[2023-06-05 13:53:44,333] [INFO] DFAST_QC pipeline started.
[2023-06-05 13:53:44,335] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 13:53:44,335] [INFO] DQC Reference Directory: /var/lib/cwl/stgd0893b05-7bdd-4a40-a3a3-53e7f173f1d9/dqc_reference
[2023-06-05 13:53:45,815] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 13:53:45,815] [INFO] Task started: Prodigal
[2023-06-05 13:53:45,816] [INFO] Running command: gunzip -c /var/lib/cwl/stg95280ed0-9faf-4fa2-a4b9-8f0e747828c8/GCA_902836585.1_MGYG-HGUT-04803_genomic.fna.gz | prodigal -d GCA_902836585.1_MGYG-HGUT-04803_genomic.fna/cds.fna -a GCA_902836585.1_MGYG-HGUT-04803_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 13:53:55,691] [INFO] Task succeeded: Prodigal
[2023-06-05 13:53:55,691] [INFO] Task started: HMMsearch
[2023-06-05 13:53:55,691] [INFO] Running command: hmmsearch --tblout GCA_902836585.1_MGYG-HGUT-04803_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd0893b05-7bdd-4a40-a3a3-53e7f173f1d9/dqc_reference/reference_markers.hmm GCA_902836585.1_MGYG-HGUT-04803_genomic.fna/protein.faa > /dev/null
[2023-06-05 13:53:55,874] [INFO] Task succeeded: HMMsearch
[2023-06-05 13:53:55,875] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg95280ed0-9faf-4fa2-a4b9-8f0e747828c8/GCA_902836585.1_MGYG-HGUT-04803_genomic.fna.gz]
[2023-06-05 13:53:55,895] [INFO] Query marker FASTA was written to GCA_902836585.1_MGYG-HGUT-04803_genomic.fna/markers.fasta
[2023-06-05 13:53:55,895] [INFO] Task started: Blastn
[2023-06-05 13:53:55,895] [INFO] Running command: blastn -query GCA_902836585.1_MGYG-HGUT-04803_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0893b05-7bdd-4a40-a3a3-53e7f173f1d9/dqc_reference/reference_markers.fasta -out GCA_902836585.1_MGYG-HGUT-04803_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 13:53:56,426] [INFO] Task succeeded: Blastn
[2023-06-05 13:53:56,429] [INFO] Selected 14 target genomes.
[2023-06-05 13:53:56,429] [INFO] Target genome list was writen to GCA_902836585.1_MGYG-HGUT-04803_genomic.fna/target_genomes.txt
[2023-06-05 13:53:56,431] [INFO] Task started: fastANI
[2023-06-05 13:53:56,431] [INFO] Running command: fastANI --query /var/lib/cwl/stg95280ed0-9faf-4fa2-a4b9-8f0e747828c8/GCA_902836585.1_MGYG-HGUT-04803_genomic.fna.gz --refList GCA_902836585.1_MGYG-HGUT-04803_genomic.fna/target_genomes.txt --output GCA_902836585.1_MGYG-HGUT-04803_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 13:54:04,091] [INFO] Task succeeded: fastANI
[2023-06-05 13:54:04,092] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd0893b05-7bdd-4a40-a3a3-53e7f173f1d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 13:54:04,092] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd0893b05-7bdd-4a40-a3a3-53e7f173f1d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 13:54:04,099] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 13:54:04,100] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 13:54:04,100] [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 copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	90.4545	404	646	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_025151535.1	165179	165179	suspected-type	True	90.3243	421	646	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_000157935.1	165179	165179	suspected-type	True	90.2807	423	646	95	below_threshold
Prevotella hominis	strain=BCRC 81118	GCA_004535825.1	2518605	2518605	type	True	82.9542	321	646	95	below_threshold
Prevotella albensis	strain=JCM 12258	GCA_000613525.1	77768	77768	type	True	77.5373	55	646	95	below_threshold
Prevotella fusca	strain=W1435	GCA_018128145.1	589436	589436	type	True	76.9698	61	646	95	below_threshold
Prevotella fusca	strain=W1435	GCA_001262015.1	589436	589436	type	True	76.9579	62	646	95	below_threshold
Prevotella brevis	strain=ATCC 19188	GCA_000621725.1	83231	83231	type	True	76.5482	56	646	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	76.4052	78	646	95	below_threshold
Prevotella herbatica	strain=WR041	GCA_017347605.1	2801997	2801997	type	True	76.3825	50	646	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 13:54:04,101] [INFO] DFAST Taxonomy check result was written to GCA_902836585.1_MGYG-HGUT-04803_genomic.fna/tc_result.tsv
[2023-06-05 13:54:04,102] [INFO] ===== Taxonomy check completed =====
