[2024-01-25 18:49:35,511] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:49:35,512] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:49:35,512] [INFO] DQC Reference Directory: /var/lib/cwl/stge18b146c-70c0-49f1-aac0-64b1da66faf7/dqc_reference
[2024-01-25 18:49:36,672] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:49:36,673] [INFO] Task started: Prodigal
[2024-01-25 18:49:36,673] [INFO] Running command: gunzip -c /var/lib/cwl/stgb2701397-c4f8-4cb3-ab4d-0fbed276100e/GCF_028539425.1_ASM2853942v1_genomic.fna.gz | prodigal -d GCF_028539425.1_ASM2853942v1_genomic.fna/cds.fna -a GCF_028539425.1_ASM2853942v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:50:01,239] [INFO] Task succeeded: Prodigal
[2024-01-25 18:50:01,240] [INFO] Task started: HMMsearch
[2024-01-25 18:50:01,240] [INFO] Running command: hmmsearch --tblout GCF_028539425.1_ASM2853942v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge18b146c-70c0-49f1-aac0-64b1da66faf7/dqc_reference/reference_markers.hmm GCF_028539425.1_ASM2853942v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:50:01,567] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:50:01,568] [INFO] Found 6/6 markers.
[2024-01-25 18:50:01,617] [INFO] Query marker FASTA was written to GCF_028539425.1_ASM2853942v1_genomic.fna/markers.fasta
[2024-01-25 18:50:01,617] [INFO] Task started: Blastn
[2024-01-25 18:50:01,618] [INFO] Running command: blastn -query GCF_028539425.1_ASM2853942v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge18b146c-70c0-49f1-aac0-64b1da66faf7/dqc_reference/reference_markers.fasta -out GCF_028539425.1_ASM2853942v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:50:02,197] [INFO] Task succeeded: Blastn
[2024-01-25 18:50:02,206] [INFO] Selected 11 target genomes.
[2024-01-25 18:50:02,207] [INFO] Target genome list was writen to GCF_028539425.1_ASM2853942v1_genomic.fna/target_genomes.txt
[2024-01-25 18:50:02,217] [INFO] Task started: fastANI
[2024-01-25 18:50:02,217] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2701397-c4f8-4cb3-ab4d-0fbed276100e/GCF_028539425.1_ASM2853942v1_genomic.fna.gz --refList GCF_028539425.1_ASM2853942v1_genomic.fna/target_genomes.txt --output GCF_028539425.1_ASM2853942v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:50:15,948] [INFO] Task succeeded: fastANI
[2024-01-25 18:50:15,948] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge18b146c-70c0-49f1-aac0-64b1da66faf7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:50:15,949] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge18b146c-70c0-49f1-aac0-64b1da66faf7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:50:15,957] [INFO] Found 11 fastANI hits (5 hits with ANI > threshold)
[2024-01-25 18:50:15,957] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:50:15,957] [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 thetaiotaomicron	strain=VPI-5482	GCA_002959695.1	818	818	type	True	99.9971	2036	2038	95	conclusive
Bacteroides thetaiotaomicron	strain=VPI 5482	GCA_022453665.1	818	818	type	True	99.9937	2038	2038	95	conclusive
Bacteroides thetaiotaomicron	strain=VPI-5482	GCA_020179495.1	818	818	type	True	99.9934	2015	2038	95	conclusive
Bacteroides thetaiotaomicron	strain=VPI-5482	GCA_000011065.1	818	818	type	True	99.9922	2032	2038	95	conclusive
Bacteroides thetaiotaomicron	strain=NCTC10582	GCA_900445595.1	818	818	type	True	99.981	2017	2038	95	conclusive
Bacteroides caecimuris	strain=I48	GCA_023277905.1	1796613	1796613	type	True	82.3481	739	2038	95	below_threshold
Bacteroides caccae	strain=ATCC 43185	GCA_025146315.1	47678	47678	suspected-type	True	81.9347	795	2038	95	below_threshold
Bacteroides ovatus	strain=FDAARGOS_1516	GCA_020149745.1	28116	28116	suspected-type	True	81.7432	927	2038	95	below_threshold
Bacteroides ovatus	strain=ATCC 8483	GCA_025146775.1	28116	28116	suspected-type	True	81.6838	942	2038	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_025147325.1	46506	46506	suspected-type	True	80.4423	329	2038	95	below_threshold
Bacteroides stercorirosoris	strain=JCM 17103	GCA_000614165.1	871324	871324	type	True	78.3462	393	2038	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:50:15,958] [INFO] DFAST Taxonomy check result was written to GCF_028539425.1_ASM2853942v1_genomic.fna/tc_result.tsv
[2024-01-25 18:50:15,961] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:50:15,961] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:50:15,961] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge18b146c-70c0-49f1-aac0-64b1da66faf7/dqc_reference/checkm_data
