[2023-06-27 04:30:31,010] [INFO] DFAST_QC pipeline started.
[2023-06-27 04:30:31,050] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 04:30:31,050] [INFO] DQC Reference Directory: /var/lib/cwl/stg1b6f800f-02a9-49ad-83a2-c168265e86ee/dqc_reference
[2023-06-27 04:30:33,447] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 04:30:33,448] [INFO] Task started: Prodigal
[2023-06-27 04:30:33,448] [INFO] Running command: gunzip -c /var/lib/cwl/stg2141e132-fe5a-4f0a-b0f8-ec2f89cfd90c/GCA_002432045.1_ASM243204v1_genomic.fna.gz | prodigal -d GCA_002432045.1_ASM243204v1_genomic.fna/cds.fna -a GCA_002432045.1_ASM243204v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 04:30:49,864] [INFO] Task succeeded: Prodigal
[2023-06-27 04:30:49,865] [INFO] Task started: HMMsearch
[2023-06-27 04:30:49,865] [INFO] Running command: hmmsearch --tblout GCA_002432045.1_ASM243204v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1b6f800f-02a9-49ad-83a2-c168265e86ee/dqc_reference/reference_markers.hmm GCA_002432045.1_ASM243204v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 04:30:50,115] [INFO] Task succeeded: HMMsearch
[2023-06-27 04:30:50,117] [INFO] Found 6/6 markers.
[2023-06-27 04:30:50,147] [INFO] Query marker FASTA was written to GCA_002432045.1_ASM243204v1_genomic.fna/markers.fasta
[2023-06-27 04:30:50,148] [INFO] Task started: Blastn
[2023-06-27 04:30:50,148] [INFO] Running command: blastn -query GCA_002432045.1_ASM243204v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b6f800f-02a9-49ad-83a2-c168265e86ee/dqc_reference/reference_markers.fasta -out GCA_002432045.1_ASM243204v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 04:30:55,013] [INFO] Task succeeded: Blastn
[2023-06-27 04:30:55,058] [INFO] Selected 17 target genomes.
[2023-06-27 04:30:55,058] [INFO] Target genome list was writen to GCA_002432045.1_ASM243204v1_genomic.fna/target_genomes.txt
[2023-06-27 04:30:55,061] [INFO] Task started: fastANI
[2023-06-27 04:30:55,061] [INFO] Running command: fastANI --query /var/lib/cwl/stg2141e132-fe5a-4f0a-b0f8-ec2f89cfd90c/GCA_002432045.1_ASM243204v1_genomic.fna.gz --refList GCA_002432045.1_ASM243204v1_genomic.fna/target_genomes.txt --output GCA_002432045.1_ASM243204v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 04:31:05,594] [INFO] Task succeeded: fastANI
[2023-06-27 04:31:05,594] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1b6f800f-02a9-49ad-83a2-c168265e86ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 04:31:05,595] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1b6f800f-02a9-49ad-83a2-c168265e86ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 04:31:05,607] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 04:31:05,607] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 04:31:05,607] [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
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	81.944	434	729	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000242335.3	52227	52227	type	True	78.1505	214	729	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000220215.1	52227	52227	type	True	78.1108	221	729	95	below_threshold
Hallella seregens	strain=ATCC 51272	GCA_000518545.1	52229	52229	type	True	78.0711	214	729	95	below_threshold
Prevotella mizrahii	strain=LKV-178-WT-2A	GCA_009695775.1	2606637	2606637	type	True	77.4539	170	729	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	77.0308	98	729	95	below_threshold
Prevotella lacticifex	strain=R5019	GCA_019973375.1	2854755	2854755	type	True	77.0	103	729	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	76.8852	132	729	95	below_threshold
Prevotella multiformis	strain=DSM 16608	GCA_000191065.1	282402	282402	type	True	76.6687	98	729	95	below_threshold
Prevotella dentasini	strain=JCM 15908	GCA_000614065.1	589537	589537	type	True	76.4675	81	729	95	below_threshold
Prevotella denticola	strain=DSM 20614	GCA_000421205.1	28129	28129	type	True	76.4311	93	729	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	76.3701	57	729	95	below_threshold
Prevotella brevis	strain=ATCC 19188	GCA_000621725.1	83231	83231	type	True	76.3018	80	729	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 04:31:05,609] [INFO] DFAST Taxonomy check result was written to GCA_002432045.1_ASM243204v1_genomic.fna/tc_result.tsv