[2023-06-05 13:54:04,102] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 13:54:04,102] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd0893b05-7bdd-4a40-a3a3-53e7f173f1d9/dqc_reference/checkm_data
[2023-06-05 13:54:04,103] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 13:54:04,130] [INFO] Task started: CheckM
[2023-06-05 13:54:04,130] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902836585.1_MGYG-HGUT-04803_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902836585.1_MGYG-HGUT-04803_genomic.fna/checkm_input GCA_902836585.1_MGYG-HGUT-04803_genomic.fna/checkm_result
[2023-06-05 13:54:35,574] [INFO] Task succeeded: CheckM
[2023-06-05 13:54:35,576] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 53.12%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-05 13:54:35,593] [INFO] ===== Completeness check finished =====
[2023-06-05 13:54:35,593] [INFO] ===== Start GTDB Search =====
[2023-06-05 13:54:35,594] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902836585.1_MGYG-HGUT-04803_genomic.fna/markers.fasta)
[2023-06-05 13:54:35,595] [INFO] Task started: Blastn
[2023-06-05 13:54:35,595] [INFO] Running command: blastn -query GCA_902836585.1_MGYG-HGUT-04803_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0893b05-7bdd-4a40-a3a3-53e7f173f1d9/dqc_reference/reference_markers_gtdb.fasta -out GCA_902836585.1_MGYG-HGUT-04803_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 13:54:36,362] [INFO] Task succeeded: Blastn
[2023-06-05 13:54:36,365] [INFO] Selected 13 target genomes.
[2023-06-05 13:54:36,365] [INFO] Target genome list was writen to GCA_902836585.1_MGYG-HGUT-04803_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 13:54:36,370] [INFO] Task started: fastANI
[2023-06-05 13:54:36,371] [INFO] Running command: fastANI --query /var/lib/cwl/stg95280ed0-9faf-4fa2-a4b9-8f0e747828c8/GCA_902836585.1_MGYG-HGUT-04803_genomic.fna.gz --refList GCA_902836585.1_MGYG-HGUT-04803_genomic.fna/target_genomes_gtdb.txt --output GCA_902836585.1_MGYG-HGUT-04803_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 13:54:44,369] [INFO] Task succeeded: fastANI
[2023-06-05 13:54:44,378] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 13:54:44,378] [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
GCF_002224675.1	s__Prevotella copri_A	90.8469	456	646	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.28	96.07	0.78	0.74	13	-
GCF_015074785.1	s__Prevotella sp015074785	90.7593	434	646	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.6733	96.50	95.88	0.80	0.71	45	-
GCA_900557255.1	s__Prevotella sp900557255	90.6444	252	646	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019249655.1	s__Prevotella sp900767615	90.4555	489	646	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.47	95.77	0.82	0.75	7	-
GCF_000157935.1	s__Prevotella copri	90.281	423	646	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.6733	96.34	95.85	0.75	0.69	97	-
GCA_900557035.1	s__Prevotella sp900557035	89.8925	310	646	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.84	97.17	0.78	0.68	3	-
GCF_019127135.1	s__Prevotella sp900551275	89.7575	431	646	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0063	98.12	96.96	0.86	0.77	7	-
GCA_900544825.1	s__Prevotella sp900544825	89.7072	404	646	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.36	98.76	0.90	0.84	3	-
GCA_900551985.1	s__Prevotella sp900551985	89.6954	369	646	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.28	99.28	0.87	0.87	2	-
GCA_900765465.1	s__Prevotella sp900765465	88.9541	259	646	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900555035.1	s__Prevotella sp900555035	86.9326	372	646	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009494395.1	s__Prevotella sp900546535	86.428	432	646	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.78	96.11	0.82	0.79	8	-
GCA_900556795.1	s__Prevotella sp900556795	86.2867	238	646	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.39	96.16	0.81	0.77	3	-
--------------------------------------------------------------------------------
[2023-06-05 13:54:44,380] [INFO] GTDB search result was written to GCA_902836585.1_MGYG-HGUT-04803_genomic.fna/result_gtdb.tsv
[2023-06-05 13:54:44,380] [INFO] ===== GTDB Search completed =====
[2023-06-05 13:54:44,383] [INFO] DFAST_QC result json was written to GCA_902836585.1_MGYG-HGUT-04803_genomic.fna/dqc_result.json
[2023-06-05 13:54:44,384] [INFO] DFAST_QC completed!
[2023-06-05 13:54:44,384] [INFO] Total running time: 0h1m0s