[2023-06-08 07:02:03,000] [INFO] DFAST_QC pipeline started.
[2023-06-08 07:02:03,002] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 07:02:03,002] [INFO] DQC Reference Directory: /var/lib/cwl/stg602978f4-addd-4e62-bf2c-9f0dcc5df86c/dqc_reference
[2023-06-08 07:02:04,404] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 07:02:04,405] [INFO] Task started: Prodigal
[2023-06-08 07:02:04,405] [INFO] Running command: gunzip -c /var/lib/cwl/stg4b7260e0-a515-4348-87fd-743418294806/GCA_902800245.1_Rumen_uncultured_genome_RUG14561_genomic.fna.gz | prodigal -d GCA_902800245.1_Rumen_uncultured_genome_RUG14561_genomic.fna/cds.fna -a GCA_902800245.1_Rumen_uncultured_genome_RUG14561_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 07:02:23,174] [INFO] Task succeeded: Prodigal
[2023-06-08 07:02:23,174] [INFO] Task started: HMMsearch
[2023-06-08 07:02:23,175] [INFO] Running command: hmmsearch --tblout GCA_902800245.1_Rumen_uncultured_genome_RUG14561_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg602978f4-addd-4e62-bf2c-9f0dcc5df86c/dqc_reference/reference_markers.hmm GCA_902800245.1_Rumen_uncultured_genome_RUG14561_genomic.fna/protein.faa > /dev/null
[2023-06-08 07:02:23,442] [INFO] Task succeeded: HMMsearch
[2023-06-08 07:02:23,444] [INFO] Found 6/6 markers.
[2023-06-08 07:02:23,478] [INFO] Query marker FASTA was written to GCA_902800245.1_Rumen_uncultured_genome_RUG14561_genomic.fna/markers.fasta
[2023-06-08 07:02:23,478] [INFO] Task started: Blastn
[2023-06-08 07:02:23,478] [INFO] Running command: blastn -query GCA_902800245.1_Rumen_uncultured_genome_RUG14561_genomic.fna/markers.fasta -db /var/lib/cwl/stg602978f4-addd-4e62-bf2c-9f0dcc5df86c/dqc_reference/reference_markers.fasta -out GCA_902800245.1_Rumen_uncultured_genome_RUG14561_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 07:02:24,068] [INFO] Task succeeded: Blastn
[2023-06-08 07:02:24,073] [INFO] Selected 31 target genomes.
[2023-06-08 07:02:24,074] [INFO] Target genome list was writen to GCA_902800245.1_Rumen_uncultured_genome_RUG14561_genomic.fna/target_genomes.txt
[2023-06-08 07:02:24,076] [INFO] Task started: fastANI
[2023-06-08 07:02:24,076] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b7260e0-a515-4348-87fd-743418294806/GCA_902800245.1_Rumen_uncultured_genome_RUG14561_genomic.fna.gz --refList GCA_902800245.1_Rumen_uncultured_genome_RUG14561_genomic.fna/target_genomes.txt --output GCA_902800245.1_Rumen_uncultured_genome_RUG14561_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 07:02:38,795] [INFO] Task succeeded: fastANI
[2023-06-08 07:02:38,796] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg602978f4-addd-4e62-bf2c-9f0dcc5df86c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 07:02:38,796] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg602978f4-addd-4e62-bf2c-9f0dcc5df86c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 07:02:38,808] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 07:02:38,808] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 07:02:38,808] [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 ruminicola	strain=ATCC 19189	GCA_900108375.1	839	839	type	True	78.4734	235	1061	95	below_threshold
Prevotella ruminicola	strain=Bryant 23	GCA_000025925.1	839	839	type	True	78.4684	234	1061	95	below_threshold
Prevotella brevis	strain=ATCC 19188	GCA_000621725.1	83231	83231	type	True	78.1719	169	1061	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	76.6771	89	1061	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_000157935.1	165179	165179	suspected-type	True	76.6214	90	1061	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	76.1771	51	1061	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	76.1625	79	1061	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 07:02:38,810] [INFO] DFAST Taxonomy check result was written to GCA_902800245.1_Rumen_uncultured_genome_RUG14561_genomic.fna/tc_result.tsv
[2023-06-08 07:02:38,811] [INFO] ===== Taxonomy check completed =====
