[2023-06-18 19:16:46,498] [INFO] DFAST_QC pipeline started.
[2023-06-18 19:16:46,501] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 19:16:46,502] [INFO] DQC Reference Directory: /var/lib/cwl/stgb1bf7daf-9a9d-46da-a50b-2b434a324252/dqc_reference
[2023-06-18 19:16:47,785] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 19:16:47,786] [INFO] Task started: Prodigal
[2023-06-18 19:16:47,786] [INFO] Running command: gunzip -c /var/lib/cwl/stg8ce1448f-c142-4977-ade2-a5e33385a7f6/GCA_018366395.1_ASM1836639v1_genomic.fna.gz | prodigal -d GCA_018366395.1_ASM1836639v1_genomic.fna/cds.fna -a GCA_018366395.1_ASM1836639v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 19:16:55,316] [INFO] Task succeeded: Prodigal
[2023-06-18 19:16:55,316] [INFO] Task started: HMMsearch
[2023-06-18 19:16:55,316] [INFO] Running command: hmmsearch --tblout GCA_018366395.1_ASM1836639v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb1bf7daf-9a9d-46da-a50b-2b434a324252/dqc_reference/reference_markers.hmm GCA_018366395.1_ASM1836639v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 19:16:55,629] [INFO] Task succeeded: HMMsearch
[2023-06-18 19:16:55,630] [INFO] Found 6/6 markers.
[2023-06-18 19:16:55,661] [INFO] Query marker FASTA was written to GCA_018366395.1_ASM1836639v1_genomic.fna/markers.fasta
[2023-06-18 19:16:55,662] [INFO] Task started: Blastn
[2023-06-18 19:16:55,662] [INFO] Running command: blastn -query GCA_018366395.1_ASM1836639v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1bf7daf-9a9d-46da-a50b-2b434a324252/dqc_reference/reference_markers.fasta -out GCA_018366395.1_ASM1836639v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 19:16:56,365] [INFO] Task succeeded: Blastn
[2023-06-18 19:16:56,371] [INFO] Selected 19 target genomes.
[2023-06-18 19:16:56,371] [INFO] Target genome list was writen to GCA_018366395.1_ASM1836639v1_genomic.fna/target_genomes.txt
[2023-06-18 19:16:56,372] [INFO] Task started: fastANI
[2023-06-18 19:16:56,372] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ce1448f-c142-4977-ade2-a5e33385a7f6/GCA_018366395.1_ASM1836639v1_genomic.fna.gz --refList GCA_018366395.1_ASM1836639v1_genomic.fna/target_genomes.txt --output GCA_018366395.1_ASM1836639v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 19:17:08,299] [INFO] Task succeeded: fastANI
[2023-06-18 19:17:08,299] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb1bf7daf-9a9d-46da-a50b-2b434a324252/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 19:17:08,299] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb1bf7daf-9a9d-46da-a50b-2b434a324252/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 19:17:08,316] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 19:17:08,317] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 19:17:08,317] [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 wexlerae	strain=DSM 19850	GCA_000484655.1	418240	418240	suspected-type	True	79.6218	246	1034	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_025148125.1	418240	418240	suspected-type	True	79.5081	250	1034	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	79.305	205	1034	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_000153905.1	40520	40520	type	True	79.2788	204	1034	95	below_threshold
Blautia caecimuris	strain=DSM 29492	GCA_024622975.1	1796615	1796615	type	True	79.2441	309	1034	95	below_threshold
Blautia massiliensis	strain=GD9	GCA_001487165.1	1737424	1737424	type	True	79.0019	225	1034	95	below_threshold
Blautia luti	strain=DSM 14534	GCA_009707925.1	89014	89014	suspected-type	True	78.9667	229	1034	95	below_threshold
Blautia intestinalis	strain=27-44	GCA_014297355.1	2763028	2763028	type	True	78.6909	215	1034	95	below_threshold
Blautia hansenii	strain=DSM 20583	GCA_025147655.1	1322	1322	type	True	78.5148	142	1034	95	below_threshold
Blautia hansenii	strain=DSM 20583	GCA_000156675.1	1322	1322	type	True	78.5078	146	1034	95	below_threshold
Blautia coccoides	strain=DSM 935	GCA_004340925.1	1532	1532	type	True	78.3843	110	1034	95	below_threshold
Blautia hansenii	strain=DSM 20583	GCA_002222595.2	1322	1322	type	True	78.3287	145	1034	95	below_threshold
Blautia producta	strain=DSM 2950	GCA_000439125.1	33035	33035	suspected-type	True	77.6522	117	1034	95	below_threshold
Blautia producta	strain=ATCC 27340	GCA_000373885.1	33035	33035	suspected-type	True	77.5699	117	1034	95	below_threshold
