[2023-06-13 17:33:32,163] [INFO] DFAST_QC pipeline started.
[2023-06-13 17:33:32,165] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 17:33:32,166] [INFO] DQC Reference Directory: /var/lib/cwl/stg9bbb84be-1c09-4b0b-a201-4e460d7546fa/dqc_reference
[2023-06-13 17:33:33,405] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 17:33:33,406] [INFO] Task started: Prodigal
[2023-06-13 17:33:33,406] [INFO] Running command: gunzip -c /var/lib/cwl/stgbdbdef7c-d3bb-4df2-9987-fbd487a91918/GCA_022797975.1_ASM2279797v1_genomic.fna.gz | prodigal -d GCA_022797975.1_ASM2279797v1_genomic.fna/cds.fna -a GCA_022797975.1_ASM2279797v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 17:33:42,638] [INFO] Task succeeded: Prodigal
[2023-06-13 17:33:42,638] [INFO] Task started: HMMsearch
[2023-06-13 17:33:42,638] [INFO] Running command: hmmsearch --tblout GCA_022797975.1_ASM2279797v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9bbb84be-1c09-4b0b-a201-4e460d7546fa/dqc_reference/reference_markers.hmm GCA_022797975.1_ASM2279797v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 17:33:42,855] [INFO] Task succeeded: HMMsearch
[2023-06-13 17:33:42,857] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgbdbdef7c-d3bb-4df2-9987-fbd487a91918/GCA_022797975.1_ASM2279797v1_genomic.fna.gz]
[2023-06-13 17:33:42,888] [INFO] Query marker FASTA was written to GCA_022797975.1_ASM2279797v1_genomic.fna/markers.fasta
[2023-06-13 17:33:42,889] [INFO] Task started: Blastn
[2023-06-13 17:33:42,889] [INFO] Running command: blastn -query GCA_022797975.1_ASM2279797v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9bbb84be-1c09-4b0b-a201-4e460d7546fa/dqc_reference/reference_markers.fasta -out GCA_022797975.1_ASM2279797v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 17:33:43,473] [INFO] Task succeeded: Blastn
[2023-06-13 17:33:43,477] [INFO] Selected 22 target genomes.
[2023-06-13 17:33:43,477] [INFO] Target genome list was writen to GCA_022797975.1_ASM2279797v1_genomic.fna/target_genomes.txt
[2023-06-13 17:33:43,478] [INFO] Task started: fastANI
[2023-06-13 17:33:43,478] [INFO] Running command: fastANI --query /var/lib/cwl/stgbdbdef7c-d3bb-4df2-9987-fbd487a91918/GCA_022797975.1_ASM2279797v1_genomic.fna.gz --refList GCA_022797975.1_ASM2279797v1_genomic.fna/target_genomes.txt --output GCA_022797975.1_ASM2279797v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 17:33:57,717] [INFO] Task succeeded: fastANI
[2023-06-13 17:33:57,718] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9bbb84be-1c09-4b0b-a201-4e460d7546fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 17:33:57,718] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9bbb84be-1c09-4b0b-a201-4e460d7546fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 17:33:57,730] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 17:33:57,731] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 17:33:57,731] [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
Massilistercora timonensis	strain=Marseille-P3756	GCA_900312975.1	2086584	2086584	type	True	76.7831	71	1192	95	below_threshold
Diplocloster agilis	strain=ASD5720	GCA_019042275.1	2850323	2850323	type	True	76.669	60	1192	95	below_threshold
Schaedlerella arabinosiphila	strain=DSM 106076	GCA_003885045.1	2044587	2044587	type	True	76.5154	93	1192	95	below_threshold
Acetatifactor muris	strain=DSM 23669	GCA_024623325.1	879566	879566	type	True	76.504	65	1192	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_000158075.1	333367	333367	type	True	76.4277	93	1192	95	below_threshold
Diplocloster modestus	strain=ASD4241	GCA_019042245.1	2850322	2850322	type	True	76.4016	67	1192	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_025149125.1	333367	333367	type	True	76.3321	92	1192	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_002959675.1	208479	208479	type	True	76.2942	77	1192	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_002234575.2	208479	208479	type	True	76.2619	77	1192	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_000154365.1	208479	208479	type	True	76.2543	73	1192	95	below_threshold
Eisenbergiella massiliensis	strain=AT11	GCA_900243045.1	1720294	1720294	type	True	75.9506	65	1192	95	below_threshold
Eisenbergiella tayi	strain=DSM 26961	GCA_001881565.1	1432052	1432052	type	True	75.8312	65	1192	95	below_threshold
Eisenbergiella porci	strain=WCA-389-WT-23B	GCA_009696275.1	2652274	2652274	type	True	75.7609	64	1192	95	below_threshold
Blautia caecimuris	strain=DSM 29492	GCA_024622975.1	1796615	1796615	type	True	75.7278	60	1192	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 17:33:57,733] [INFO] DFAST Taxonomy check result was written to GCA_022797975.1_ASM2279797v1_genomic.fna/tc_result.tsv
[2023-06-13 17:33:57,734] [INFO] ===== Taxonomy check completed =====