[2023-06-08 07:02:38,811] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 07:02:38,811] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg602978f4-addd-4e62-bf2c-9f0dcc5df86c/dqc_reference/checkm_data
[2023-06-08 07:02:38,812] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 07:02:38,850] [INFO] Task started: CheckM
[2023-06-08 07:02:38,851] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902800245.1_Rumen_uncultured_genome_RUG14561_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902800245.1_Rumen_uncultured_genome_RUG14561_genomic.fna/checkm_input GCA_902800245.1_Rumen_uncultured_genome_RUG14561_genomic.fna/checkm_result
[2023-06-08 07:03:33,750] [INFO] Task succeeded: CheckM
[2023-06-08 07:03:33,751] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 07:03:33,779] [INFO] ===== Completeness check finished =====
[2023-06-08 07:03:33,780] [INFO] ===== Start GTDB Search =====
[2023-06-08 07:03:33,780] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902800245.1_Rumen_uncultured_genome_RUG14561_genomic.fna/markers.fasta)
[2023-06-08 07:03:33,780] [INFO] Task started: Blastn
[2023-06-08 07:03:33,781] [INFO] Running command: blastn -query GCA_902800245.1_Rumen_uncultured_genome_RUG14561_genomic.fna/markers.fasta -db /var/lib/cwl/stg602978f4-addd-4e62-bf2c-9f0dcc5df86c/dqc_reference/reference_markers_gtdb.fasta -out GCA_902800245.1_Rumen_uncultured_genome_RUG14561_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 07:03:34,665] [INFO] Task succeeded: Blastn
[2023-06-08 07:03:34,670] [INFO] Selected 11 target genomes.
[2023-06-08 07:03:34,670] [INFO] Target genome list was writen to GCA_902800245.1_Rumen_uncultured_genome_RUG14561_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 07:03:34,672] [INFO] Task started: fastANI
[2023-06-08 07:03:34,672] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b7260e0-a515-4348-87fd-743418294806/GCA_902800245.1_Rumen_uncultured_genome_RUG14561_genomic.fna.gz --refList GCA_902800245.1_Rumen_uncultured_genome_RUG14561_genomic.fna/target_genomes_gtdb.txt --output GCA_902800245.1_Rumen_uncultured_genome_RUG14561_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 07:03:41,801] [INFO] Task succeeded: fastANI
[2023-06-08 07:03:41,813] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 07:03:41,813] [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_902800245.1	s__Prevotella sp902800245	100.0	1050	1061	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900318885.1	s__Prevotella sp900318885	92.7018	734	1061	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.27	96.53	0.88	0.77	3	-
GCA_902774925.1	s__Prevotella sp902774925	92.2327	776	1061	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.74	98.74	0.87	0.87	2	-
GCA_900318555.1	s__Prevotella sp900318555	91.7658	753	1061	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.81	96.13	0.85	0.78	8	-
GCA_017447515.1	s__Prevotella sp017447515	86.1763	432	1061	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902772585.1	s__Prevotella sp902772585	81.154	367	1061	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902762565.1	s__Prevotella sp902762565	81.0944	415	1061	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.04	97.04	0.79	0.79	2	-
GCA_016291085.1	s__Prevotella sp016291085	80.597	516	1061	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902800925.1	s__Prevotella sp902800925	80.2084	322	1061	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900314985.1	s__Prevotella sp900314985	79.4506	336	1061	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.71	97.24	0.86	0.81	12	-
GCA_002363695.1	s__Prevotella sp002363695	78.8402	213	1061	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 07:03:41,815] [INFO] GTDB search result was written to GCA_902800245.1_Rumen_uncultured_genome_RUG14561_genomic.fna/result_gtdb.tsv
[2023-06-08 07:03:41,816] [INFO] ===== GTDB Search completed =====
[2023-06-08 07:03:41,819] [INFO] DFAST_QC result json was written to GCA_902800245.1_Rumen_uncultured_genome_RUG14561_genomic.fna/dqc_result.json
[2023-06-08 07:03:41,819] [INFO] DFAST_QC completed!
[2023-06-08 07:03:41,820] [INFO] Total running time: 0h1m39s