[2024-01-25 18:50:15,962] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:50:16,019] [INFO] Task started: CheckM
[2024-01-25 18:50:16,019] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028539425.1_ASM2853942v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028539425.1_ASM2853942v1_genomic.fna/checkm_input GCF_028539425.1_ASM2853942v1_genomic.fna/checkm_result
[2024-01-25 18:51:24,061] [INFO] Task succeeded: CheckM
[2024-01-25 18:51:24,062] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:51:24,081] [INFO] ===== Completeness check finished =====
[2024-01-25 18:51:24,081] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:51:24,082] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028539425.1_ASM2853942v1_genomic.fna/markers.fasta)
[2024-01-25 18:51:24,082] [INFO] Task started: Blastn
[2024-01-25 18:51:24,082] [INFO] Running command: blastn -query GCF_028539425.1_ASM2853942v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge18b146c-70c0-49f1-aac0-64b1da66faf7/dqc_reference/reference_markers_gtdb.fasta -out GCF_028539425.1_ASM2853942v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:51:24,998] [INFO] Task succeeded: Blastn
[2024-01-25 18:51:25,001] [INFO] Selected 16 target genomes.
[2024-01-25 18:51:25,001] [INFO] Target genome list was writen to GCF_028539425.1_ASM2853942v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:51:25,022] [INFO] Task started: fastANI
[2024-01-25 18:51:25,022] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2701397-c4f8-4cb3-ab4d-0fbed276100e/GCF_028539425.1_ASM2853942v1_genomic.fna.gz --refList GCF_028539425.1_ASM2853942v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028539425.1_ASM2853942v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:51:44,422] [INFO] Task succeeded: fastANI
[2024-01-25 18:51:44,432] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:51:44,432] [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_000011065.1	s__Bacteroides thetaiotaomicron	99.9922	2032	2038	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.45	97.24	0.84	0.75	121	conclusive
GCF_900106755.1	s__Bacteroides faecis	89.3356	1422	2038	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.27	98.92	0.88	0.84	29	-
GCA_900755095.1	s__Bacteroides sp900755095	88.6632	670	2038	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900761785.1	s__Bacteroides sp900761785	84.9139	999	2038	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000210075.1	s__Bacteroides xylanisolvens	82.6743	973	2038	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.52	96.81	0.77	0.68	125	-
GCF_000156195.1	s__Bacteroides finegoldii	82.2678	760	2038	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.8579	98.84	97.86	0.83	0.75	21	-
GCF_900130125.1	s__Bacteroides congonensis	82.0958	936	2038	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.81	97.60	0.79	0.75	6	-
GCF_009193295.2	s__Bacteroides luhongzhouii	82.0106	911	2038	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.19	98.73	0.86	0.78	4	-
GCF_002222615.2	s__Bacteroides caccae	81.9557	793	2038	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.30	98.91	0.88	0.81	77	-
GCF_012113595.1	s__Bacteroides sp012113595	81.7231	980	2038	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014334015.1	s__Bacteroides intestinigallinarum	81.6957	942	2038	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.71	95.47	0.80	0.53	8	-
GCF_001314995.1	s__Bacteroides ovatus	81.6769	945	2038	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.48	95.28	0.79	0.72	126	-
GCF_014750685.1	s__Bacteroides sp014750685	81.5948	974	2038	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902362375.1	s__Bacteroides sp902362375	81.5578	924	2038	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.74	98.46	0.82	0.77	13	-
GCF_009193325.2	s__Bacteroides zhangwenhongi	81.4733	763	2038	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.8579	97.65	96.82	0.72	0.66	9	-
GCA_900556625.1	s__Bacteroides sp900556625	80.9979	482	2038	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.84	99.84	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:51:44,434] [INFO] GTDB search result was written to GCF_028539425.1_ASM2853942v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:51:44,435] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:51:44,439] [INFO] DFAST_QC result json was written to GCF_028539425.1_ASM2853942v1_genomic.fna/dqc_result.json
[2024-01-25 18:51:44,439] [INFO] DFAST_QC completed!
[2024-01-25 18:51:44,439] [INFO] Total running time: 0h2m9s