[2023-06-30 14:54:08,813] [INFO] DFAST_QC pipeline started.
[2023-06-30 14:54:08,821] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 14:54:08,821] [INFO] DQC Reference Directory: /var/lib/cwl/stgf5e1efee-b44e-4f50-8cb6-582ae7b2806d/dqc_reference
[2023-06-30 14:54:12,020] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 14:54:12,022] [INFO] Task started: Prodigal
[2023-06-30 14:54:12,022] [INFO] Running command: gunzip -c /var/lib/cwl/stg7351a325-42cb-4186-ba01-0430e77de312/GCA_019114545.1_ASM1911454v1_genomic.fna.gz | prodigal -d GCA_019114545.1_ASM1911454v1_genomic.fna/cds.fna -a GCA_019114545.1_ASM1911454v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 14:54:18,165] [INFO] Task succeeded: Prodigal
[2023-06-30 14:54:18,166] [INFO] Task started: HMMsearch
[2023-06-30 14:54:18,166] [INFO] Running command: hmmsearch --tblout GCA_019114545.1_ASM1911454v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf5e1efee-b44e-4f50-8cb6-582ae7b2806d/dqc_reference/reference_markers.hmm GCA_019114545.1_ASM1911454v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 14:54:18,511] [INFO] Task succeeded: HMMsearch
[2023-06-30 14:54:18,512] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7351a325-42cb-4186-ba01-0430e77de312/GCA_019114545.1_ASM1911454v1_genomic.fna.gz]
[2023-06-30 14:54:18,544] [INFO] Query marker FASTA was written to GCA_019114545.1_ASM1911454v1_genomic.fna/markers.fasta
[2023-06-30 14:54:18,544] [INFO] Task started: Blastn
[2023-06-30 14:54:18,544] [INFO] Running command: blastn -query GCA_019114545.1_ASM1911454v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf5e1efee-b44e-4f50-8cb6-582ae7b2806d/dqc_reference/reference_markers.fasta -out GCA_019114545.1_ASM1911454v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 14:54:19,215] [INFO] Task succeeded: Blastn
[2023-06-30 14:54:19,219] [INFO] Selected 16 target genomes.
[2023-06-30 14:54:19,220] [INFO] Target genome list was writen to GCA_019114545.1_ASM1911454v1_genomic.fna/target_genomes.txt
[2023-06-30 14:54:19,223] [INFO] Task started: fastANI
[2023-06-30 14:54:19,224] [INFO] Running command: fastANI --query /var/lib/cwl/stg7351a325-42cb-4186-ba01-0430e77de312/GCA_019114545.1_ASM1911454v1_genomic.fna.gz --refList GCA_019114545.1_ASM1911454v1_genomic.fna/target_genomes.txt --output GCA_019114545.1_ASM1911454v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 14:54:31,590] [INFO] Task succeeded: fastANI
[2023-06-30 14:54:31,590] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf5e1efee-b44e-4f50-8cb6-582ae7b2806d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 14:54:31,591] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf5e1efee-b44e-4f50-8cb6-582ae7b2806d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 14:54:31,603] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 14:54:31,604] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 14:54:31,604] [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
Blautia hansenii	strain=DSM 20583	GCA_000156675.1	1322	1322	type	True	77.7981	153	862	95	below_threshold
Blautia argi	strain=KCTC 15426	GCA_003287895.1	1912897	1912897	type	True	77.7362	209	862	95	below_threshold
Blautia hansenii	strain=DSM 20583	GCA_002222595.2	1322	1322	type	True	77.7285	150	862	95	below_threshold
Blautia hansenii	strain=DSM 20583	GCA_025147655.1	1322	1322	type	True	77.7037	153	862	95	below_threshold
Blautia pseudococcoides	strain=YL58	GCA_001689125.2	1796616	1796616	type	True	77.2817	164	862	95	below_threshold
Blautia marasmi	strain=Marseille-P2377	GCA_900258535.1	1917868	1917868	suspected-type	True	77.2704	176	862	95	below_threshold
Blautia pseudococcoides	strain=YL58	GCA_002221555.2	1796616	1796616	type	True	77.2118	169	862	95	below_threshold
Blautia producta	strain=ATCC 27340	GCA_000373885.1	33035	33035	suspected-type	True	77.1701	185	862	95	below_threshold
Blautia producta	strain=DSM 2950	GCA_014131715.1	33035	33035	suspected-type	True	77.1483	181	862	95	below_threshold
Blautia producta	strain=DSM 2950	GCA_000439125.1	33035	33035	suspected-type	True	77.1355	183	862	95	below_threshold
Blautia coccoides	strain=DSM 935	GCA_004340925.1	1532	1532	type	True	77.1236	175	862	95	below_threshold