[2023-06-27 04:31:05,610] [INFO] ===== Taxonomy check completed =====
[2023-06-27 04:31:05,610] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 04:31:05,610] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1b6f800f-02a9-49ad-83a2-c168265e86ee/dqc_reference/checkm_data
[2023-06-27 04:31:05,611] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 04:31:05,646] [INFO] Task started: CheckM
[2023-06-27 04:31:05,646] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002432045.1_ASM243204v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002432045.1_ASM243204v1_genomic.fna/checkm_input GCA_002432045.1_ASM243204v1_genomic.fna/checkm_result
[2023-06-27 04:31:53,152] [INFO] Task succeeded: CheckM
[2023-06-27 04:31:53,160] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 41.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 04:31:53,193] [INFO] ===== Completeness check finished =====
[2023-06-27 04:31:53,194] [INFO] ===== Start GTDB Search =====
[2023-06-27 04:31:53,194] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002432045.1_ASM243204v1_genomic.fna/markers.fasta)
[2023-06-27 04:31:53,195] [INFO] Task started: Blastn
[2023-06-27 04:31:53,195] [INFO] Running command: blastn -query GCA_002432045.1_ASM243204v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b6f800f-02a9-49ad-83a2-c168265e86ee/dqc_reference/reference_markers_gtdb.fasta -out GCA_002432045.1_ASM243204v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 04:31:54,127] [INFO] Task succeeded: Blastn
[2023-06-27 04:31:54,134] [INFO] Selected 10 target genomes.
[2023-06-27 04:31:54,134] [INFO] Target genome list was writen to GCA_002432045.1_ASM243204v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 04:31:54,167] [INFO] Task started: fastANI
[2023-06-27 04:31:54,168] [INFO] Running command: fastANI --query /var/lib/cwl/stg2141e132-fe5a-4f0a-b0f8-ec2f89cfd90c/GCA_002432045.1_ASM243204v1_genomic.fna.gz --refList GCA_002432045.1_ASM243204v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002432045.1_ASM243204v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 04:31:59,683] [INFO] Task succeeded: fastANI
[2023-06-27 04:31:59,695] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 04:31:59,695] [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_002437285.1	s__Prevotella sp002437285	99.6256	679	729	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.68	99.38	0.93	0.88	13	conclusive
GCA_002437115.1	s__Prevotella sp002437115	84.1607	472	729	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018789675.1	s__Prevotella sp002300055	81.9372	435	729	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.15	99.02	0.92	0.90	6	-
GCA_900762125.1	s__Prevotella sp900762125	78.5558	205	729	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900315835.1	s__Prevotella sp900315835	78.0833	211	729	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.59	98.19	0.88	0.85	9	-
GCF_000518545.1	s__Prevotella seregens	78.0711	214	729	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.68	98.64	0.90	0.90	3	-
GCA_002481295.1	s__Prevotella sp002481295	77.7435	170	729	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.83	96.70	0.87	0.78	4	-
GCA_000431975.1	s__Prevotella sp000431975	77.5939	120	729	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.89	99.89	0.92	0.91	3	-
GCA_002317385.1	s__Prevotella sp002317385	77.4657	178	729	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900317685.1	s__Prevotella sp900317685	77.4577	186	729	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.13	96.10	0.84	0.76	12	-
--------------------------------------------------------------------------------
[2023-06-27 04:31:59,720] [INFO] GTDB search result was written to GCA_002432045.1_ASM243204v1_genomic.fna/result_gtdb.tsv
[2023-06-27 04:31:59,721] [INFO] ===== GTDB Search completed =====
[2023-06-27 04:31:59,727] [INFO] DFAST_QC result json was written to GCA_002432045.1_ASM243204v1_genomic.fna/dqc_result.json
[2023-06-27 04:31:59,728] [INFO] DFAST_QC completed!
[2023-06-27 04:31:59,728] [INFO] Total running time: 0h1m29s