[2024-01-24 14:05:53,394] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:53,397] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:53,397] [INFO] DQC Reference Directory: /var/lib/cwl/stge9bd71a2-a055-47be-9bc5-8b31f5231a2a/dqc_reference
[2024-01-24 14:05:54,851] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:54,852] [INFO] Task started: Prodigal
[2024-01-24 14:05:54,853] [INFO] Running command: gunzip -c /var/lib/cwl/stgc4487a6a-ea3d-44c4-98e9-af23ff3a7d05/GCF_021730445.1_ASM2173044v1_genomic.fna.gz | prodigal -d GCF_021730445.1_ASM2173044v1_genomic.fna/cds.fna -a GCF_021730445.1_ASM2173044v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:18,130] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:18,130] [INFO] Task started: HMMsearch
[2024-01-24 14:06:18,130] [INFO] Running command: hmmsearch --tblout GCF_021730445.1_ASM2173044v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge9bd71a2-a055-47be-9bc5-8b31f5231a2a/dqc_reference/reference_markers.hmm GCF_021730445.1_ASM2173044v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:18,410] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:18,411] [INFO] Found 6/6 markers.
[2024-01-24 14:06:18,448] [INFO] Query marker FASTA was written to GCF_021730445.1_ASM2173044v1_genomic.fna/markers.fasta
[2024-01-24 14:06:18,448] [INFO] Task started: Blastn
[2024-01-24 14:06:18,448] [INFO] Running command: blastn -query GCF_021730445.1_ASM2173044v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge9bd71a2-a055-47be-9bc5-8b31f5231a2a/dqc_reference/reference_markers.fasta -out GCF_021730445.1_ASM2173044v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:19,080] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:19,083] [INFO] Selected 11 target genomes.
[2024-01-24 14:06:19,084] [INFO] Target genome list was writen to GCF_021730445.1_ASM2173044v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:19,095] [INFO] Task started: fastANI
[2024-01-24 14:06:19,095] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4487a6a-ea3d-44c4-98e9-af23ff3a7d05/GCF_021730445.1_ASM2173044v1_genomic.fna.gz --refList GCF_021730445.1_ASM2173044v1_genomic.fna/target_genomes.txt --output GCF_021730445.1_ASM2173044v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:30,837] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:30,838] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge9bd71a2-a055-47be-9bc5-8b31f5231a2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:30,838] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge9bd71a2-a055-47be-9bc5-8b31f5231a2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:30,848] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:30,848] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:30,848] [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
Phocaeicola faecalis	strain=FXJYN30E22	GCA_021730445.1	2786956	2786956	type	True	100.0	1413	1417	95	conclusive
Phocaeicola massiliensis	strain=DSM 17679	GCA_000373085.1	204516	204516	type	True	90.2486	1027	1417	95	below_threshold
Phocaeicola massiliensis	strain=DSM 17679	GCA_000382445.1	204516	204516	suspected-type	True	90.2121	1039	1417	95	below_threshold
Phocaeicola dorei	strain=DSM 17855	GCA_025146415.1	357276	357276	type	True	81.3964	630	1417	95	below_threshold
Phocaeicola vulgatus	strain=FDAARGOS_1098	GCA_016766915.1	821	821	type	True	80.7411	590	1417	95	below_threshold
Parabacteroides merdae	strain=ATCC 43184	GCA_025151215.1	46503	46503	type	True	80.7292	102	1417	95	below_threshold
Phocaeicola vulgatus	strain=ATCC 8482	GCA_000012825.1	821	821	type	True	80.7208	593	1417	95	below_threshold
Phocaeicola sartorii	strain=JCM 17136	GCA_000614185.1	671267	671267	type	True	80.6931	595	1417	95	below_threshold
Phocaeicola sartorii	strain=DSM 21941	GCA_024622025.1	671267	671267	type	True	80.6355	592	1417	95	below_threshold
Bacteroides humanifaecis	strain=KGMB07931	GCA_017309675.2	2792859	2792859	type	True	79.6135	201	1417	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:30,850] [INFO] DFAST Taxonomy check result was written to GCF_021730445.1_ASM2173044v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:30,850] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:30,851] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:30,851] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge9bd71a2-a055-47be-9bc5-8b31f5231a2a/dqc_reference/checkm_data
[2024-01-24 14:06:30,852] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:30,907] [INFO] Task started: CheckM
[2024-01-24 14:06:30,907] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021730445.1_ASM2173044v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021730445.1_ASM2173044v1_genomic.fna/checkm_input GCF_021730445.1_ASM2173044v1_genomic.fna/checkm_result
[2024-01-24 14:07:36,315] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:36,316] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:36,338] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:36,339] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:36,339] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021730445.1_ASM2173044v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:36,339] [INFO] Task started: Blastn
[2024-01-24 14:07:36,339] [INFO] Running command: blastn -query GCF_021730445.1_ASM2173044v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge9bd71a2-a055-47be-9bc5-8b31f5231a2a/dqc_reference/reference_markers_gtdb.fasta -out GCF_021730445.1_ASM2173044v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:37,169] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:37,174] [INFO] Selected 13 target genomes.
[2024-01-24 14:07:37,174] [INFO] Target genome list was writen to GCF_021730445.1_ASM2173044v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:37,204] [INFO] Task started: fastANI
[2024-01-24 14:07:37,204] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4487a6a-ea3d-44c4-98e9-af23ff3a7d05/GCF_021730445.1_ASM2173044v1_genomic.fna.gz --refList GCF_021730445.1_ASM2173044v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021730445.1_ASM2173044v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:47,387] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:47,401] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:47,401] [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_002493165.1	s__Phocaeicola sp002493165	98.5721	1048	1417	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.20	98.75	0.86	0.83	5	conclusive
GCF_000382445.1	s__Phocaeicola massiliensis	90.1826	1042	1417	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.84	98.03	0.86	0.62	25	-
GCA_900760795.1	s__Phocaeicola sp900760795	87.1924	723	1417	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013009555.1	s__Phocaeicola dorei	81.3178	628	1417	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.359	99.04	97.27	0.84	0.54	104	-
GCF_000012825.1	s__Phocaeicola vulgatus	80.7102	594	1417	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.359	98.84	95.43	0.81	0.61	263	-
GCA_011959205.1	s__Phocaeicola sp011959205	80.7096	509	1417	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.87	99.87	0.90	0.90	2	-
GCF_000614185.1	s__Phocaeicola sartorii	80.6947	594	1417	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.95	98.44	0.85	0.76	7	-
GCA_902388365.1	s__Phocaeicola sp902388365	80.1288	618	1417	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.75	97.52	0.90	0.83	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:47,403] [INFO] GTDB search result was written to GCF_021730445.1_ASM2173044v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:47,404] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:47,407] [INFO] DFAST_QC result json was written to GCF_021730445.1_ASM2173044v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:47,407] [INFO] DFAST_QC completed!
[2024-01-24 14:07:47,407] [INFO] Total running time: 0h1m54s