[2023-06-05 19:01:48,731] [INFO] DFAST_QC pipeline started.
[2023-06-05 19:01:48,733] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 19:01:48,733] [INFO] DQC Reference Directory: /var/lib/cwl/stg376f6a6f-96bd-484e-9122-bae792133acc/dqc_reference
[2023-06-05 19:01:50,394] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 19:01:50,398] [INFO] Task started: Prodigal
[2023-06-05 19:01:50,398] [INFO] Running command: gunzip -c /var/lib/cwl/stg1f3cb6f2-6144-4e3e-bfc1-b8bb1df04015/GCA_902758745.1_Rumen_uncultured_genome_RUG10402_genomic.fna.gz | prodigal -d GCA_902758745.1_Rumen_uncultured_genome_RUG10402_genomic.fna/cds.fna -a GCA_902758745.1_Rumen_uncultured_genome_RUG10402_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 19:02:09,300] [INFO] Task succeeded: Prodigal
[2023-06-05 19:02:09,301] [INFO] Task started: HMMsearch
[2023-06-05 19:02:09,301] [INFO] Running command: hmmsearch --tblout GCA_902758745.1_Rumen_uncultured_genome_RUG10402_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg376f6a6f-96bd-484e-9122-bae792133acc/dqc_reference/reference_markers.hmm GCA_902758745.1_Rumen_uncultured_genome_RUG10402_genomic.fna/protein.faa > /dev/null
[2023-06-05 19:02:09,567] [INFO] Task succeeded: HMMsearch
[2023-06-05 19:02:09,569] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1f3cb6f2-6144-4e3e-bfc1-b8bb1df04015/GCA_902758745.1_Rumen_uncultured_genome_RUG10402_genomic.fna.gz]
[2023-06-05 19:02:09,604] [INFO] Query marker FASTA was written to GCA_902758745.1_Rumen_uncultured_genome_RUG10402_genomic.fna/markers.fasta
[2023-06-05 19:02:09,605] [INFO] Task started: Blastn
[2023-06-05 19:02:09,605] [INFO] Running command: blastn -query GCA_902758745.1_Rumen_uncultured_genome_RUG10402_genomic.fna/markers.fasta -db /var/lib/cwl/stg376f6a6f-96bd-484e-9122-bae792133acc/dqc_reference/reference_markers.fasta -out GCA_902758745.1_Rumen_uncultured_genome_RUG10402_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 19:02:10,245] [INFO] Task succeeded: Blastn
[2023-06-05 19:02:10,249] [INFO] Selected 16 target genomes.
[2023-06-05 19:02:10,250] [INFO] Target genome list was writen to GCA_902758745.1_Rumen_uncultured_genome_RUG10402_genomic.fna/target_genomes.txt
[2023-06-05 19:02:10,251] [INFO] Task started: fastANI
[2023-06-05 19:02:10,251] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f3cb6f2-6144-4e3e-bfc1-b8bb1df04015/GCA_902758745.1_Rumen_uncultured_genome_RUG10402_genomic.fna.gz --refList GCA_902758745.1_Rumen_uncultured_genome_RUG10402_genomic.fna/target_genomes.txt --output GCA_902758745.1_Rumen_uncultured_genome_RUG10402_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 19:02:19,245] [INFO] Task succeeded: fastANI
[2023-06-05 19:02:19,245] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg376f6a6f-96bd-484e-9122-bae792133acc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 19:02:19,246] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg376f6a6f-96bd-484e-9122-bae792133acc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 19:02:19,261] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 19:02:19,262] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 19:02:19,262] [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=Bryant 23	GCA_000025925.1	839	839	type	True	79.3463	359	1132	95	below_threshold
Prevotella ruminicola	strain=ATCC 19189	GCA_900108375.1	839	839	type	True	79.2642	359	1132	95	below_threshold
Prevotella brevis	strain=ATCC 19188	GCA_000621725.1	83231	83231	type	True	78.5573	200	1132	95	below_threshold
Prevotella pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	76.896	75	1132	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	76.6254	72	1132	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	76.5347	92	1132	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	76.493	69	1132	95	below_threshold
Prevotella fusca	strain=W1435	GCA_018128145.1	589436	589436	type	True	76.4644	73	1132	95	below_threshold
Prevotella fusca	strain=W1435	GCA_001262015.1	589436	589436	type	True	76.3991	72	1132	95	below_threshold
Prevotella albensis	strain=DSM 11370	GCA_000426565.1	77768	77768	type	True	76.3703	64	1132	95	below_threshold
Prevotella hominis	strain=BCRC 81118	GCA_004535825.1	2518605	2518605	type	True	76.3644	99	1132	95	below_threshold
Prevotella albensis	strain=JCM 12258	GCA_000613525.1	77768	77768	type	True	76.3551	62	1132	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	76.3385	85	1132	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 19:02:19,264] [INFO] DFAST Taxonomy check result was written to GCA_902758745.1_Rumen_uncultured_genome_RUG10402_genomic.fna/tc_result.tsv
[2023-06-05 19:02:19,264] [INFO] ===== Taxonomy check completed =====
