[2024-01-25 18:51:50,496] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:51:50,497] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:51:50,497] [INFO] DQC Reference Directory: /var/lib/cwl/stg9c9c2f48-1ef7-4686-9295-3843a7649cd4/dqc_reference
[2024-01-25 18:51:51,698] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:51:51,699] [INFO] Task started: Prodigal
[2024-01-25 18:51:51,699] [INFO] Running command: gunzip -c /var/lib/cwl/stgf920d373-f829-43ee-8f83-39b0f50d3dcc/GCF_000430565.1_ASM43056v1_genomic.fna.gz | prodigal -d GCF_000430565.1_ASM43056v1_genomic.fna/cds.fna -a GCF_000430565.1_ASM43056v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:52:05,590] [INFO] Task succeeded: Prodigal
[2024-01-25 18:52:05,590] [INFO] Task started: HMMsearch
[2024-01-25 18:52:05,590] [INFO] Running command: hmmsearch --tblout GCF_000430565.1_ASM43056v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9c9c2f48-1ef7-4686-9295-3843a7649cd4/dqc_reference/reference_markers.hmm GCF_000430565.1_ASM43056v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:52:05,865] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:52:05,868] [INFO] Found 6/6 markers.
[2024-01-25 18:52:05,897] [INFO] Query marker FASTA was written to GCF_000430565.1_ASM43056v1_genomic.fna/markers.fasta
[2024-01-25 18:52:05,898] [INFO] Task started: Blastn
[2024-01-25 18:52:05,898] [INFO] Running command: blastn -query GCF_000430565.1_ASM43056v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c9c2f48-1ef7-4686-9295-3843a7649cd4/dqc_reference/reference_markers.fasta -out GCF_000430565.1_ASM43056v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:52:06,509] [INFO] Task succeeded: Blastn
[2024-01-25 18:52:06,512] [INFO] Selected 14 target genomes.
[2024-01-25 18:52:06,512] [INFO] Target genome list was writen to GCF_000430565.1_ASM43056v1_genomic.fna/target_genomes.txt
[2024-01-25 18:52:06,523] [INFO] Task started: fastANI
[2024-01-25 18:52:06,523] [INFO] Running command: fastANI --query /var/lib/cwl/stgf920d373-f829-43ee-8f83-39b0f50d3dcc/GCF_000430565.1_ASM43056v1_genomic.fna.gz --refList GCF_000430565.1_ASM43056v1_genomic.fna/target_genomes.txt --output GCF_000430565.1_ASM43056v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:52:14,928] [INFO] Task succeeded: fastANI
[2024-01-25 18:52:14,929] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9c9c2f48-1ef7-4686-9295-3843a7649cd4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:52:14,929] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9c9c2f48-1ef7-4686-9295-3843a7649cd4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:52:14,937] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 18:52:14,937] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:52:14,937] [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 timonensis	strain=DSM 22865	GCA_000430565.1	386414	386414	suspected-type	True	100.0	973	986	95	conclusive
Prevotella timonensis	strain=4401737	GCA_000455445.1	386414	386414	type	True	99.9538	961	986	95	conclusive
Prevotella timonensis	strain=JCM 15640	GCA_000614005.1	386414	386414	type	True	99.8793	915	986	95	conclusive
Prevotella illustrans	strain=A2931	GCA_017426725.1	2800387	2800387	type	True	81.9699	112	986	95	below_threshold
Prevotella pleuritidis	strain=JCM 14110	GCA_000613725.1	407975	407975	type	True	78.7368	85	986	95	below_threshold
Prevotella oris	strain=DSM 18711	GCA_000377685.1	28135	28135	type	True	78.5563	94	986	95	below_threshold
Prevotella phocaeensis	strain=SN19	GCA_900065875.1	1776388	1776388	type	True	78.296	80	986	95	below_threshold
Prevotella loescheii	strain=DSM 19665	GCA_000378085.1	840	840	type	True	78.0505	75	986	95	below_threshold
Prevotella loescheii	strain=ATCC 15930	GCA_000698925.1	840	840	type	True	77.9791	68	986	95	below_threshold
Prevotella dentasini	strain=JCM 15908	GCA_000614065.1	589537	589537	type	True	77.9357	67	986	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:52:14,939] [INFO] DFAST Taxonomy check result was written to GCF_000430565.1_ASM43056v1_genomic.fna/tc_result.tsv
