[2023-06-07 21:13:35,363] [INFO] DFAST_QC pipeline started.
[2023-06-07 21:13:35,369] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 21:13:35,369] [INFO] DQC Reference Directory: /var/lib/cwl/stgef8621d7-05f8-4c89-952a-98c6102be5ad/dqc_reference
[2023-06-07 21:13:36,733] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 21:13:36,734] [INFO] Task started: Prodigal
[2023-06-07 21:13:36,737] [INFO] Running command: gunzip -c /var/lib/cwl/stgd94699c4-44e8-4929-8d85-250c3451ee75/GCA_902835565.1_MGYG-HGUT-04827_genomic.fna.gz | prodigal -d GCA_902835565.1_MGYG-HGUT-04827_genomic.fna/cds.fna -a GCA_902835565.1_MGYG-HGUT-04827_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 21:13:56,712] [INFO] Task succeeded: Prodigal
[2023-06-07 21:13:56,713] [INFO] Task started: HMMsearch
[2023-06-07 21:13:56,713] [INFO] Running command: hmmsearch --tblout GCA_902835565.1_MGYG-HGUT-04827_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgef8621d7-05f8-4c89-952a-98c6102be5ad/dqc_reference/reference_markers.hmm GCA_902835565.1_MGYG-HGUT-04827_genomic.fna/protein.faa > /dev/null
[2023-06-07 21:13:57,008] [INFO] Task succeeded: HMMsearch
[2023-06-07 21:13:57,010] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgd94699c4-44e8-4929-8d85-250c3451ee75/GCA_902835565.1_MGYG-HGUT-04827_genomic.fna.gz]
[2023-06-07 21:13:57,053] [INFO] Query marker FASTA was written to GCA_902835565.1_MGYG-HGUT-04827_genomic.fna/markers.fasta
[2023-06-07 21:13:57,053] [INFO] Task started: Blastn
[2023-06-07 21:13:57,054] [INFO] Running command: blastn -query GCA_902835565.1_MGYG-HGUT-04827_genomic.fna/markers.fasta -db /var/lib/cwl/stgef8621d7-05f8-4c89-952a-98c6102be5ad/dqc_reference/reference_markers.fasta -out GCA_902835565.1_MGYG-HGUT-04827_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 21:13:57,692] [INFO] Task succeeded: Blastn
[2023-06-07 21:13:57,697] [INFO] Selected 15 target genomes.
[2023-06-07 21:13:57,698] [INFO] Target genome list was writen to GCA_902835565.1_MGYG-HGUT-04827_genomic.fna/target_genomes.txt
[2023-06-07 21:13:57,700] [INFO] Task started: fastANI
[2023-06-07 21:13:57,700] [INFO] Running command: fastANI --query /var/lib/cwl/stgd94699c4-44e8-4929-8d85-250c3451ee75/GCA_902835565.1_MGYG-HGUT-04827_genomic.fna.gz --refList GCA_902835565.1_MGYG-HGUT-04827_genomic.fna/target_genomes.txt --output GCA_902835565.1_MGYG-HGUT-04827_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 21:14:10,695] [INFO] Task succeeded: fastANI
[2023-06-07 21:14:10,695] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgef8621d7-05f8-4c89-952a-98c6102be5ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 21:14:10,696] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgef8621d7-05f8-4c89-952a-98c6102be5ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 21:14:10,710] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 21:14:10,710] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-07 21:14:10,711] [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
Bacteroides ovatus	strain=ATCC 8483	GCA_002959635.1	28116	28116	suspected-type	True	92.3478	816	1260	95	below_threshold
Bacteroides ovatus	strain=NCTC11153	GCA_900445505.1	28116	28116	suspected-type	True	92.3454	814	1260	95	below_threshold
Bacteroides ovatus	strain=ATCC 8483	GCA_001314995.1	28116	28116	suspected-type	True	92.3407	817	1260	95	below_threshold
Bacteroides xylanisolvens	strain=XB1A	GCA_000210075.1	371601	371601	suspected-type	True	92.0018	802	1260	95	below_threshold
Bacteroides caccae	strain=ATCC 43185	GCA_002959715.1	47678	47678	suspected-type	True	92.0008	582	1260	95	below_threshold
Bacteroides caccae	strain=ATCC 43185	GCA_025146315.1	47678	47678	suspected-type	True	91.8999	584	1260	95	below_threshold
Bacteroides caccae	strain=ATCC 43185	GCA_002222615.2	47678	47678	suspected-type	True	91.8924	584	1260	95	below_threshold
Bacteroides caccae	strain=ATCC 43185	GCA_000169015.1	47678	47678	suspected-type	True	91.8556	589	1260	95	below_threshold
Bacteroides caccae	strain=FDAARGOS_1097	GCA_016726305.1	47678	47678	suspected-type	True	91.7704	592	1260	95	below_threshold
Bacteroides luhongzhouii	strain=HF-5141	GCA_009193295.2	2650158	2650158	type	True	89.3985	718	1260	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_001688725.2	1796613	1796613	type	True	89.0899	560	1260	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_016697125.1	1796613	1796613	type	True	89.0023	565	1260	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_002221665.1	1796613	1796613	type	True	88.9654	555	1260	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_023277905.1	1796613	1796613	type	True	88.9288	557	1260	95	below_threshold