[2023-06-05 19:02:19,265] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 19:02:19,265] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg376f6a6f-96bd-484e-9122-bae792133acc/dqc_reference/checkm_data
[2023-06-05 19:02:19,266] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 19:02:19,301] [INFO] Task started: CheckM
[2023-06-05 19:02:19,302] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902758745.1_Rumen_uncultured_genome_RUG10402_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902758745.1_Rumen_uncultured_genome_RUG10402_genomic.fna/checkm_input GCA_902758745.1_Rumen_uncultured_genome_RUG10402_genomic.fna/checkm_result
[2023-06-05 19:03:15,620] [INFO] Task succeeded: CheckM
[2023-06-05 19:03:15,622] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.90%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 19:03:15,645] [INFO] ===== Completeness check finished =====
[2023-06-05 19:03:15,645] [INFO] ===== Start GTDB Search =====
[2023-06-05 19:03:15,646] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902758745.1_Rumen_uncultured_genome_RUG10402_genomic.fna/markers.fasta)
[2023-06-05 19:03:15,646] [INFO] Task started: Blastn
[2023-06-05 19:03:15,646] [INFO] Running command: blastn -query GCA_902758745.1_Rumen_uncultured_genome_RUG10402_genomic.fna/markers.fasta -db /var/lib/cwl/stg376f6a6f-96bd-484e-9122-bae792133acc/dqc_reference/reference_markers_gtdb.fasta -out GCA_902758745.1_Rumen_uncultured_genome_RUG10402_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 19:03:16,726] [INFO] Task succeeded: Blastn
[2023-06-05 19:03:16,730] [INFO] Selected 16 target genomes.
[2023-06-05 19:03:16,730] [INFO] Target genome list was writen to GCA_902758745.1_Rumen_uncultured_genome_RUG10402_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 19:03:16,732] [INFO] Task started: fastANI
[2023-06-05 19:03:16,732] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f3cb6f2-6144-4e3e-bfc1-b8bb1df04015/GCA_902758745.1_Rumen_uncultured_genome_RUG10402_genomic.fna.gz --refList GCA_902758745.1_Rumen_uncultured_genome_RUG10402_genomic.fna/target_genomes_gtdb.txt --output GCA_902758745.1_Rumen_uncultured_genome_RUG10402_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 19:03:28,388] [INFO] Task succeeded: fastANI
[2023-06-05 19:03:28,406] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 19:03:28,406] [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_900318395.1	s__Prevotella sp900318395	100.0	1127	1132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.69	96.89	0.88	0.81	6	conclusive
GCA_016286575.1	s__Prevotella sp016286575	84.2043	571	1132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017443345.1	s__Prevotella sp017443345	83.023	661	1132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110085.1	s__Prevotella sp900110085	81.0096	534	1132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.96	96.96	0.82	0.82	3	-
GCA_902799765.1	s__Prevotella sp902799765	80.2851	478	1132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.49	95.44	0.80	0.73	3	-
GCA_900315695.1	s__Prevotella sp900315695	80.2819	442	1132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.90	97.22	0.82	0.74	6	-
GCA_900315525.1	s__Prevotella sp900315525	80.1581	447	1132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.95	96.00	0.84	0.76	10	-
GCA_017428805.1	s__Prevotella sp017428805	80.0932	394	1132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900315035.1	s__Prevotella sp900315035	80.0886	452	1132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.18	98.35	0.94	0.89	3	-
GCA_905234145.1	s__Prevotella sp905234145	79.8594	365	1132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.84	97.84	0.73	0.73	2	-
GCA_902798285.1	s__Prevotella sp902798285	79.7486	444	1132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.28	98.28	0.87	0.87	2	-
GCA_902784065.1	s__Prevotella sp902784065	79.7	390	1132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017965475.1	s__Prevotella sp017965475	79.5859	373	1132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016284635.1	s__Prevotella sp016284635	79.5683	401	1132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109055.1	s__Prevotella sp900109055	79.4831	405	1132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.78	98.70	0.94	0.92	3	-
GCA_002379425.1	s__Prevotella sp002379425	79.4777	246	1132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 19:03:28,408] [INFO] GTDB search result was written to GCA_902758745.1_Rumen_uncultured_genome_RUG10402_genomic.fna/result_gtdb.tsv
[2023-06-05 19:03:28,409] [INFO] ===== GTDB Search completed =====
[2023-06-05 19:03:28,413] [INFO] DFAST_QC result json was written to GCA_902758745.1_Rumen_uncultured_genome_RUG10402_genomic.fna/dqc_result.json
[2023-06-05 19:03:28,413] [INFO] DFAST_QC completed!
[2023-06-05 19:03:28,413] [INFO] Total running time: 0h1m40s