[2024-01-25 18:52:14,939] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:52:14,939] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:52:14,940] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9c9c2f48-1ef7-4686-9295-3843a7649cd4/dqc_reference/checkm_data
[2024-01-25 18:52:14,941] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:52:14,973] [INFO] Task started: CheckM
[2024-01-25 18:52:14,973] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000430565.1_ASM43056v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000430565.1_ASM43056v1_genomic.fna/checkm_input GCF_000430565.1_ASM43056v1_genomic.fna/checkm_result
[2024-01-25 18:52:56,665] [INFO] Task succeeded: CheckM
[2024-01-25 18:52:56,667] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:52:56,683] [INFO] ===== Completeness check finished =====
[2024-01-25 18:52:56,683] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:52:56,684] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000430565.1_ASM43056v1_genomic.fna/markers.fasta)
[2024-01-25 18:52:56,684] [INFO] Task started: Blastn
[2024-01-25 18:52:56,684] [INFO] Running command: blastn -query GCF_000430565.1_ASM43056v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c9c2f48-1ef7-4686-9295-3843a7649cd4/dqc_reference/reference_markers_gtdb.fasta -out GCF_000430565.1_ASM43056v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:52:57,472] [INFO] Task succeeded: Blastn
[2024-01-25 18:52:57,475] [INFO] Selected 17 target genomes.
[2024-01-25 18:52:57,475] [INFO] Target genome list was writen to GCF_000430565.1_ASM43056v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:52:57,487] [INFO] Task started: fastANI
[2024-01-25 18:52:57,487] [INFO] Running command: fastANI --query /var/lib/cwl/stgf920d373-f829-43ee-8f83-39b0f50d3dcc/GCF_000430565.1_ASM43056v1_genomic.fna.gz --refList GCF_000430565.1_ASM43056v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000430565.1_ASM43056v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:53:06,862] [INFO] Task succeeded: fastANI
[2024-01-25 18:53:06,870] [INFO] Found 10 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-25 18:53:06,870] [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_000455445.1	s__Prevotella timonensis	99.9538	961	986	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0025	97.81	95.47	0.90	0.82	5	inconclusive
GCF_000762405.1	s__Prevotella timonensis_A	95.128	731	986	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0025	96.56	96.39	0.83	0.81	3	inconclusive
GCF_000177075.1	s__Prevotella buccalis	85.6066	384	986	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	95.19	95.19	0.85	0.85	2	-
GCF_000479005.1	s__Prevotella sp000479005	84.5518	369	986	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.86	96.42	0.92	0.87	3	-
GCA_900547085.1	s__Prevotella sp900547085	84.1806	268	986	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000599605.1	s__Prevotella sp000599605	80.991	106	986	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.66	96.63	0.93	0.92	3	-
GCF_000378085.1	s__Prevotella loescheii	78.2457	77	986	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.09	95.73	0.96	0.93	5	-
GCF_000614065.1	s__Prevotella dentasini	77.9871	66	986	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900199655.1	s__Prevotella sp900199655	77.8785	78	986	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.91	99.91	0.98	0.98	2	-
GCA_002449845.1	s__Prevotella sp002449845	76.2777	61	986	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.15	96.99	0.89	0.86	3	-
--------------------------------------------------------------------------------
[2024-01-25 18:53:06,871] [INFO] GTDB search result was written to GCF_000430565.1_ASM43056v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:53:06,872] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:53:06,874] [INFO] DFAST_QC result json was written to GCF_000430565.1_ASM43056v1_genomic.fna/dqc_result.json
[2024-01-25 18:53:06,874] [INFO] DFAST_QC completed!
[2024-01-25 18:53:06,874] [INFO] Total running time: 0h1m16s