCA_902768125.1	s__UBA4334 sp902768125	79.788	383	1190	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	98.29	98.29	0.89	0.89	2	-
GCA_900316975.1	s__UBA4334 sp900316975	79.7696	406	1190	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	97.97	97.29	0.86	0.80	13	-
GCA_900316505.1	s__UBA4334 sp900316505	79.7413	404	1190	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	97.97	97.14	0.89	0.83	54	-
GCA_905235525.1	s__UBA4334 sp905235525	79.7023	359	1190	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	99.02	99.02	0.89	0.89	2	-
GCA_017651245.1	s__UBA4334 sp017651245	79.503	383	1190	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017617805.1	s__UBA4334 sp017617805	79.3608	306	1190	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009177185.1	s__UBA4334 sp009177185	79.0765	309	1190	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902789725.1	s__UBA4334 sp002363115	78.7343	348	1190	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	99.06	99.06	0.84	0.84	2	-
GCA_017507385.1	s__UBA4334 sp017507385	78.0737	202	1190	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904501945.1	s__UBA4334 sp904501945	77.9908	203	1190	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	100.00	100.00	0.99	0.99	2	-
GCA_017534705.1	s__RUG11857 sp017534705	76.9078	96	1190	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__RUG11857	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 04:45:04,377] [INFO] GTDB search result was written to GCA_902800305.1_Rumen_uncultured_genome_RUG14560_genomic.fna/result_gtdb.tsv
[2023-06-08 04:45:04,377] [INFO] ===== GTDB Search completed =====
[2023-06-08 04:45:04,381] [INFO] DFAST_QC result json was written to GCA_902800305.1_Rumen_uncultured_genome_RUG14560_genomic.fna/dqc_result.json
[2023-06-08 04:45:04,381] [INFO] DFAST_QC completed!
[2023-06-08 04:45:04,381] [INFO] Total running time: 0h2m1s