Bacteroides thetaiotaomicron	strain=VPI 5482	GCA_022453665.1	818	818	type	True	81.6392	535	1260	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-07 21:14:10,713] [INFO] DFAST Taxonomy check result was written to GCA_902835565.1_MGYG-HGUT-04827_genomic.fna/tc_result.tsv
[2023-06-07 21:14:10,713] [INFO] ===== Taxonomy check completed =====
[2023-06-07 21:14:10,713] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 21:14:10,713] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgef8621d7-05f8-4c89-952a-98c6102be5ad/dqc_reference/checkm_data
[2023-06-07 21:14:10,714] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 21:14:10,759] [INFO] Task started: CheckM
[2023-06-07 21:14:10,759] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902835565.1_MGYG-HGUT-04827_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902835565.1_MGYG-HGUT-04827_genomic.fna/checkm_input GCA_902835565.1_MGYG-HGUT-04827_genomic.fna/checkm_result
[2023-06-07 21:15:08,357] [INFO] Task succeeded: CheckM
[2023-06-07 21:15:08,358] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 49.64%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 21:15:08,379] [INFO] ===== Completeness check finished =====
[2023-06-07 21:15:08,380] [INFO] ===== Start GTDB Search =====
[2023-06-07 21:15:08,380] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902835565.1_MGYG-HGUT-04827_genomic.fna/markers.fasta)
[2023-06-07 21:15:08,380] [INFO] Task started: Blastn
[2023-06-07 21:15:08,380] [INFO] Running command: blastn -query GCA_902835565.1_MGYG-HGUT-04827_genomic.fna/markers.fasta -db /var/lib/cwl/stgef8621d7-05f8-4c89-952a-98c6102be5ad/dqc_reference/reference_markers_gtdb.fasta -out GCA_902835565.1_MGYG-HGUT-04827_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 21:15:09,269] [INFO] Task succeeded: Blastn
[2023-06-07 21:15:09,273] [INFO] Selected 12 target genomes.
[2023-06-07 21:15:09,273] [INFO] Target genome list was writen to GCA_902835565.1_MGYG-HGUT-04827_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 21:15:09,274] [INFO] Task started: fastANI
[2023-06-07 21:15:09,274] [INFO] Running command: fastANI --query /var/lib/cwl/stgd94699c4-44e8-4929-8d85-250c3451ee75/GCA_902835565.1_MGYG-HGUT-04827_genomic.fna.gz --refList GCA_902835565.1_MGYG-HGUT-04827_genomic.fna/target_genomes_gtdb.txt --output GCA_902835565.1_MGYG-HGUT-04827_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 21:15:21,419] [INFO] Task succeeded: fastANI
[2023-06-07 21:15:21,440] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-07 21:15:21,441] [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_001314995.1	s__Bacteroides ovatus	92.2809	820	1260	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.48	95.28	0.79	0.72	126	-
GCF_000210075.1	s__Bacteroides xylanisolvens	92.0018	802	1260	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.52	96.81	0.77	0.68	125	-
GCF_002222615.2	s__Bacteroides caccae	91.9298	583	1260	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.30	98.91	0.88	0.81	77	-
GCF_014334015.1	s__Bacteroides intestinigallinarum	89.7337	814	1260	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.71	95.47	0.80	0.53	8	-
GCF_009193295.2	s__Bacteroides luhongzhouii	89.3984	718	1260	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.19	98.73	0.86	0.78	4	-
GCF_001688725.2	s__Bacteroides caecimuris	89.1161	559	1260	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.14	95.76	0.86	0.68	7	-
GCA_902362375.1	s__Bacteroides sp902362375	88.6039	771	1260	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.74	98.46	0.82	0.77	13	-
GCA_900755095.1	s__Bacteroides sp900755095	84.3447	359	1260	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014750685.1	s__Bacteroides sp014750685	82.8075	699	1260	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000011065.1	s__Bacteroides thetaiotaomicron	81.6606	537	1260	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.45	97.24	0.84	0.75	121	-
GCF_900106755.1	s__Bacteroides faecis	81.1818	498	1260	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.27	98.92	0.88	0.84	29	-
GCA_900547205.1	s__Bacteroides sp900547205	81.1786	436	1260	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.99	99.99	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2023-06-07 21:15:21,443] [INFO] GTDB search result was written to GCA_902835565.1_MGYG-HGUT-04827_genomic.fna/result_gtdb.tsv
[2023-06-07 21:15:21,443] [INFO] ===== GTDB Search completed =====
[2023-06-07 21:15:21,447] [INFO] DFAST_QC result json was written to GCA_902835565.1_MGYG-HGUT-04827_genomic.fna/dqc_result.json
[2023-06-07 21:15:21,447] [INFO] DFAST_QC completed!
[2023-06-07 21:15:21,447] [INFO] Total running time: 0h1m46s