Blautia marasmi	strain=Marseille-P2377	GCA_900258535.1	1917868	1917868	suspected-type	True	77.4098	96	1034	95	below_threshold
Konateibacter massiliensis	strain=Marseille-P3773	GCA_900184995.1	2002841	2002841	type	True	76.2792	63	1034	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 19:17:08,320] [INFO] DFAST Taxonomy check result was written to GCA_018366395.1_ASM1836639v1_genomic.fna/tc_result.tsv
[2023-06-18 19:17:08,321] [INFO] ===== Taxonomy check completed =====
[2023-06-18 19:17:08,321] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 19:17:08,321] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb1bf7daf-9a9d-46da-a50b-2b434a324252/dqc_reference/checkm_data
[2023-06-18 19:17:08,322] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 19:17:08,383] [INFO] Task started: CheckM
[2023-06-18 19:17:08,383] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018366395.1_ASM1836639v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018366395.1_ASM1836639v1_genomic.fna/checkm_input GCA_018366395.1_ASM1836639v1_genomic.fna/checkm_result
[2023-06-18 19:17:37,654] [INFO] Task succeeded: CheckM
[2023-06-18 19:17:37,656] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 19:17:37,679] [INFO] ===== Completeness check finished =====
[2023-06-18 19:17:37,679] [INFO] ===== Start GTDB Search =====
[2023-06-18 19:17:37,680] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018366395.1_ASM1836639v1_genomic.fna/markers.fasta)
[2023-06-18 19:17:37,680] [INFO] Task started: Blastn
[2023-06-18 19:17:37,680] [INFO] Running command: blastn -query GCA_018366395.1_ASM1836639v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1bf7daf-9a9d-46da-a50b-2b434a324252/dqc_reference/reference_markers_gtdb.fasta -out GCA_018366395.1_ASM1836639v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 19:17:38,719] [INFO] Task succeeded: Blastn
[2023-06-18 19:17:38,728] [INFO] Selected 11 target genomes.
[2023-06-18 19:17:38,729] [INFO] Target genome list was writen to GCA_018366395.1_ASM1836639v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 19:17:38,743] [INFO] Task started: fastANI
[2023-06-18 19:17:38,743] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ce1448f-c142-4977-ade2-a5e33385a7f6/GCA_018366395.1_ASM1836639v1_genomic.fna.gz --refList GCA_018366395.1_ASM1836639v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018366395.1_ASM1836639v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 19:17:45,926] [INFO] Task succeeded: fastANI
[2023-06-18 19:17:45,941] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 19:17:45,941] [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_900547615.1	s__Blautia_A sp900547615	97.4555	679	1034	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.55	97.48	0.84	0.79	4	conclusive
GCA_900549015.1	s__Blautia_A sp900549015	94.1072	697	1034	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.81	98.01	0.88	0.88	3	-
GCA_900540785.1	s__Blautia_A sp900540785	93.3051	766	1034	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900541345.1	s__Blautia_A sp900541345	89.7466	654	1034	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	97.52	96.26	0.83	0.75	5	-
GCF_013302405.1	s__Blautia_A caecimuris	79.9264	307	1034	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	97.97	96.45	0.87	0.70	11	-
GCF_018919065.1	s__Blautia_A sp018919065	78.8104	190	1034	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000285855.2	s__Blautia_A sp000285855	78.7266	238	1034	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	97.62	95.80	0.88	0.79	6	-
GCA_900541985.1	s__Blautia_A sp900541985	78.5841	221	1034	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	99.92	99.92	0.93	0.93	2	-
GCA_019118425.1	s__Blautia_A faecavium	78.2044	177	1034	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.91	98.91	0.82	0.82	2	-
GCA_900553515.1	s__Blautia_A sp900553515	78.0804	219	1034	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905209435.1	s__Blautia_A sp905209435	76.986	178	1034	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 19:17:45,943] [INFO] GTDB search result was written to GCA_018366395.1_ASM1836639v1_genomic.fna/result_gtdb.tsv
[2023-06-18 19:17:45,944] [INFO] ===== GTDB Search completed =====
[2023-06-18 19:17:45,948] [INFO] DFAST_QC result json was written to GCA_018366395.1_ASM1836639v1_genomic.fna/dqc_result.json
[2023-06-18 19:17:45,948] [INFO] DFAST_QC completed!
[2023-06-18 19:17:45,948] [INFO] Total running time: 0h0m59s