[2023-06-13 17:33:57,734] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 17:33:57,734] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9bbb84be-1c09-4b0b-a201-4e460d7546fa/dqc_reference/checkm_data
[2023-06-13 17:33:57,735] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 17:33:57,775] [INFO] Task started: CheckM
[2023-06-13 17:33:57,775] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022797975.1_ASM2279797v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022797975.1_ASM2279797v1_genomic.fna/checkm_input GCA_022797975.1_ASM2279797v1_genomic.fna/checkm_result
[2023-06-13 17:34:28,619] [INFO] Task succeeded: CheckM
[2023-06-13 17:34:28,620] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 17:34:28,642] [INFO] ===== Completeness check finished =====
[2023-06-13 17:34:28,642] [INFO] ===== Start GTDB Search =====
[2023-06-13 17:34:28,643] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022797975.1_ASM2279797v1_genomic.fna/markers.fasta)
[2023-06-13 17:34:28,643] [INFO] Task started: Blastn
[2023-06-13 17:34:28,643] [INFO] Running command: blastn -query GCA_022797975.1_ASM2279797v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9bbb84be-1c09-4b0b-a201-4e460d7546fa/dqc_reference/reference_markers_gtdb.fasta -out GCA_022797975.1_ASM2279797v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 17:34:29,486] [INFO] Task succeeded: Blastn
[2023-06-13 17:34:29,490] [INFO] Selected 21 target genomes.
[2023-06-13 17:34:29,490] [INFO] Target genome list was writen to GCA_022797975.1_ASM2279797v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 17:34:29,491] [INFO] Task started: fastANI
[2023-06-13 17:34:29,491] [INFO] Running command: fastANI --query /var/lib/cwl/stgbdbdef7c-d3bb-4df2-9987-fbd487a91918/GCA_022797975.1_ASM2279797v1_genomic.fna.gz --refList GCA_022797975.1_ASM2279797v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022797975.1_ASM2279797v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 17:34:40,917] [INFO] Task succeeded: fastANI
[2023-06-13 17:34:40,932] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 17:34:40,932] [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_910576205.1	s__RGIG4284 sp910576205	78.8019	402	1192	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RGIG4284	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910575725.1	s__Merdisoma sp011959465	77.7757	234	1192	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdisoma	95.0	99.24	98.50	0.89	0.80	3	-
GCA_017464645.1	s__RGIG4284 sp017464645	77.6797	121	1192	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RGIG4284	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910586955.1	s__Merdisoma sp910586955	77.5173	210	1192	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009917555.1	s__Merdisoma sp009917555	77.4286	226	1192	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdisoma	95.0	99.22	99.22	0.93	0.93	2	-
GCA_910576325.1	s__Merdisoma sp910576325	77.4275	212	1192	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdisoma	95.0	100.00	99.99	1.00	1.00	6	-
GCA_910587955.1	s__Merdisoma sp910587955	77.3802	210	1192	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002160765.1	s__Merdisoma faecalis	77.2963	181	1192	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdisoma	95.0	98.59	98.32	0.91	0.81	8	-
GCF_002160825.1	s__Merdisoma sp002160825	77.29	160	1192	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdisoma	95.0	99.04	99.04	0.92	0.92	2	-
GCF_014290175.1	s__Merdisoma sp014290175	77.0159	155	1192	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdisoma	95.0	99.98	99.96	0.81	0.62	3	-
GCA_910574255.1	s__Merdisoma sp910574255	77.0053	196	1192	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdisoma	95.0	98.74	98.74	0.82	0.82	2	-
GCA_910588285.1	s__14-2 sp910588285	76.6728	122	1192	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__14-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577765.1	s__Ventrimonas sp910577765	76.3049	82	1192	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018716305.1	s__Scatomonas merdigallinarum	76.2783	103	1192	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Scatomonas	95.0	99.11	99.10	0.93	0.92	3	-
GCA_900542045.1	s__Blautia_A gallistercoris	76.1739	69	1192	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.42	98.42	0.88	0.88	2	-
GCA_910585075.1	s__CAG-95 sp910585075	75.8097	54	1192	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017624175.1	s__Acetatifactor sp017624175	75.6314	54	1192	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 17:34:40,934] [INFO] GTDB search result was written to GCA_022797975.1_ASM2279797v1_genomic.fna/result_gtdb.tsv
[2023-06-13 17:34:40,935] [INFO] ===== GTDB Search completed =====
[2023-06-13 17:34:40,940] [INFO] DFAST_QC result json was written to GCA_022797975.1_ASM2279797v1_genomic.fna/dqc_result.json
[2023-06-13 17:34:40,940] [INFO] DFAST_QC completed!
[2023-06-13 17:34:40,940] [INFO] Total running time: 0h1m9s