[2024-01-24 13:27:46,501] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:46,503] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:46,503] [INFO] DQC Reference Directory: /var/lib/cwl/stgb2f4a96e-6dd6-4f60-ad3d-62768042a4e6/dqc_reference
[2024-01-24 13:27:47,928] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:47,929] [INFO] Task started: Prodigal
[2024-01-24 13:27:47,930] [INFO] Running command: gunzip -c /var/lib/cwl/stgaac79e6a-2649-4a2b-813a-fbdcbeef9398/GCF_000614205.1_ASM61420v1_genomic.fna.gz | prodigal -d GCF_000614205.1_ASM61420v1_genomic.fna/cds.fna -a GCF_000614205.1_ASM61420v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:02,962] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:02,963] [INFO] Task started: HMMsearch
[2024-01-24 13:28:02,963] [INFO] Running command: hmmsearch --tblout GCF_000614205.1_ASM61420v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb2f4a96e-6dd6-4f60-ad3d-62768042a4e6/dqc_reference/reference_markers.hmm GCF_000614205.1_ASM61420v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:03,265] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:03,266] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgaac79e6a-2649-4a2b-813a-fbdcbeef9398/GCF_000614205.1_ASM61420v1_genomic.fna.gz]
[2024-01-24 13:28:03,292] [INFO] Query marker FASTA was written to GCF_000614205.1_ASM61420v1_genomic.fna/markers.fasta
[2024-01-24 13:28:03,292] [INFO] Task started: Blastn
[2024-01-24 13:28:03,293] [INFO] Running command: blastn -query GCF_000614205.1_ASM61420v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2f4a96e-6dd6-4f60-ad3d-62768042a4e6/dqc_reference/reference_markers.fasta -out GCF_000614205.1_ASM61420v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:03,876] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:03,879] [INFO] Selected 20 target genomes.
[2024-01-24 13:28:03,880] [INFO] Target genome list was writen to GCF_000614205.1_ASM61420v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:03,890] [INFO] Task started: fastANI
[2024-01-24 13:28:03,890] [INFO] Running command: fastANI --query /var/lib/cwl/stgaac79e6a-2649-4a2b-813a-fbdcbeef9398/GCF_000614205.1_ASM61420v1_genomic.fna.gz --refList GCF_000614205.1_ASM61420v1_genomic.fna/target_genomes.txt --output GCF_000614205.1_ASM61420v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:14,100] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:14,100] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb2f4a96e-6dd6-4f60-ad3d-62768042a4e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:14,101] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb2f4a96e-6dd6-4f60-ad3d-62768042a4e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:14,113] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:14,113] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:14,113] [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 saccharolytica	strain=JCM 17484	GCA_000614205.1	633701	633701	type	True	100.0	950	954	95	conclusive
Prevotella nigrescens	strain=FDAARGOS_1486	GCA_019930605.1	28133	28133	type	True	83.1411	68	954	95	below_threshold
Prevotella nigrescens	strain=NCTC9336	GCA_900454985.1	28133	28133	type	True	83.1146	69	954	95	below_threshold
Prevotella nigrescens	strain=ATCC 33563	GCA_000220235.1	28133	28133	type	True	82.9993	69	954	95	below_threshold
Prevotella oris	strain=DSM 18711	GCA_000377685.1	28135	28135	type	True	81.8843	99	954	95	below_threshold
Prevotella oulorum	strain=ATCC 43324	GCA_900167385.1	28136	28136	type	True	81.8236	86	954	95	below_threshold
Prevotella oulorum	strain=JCM 14966	GCA_000613785.1	28136	28136	type	True	81.6057	85	954	95	below_threshold
Prevotella oris	strain=JCM 12252	GCA_000613505.1	28135	28135	type	True	81.5104	92	954	95	below_threshold
Prevotella aurantiaca	strain=JCM 15754	GCA_000614025.1	596085	596085	type	True	78.0354	57	954	95	below_threshold
Prevotella disiens	strain=NCTC11157	GCA_900454955.1	28130	28130	type	True	77.6323	73	954	95	below_threshold
Prevotella disiens	strain=ATCC 29426	GCA_000467875.1	28130	28130	type	True	77.2901	65	954	95	below_threshold
Prevotella pleuritidis	strain=JCM 14110	GCA_000613725.1	407975	407975	type	True	77.202	77	954	95	below_threshold
Prevotella timonensis	strain=DSM 22865	GCA_000430565.1	386414	386414	suspected-type	True	77.0706	72	954	95	below_threshold
Prevotella timonensis	strain=4401737	GCA_000455445.1	386414	386414	type	True	77.0166	75	954	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:14,115] [INFO] DFAST Taxonomy check result was written to GCF_000614205.1_ASM61420v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:14,115] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:14,116] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:14,116] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb2f4a96e-6dd6-4f60-ad3d-62768042a4e6/dqc_reference/checkm_data
[2024-01-24 13:28:14,117] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:14,152] [INFO] Task started: CheckM
[2024-01-24 13:28:14,152] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000614205.1_ASM61420v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000614205.1_ASM61420v1_genomic.fna/checkm_input GCF_000614205.1_ASM61420v1_genomic.fna/checkm_result
[2024-01-24 13:29:00,515] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:00,516] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:00,536] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:00,536] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:00,537] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000614205.1_ASM61420v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:00,537] [INFO] Task started: Blastn
[2024-01-24 13:29:00,537] [INFO] Running command: blastn -query GCF_000614205.1_ASM61420v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2f4a96e-6dd6-4f60-ad3d-62768042a4e6/dqc_reference/reference_markers_gtdb.fasta -out GCF_000614205.1_ASM61420v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:01,276] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:01,279] [INFO] Selected 21 target genomes.
[2024-01-24 13:29:01,279] [INFO] Target genome list was writen to GCF_000614205.1_ASM61420v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:01,297] [INFO] Task started: fastANI
[2024-01-24 13:29:01,297] [INFO] Running command: fastANI --query /var/lib/cwl/stgaac79e6a-2649-4a2b-813a-fbdcbeef9398/GCF_000614205.1_ASM61420v1_genomic.fna.gz --refList GCF_000614205.1_ASM61420v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000614205.1_ASM61420v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:11,278] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:11,291] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:11,291] [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_000614205.1	s__Prevotella saccharolytica	100.0	950	954	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.90	96.70	0.90	0.88	3	conclusive
GCF_900637655.1	s__Prevotella oris	81.8373	93	954	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.96	97.06	0.90	0.82	10	-
GCF_000613785.1	s__Prevotella oulorum	81.6826	85	954	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.00	96.91	0.92	0.84	5	-
GCF_000599605.1	s__Prevotella sp000599605	79.8413	82	954	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.66	96.63	0.93	0.92	3	-
GCF_000613725.1	s__Prevotella pleuritidis	77.2726	75	954	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.72	98.65	0.96	0.96	4	-
GCF_900290275.1	s__Prevotella sp900290275	76.271	52	954	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.80	97.71	0.90	0.86	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:11,293] [INFO] GTDB search result was written to GCF_000614205.1_ASM61420v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:11,294] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:11,297] [INFO] DFAST_QC result json was written to GCF_000614205.1_ASM61420v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:11,297] [INFO] DFAST_QC completed!
[2024-01-24 13:29:11,297] [INFO] Total running time: 0h1m25s