Blautia coccoides	strain=NCTC11035	GCA_900461125.1	1532	1532	type	True	77.1109	176	862	95	below_threshold
Jingyaoa shaoxingensis	strain=NSJ-46	GCA_014385005.1	2763671	2763671	type	True	76.6679	58	862	95	below_threshold
Murimonas intestini	strain=DSM 26524	GCA_024622195.1	1337051	1337051	type	True	76.4354	64	862	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 14:54:31,606] [INFO] DFAST Taxonomy check result was written to GCA_019114545.1_ASM1911454v1_genomic.fna/tc_result.tsv
[2023-06-30 14:54:31,607] [INFO] ===== Taxonomy check completed =====
[2023-06-30 14:54:31,607] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 14:54:31,607] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf5e1efee-b44e-4f50-8cb6-582ae7b2806d/dqc_reference/checkm_data
[2023-06-30 14:54:31,608] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 14:54:31,642] [INFO] Task started: CheckM
[2023-06-30 14:54:31,643] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019114545.1_ASM1911454v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019114545.1_ASM1911454v1_genomic.fna/checkm_input GCA_019114545.1_ASM1911454v1_genomic.fna/checkm_result
[2023-06-30 14:54:57,829] [INFO] Task succeeded: CheckM
[2023-06-30 14:54:57,831] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 13.92%
Strain heterogeneity: 80.00%
--------------------------------------------------------------------------------
[2023-06-30 14:54:57,858] [INFO] ===== Completeness check finished =====
[2023-06-30 14:54:57,858] [INFO] ===== Start GTDB Search =====
[2023-06-30 14:54:57,858] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019114545.1_ASM1911454v1_genomic.fna/markers.fasta)
[2023-06-30 14:54:57,859] [INFO] Task started: Blastn
[2023-06-30 14:54:57,859] [INFO] Running command: blastn -query GCA_019114545.1_ASM1911454v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf5e1efee-b44e-4f50-8cb6-582ae7b2806d/dqc_reference/reference_markers_gtdb.fasta -out GCA_019114545.1_ASM1911454v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 14:54:58,800] [INFO] Task succeeded: Blastn
[2023-06-30 14:54:58,805] [INFO] Selected 7 target genomes.
[2023-06-30 14:54:58,805] [INFO] Target genome list was writen to GCA_019114545.1_ASM1911454v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 14:54:58,810] [INFO] Task started: fastANI
[2023-06-30 14:54:58,810] [INFO] Running command: fastANI --query /var/lib/cwl/stg7351a325-42cb-4186-ba01-0430e77de312/GCA_019114545.1_ASM1911454v1_genomic.fna.gz --refList GCA_019114545.1_ASM1911454v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019114545.1_ASM1911454v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 14:55:03,834] [INFO] Task succeeded: fastANI
[2023-06-30 14:55:03,848] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 14:55:03,849] [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_019114545.1	s__Blautia pullistercoris	100.0	852	862	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	98.87	98.79	0.80	0.76	4	conclusive
GCA_019112785.1	s__Blautia stercorigallinarum	88.4475	661	862	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	99.88	99.88	0.94	0.94	2	-
GCA_019118685.1	s__Blautia merdipullorum	87.5732	580	862	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019120515.1	s__Blautia avicola	87.4826	567	862	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002161285.1	s__Blautia ornithocaccae	86.6285	664	862	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	98.34	98.05	0.87	0.83	4	-
GCA_900543715.1	s__Blautia merdigallinarum	86.3378	630	862	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	98.67	98.67	0.84	0.84	2	-
GCA_019120545.1	s__Blautia stercoripullorum	84.1579	523	862	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 14:55:03,851] [INFO] GTDB search result was written to GCA_019114545.1_ASM1911454v1_genomic.fna/result_gtdb.tsv
[2023-06-30 14:55:03,851] [INFO] ===== GTDB Search completed =====
[2023-06-30 14:55:03,855] [INFO] DFAST_QC result json was written to GCA_019114545.1_ASM1911454v1_genomic.fna/dqc_result.json
[2023-06-30 14:55:03,855] [INFO] DFAST_QC completed!
[2023-06-30 14:55:03,855] [INFO] Total running time: 0h0m55s