[2023-06-28 22:43:25,137] [INFO] DFAST_QC pipeline started.
[2023-06-28 22:43:25,139] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 22:43:25,140] [INFO] DQC Reference Directory: /var/lib/cwl/stgca9d8180-ba23-425f-b39c-d9ca2085c727/dqc_reference
[2023-06-28 22:43:27,476] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 22:43:27,477] [INFO] Task started: Prodigal
[2023-06-28 22:43:27,477] [INFO] Running command: gunzip -c /var/lib/cwl/stg2dd84a80-3e16-40d4-b3e1-43e86ea893d5/GCA_017430545.1_ASM1743054v1_genomic.fna.gz | prodigal -d GCA_017430545.1_ASM1743054v1_genomic.fna/cds.fna -a GCA_017430545.1_ASM1743054v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 22:43:32,262] [INFO] Task succeeded: Prodigal
[2023-06-28 22:43:32,262] [INFO] Task started: HMMsearch
[2023-06-28 22:43:32,263] [INFO] Running command: hmmsearch --tblout GCA_017430545.1_ASM1743054v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgca9d8180-ba23-425f-b39c-d9ca2085c727/dqc_reference/reference_markers.hmm GCA_017430545.1_ASM1743054v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 22:43:32,497] [INFO] Task succeeded: HMMsearch
[2023-06-28 22:43:32,498] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2dd84a80-3e16-40d4-b3e1-43e86ea893d5/GCA_017430545.1_ASM1743054v1_genomic.fna.gz]
[2023-06-28 22:43:32,526] [INFO] Query marker FASTA was written to GCA_017430545.1_ASM1743054v1_genomic.fna/markers.fasta
[2023-06-28 22:43:32,527] [INFO] Task started: Blastn
[2023-06-28 22:43:32,527] [INFO] Running command: blastn -query GCA_017430545.1_ASM1743054v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca9d8180-ba23-425f-b39c-d9ca2085c727/dqc_reference/reference_markers.fasta -out GCA_017430545.1_ASM1743054v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 22:43:33,108] [INFO] Task succeeded: Blastn
[2023-06-28 22:43:33,114] [INFO] Selected 19 target genomes.
[2023-06-28 22:43:33,114] [INFO] Target genome list was writen to GCA_017430545.1_ASM1743054v1_genomic.fna/target_genomes.txt
[2023-06-28 22:43:33,116] [INFO] Task started: fastANI
[2023-06-28 22:43:33,116] [INFO] Running command: fastANI --query /var/lib/cwl/stg2dd84a80-3e16-40d4-b3e1-43e86ea893d5/GCA_017430545.1_ASM1743054v1_genomic.fna.gz --refList GCA_017430545.1_ASM1743054v1_genomic.fna/target_genomes.txt --output GCA_017430545.1_ASM1743054v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 22:43:43,778] [INFO] Task succeeded: fastANI
[2023-06-28 22:43:43,779] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgca9d8180-ba23-425f-b39c-d9ca2085c727/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 22:43:43,779] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgca9d8180-ba23-425f-b39c-d9ca2085c727/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 22:43:43,787] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 22:43:43,788] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 22:43:43,788] [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
Butyrivibrio hungatei	strain=DSM 14810	GCA_900143205.1	185008	185008	type	True	79.5216	268	657	95	below_threshold
Butyrivibrio proteoclasticus	strain=B316	GCA_000145035.1	43305	43305	type	True	78.9512	234	657	95	below_threshold
Butyrivibrio fibrisolvens	strain=DSM 3071	GCA_900129945.1	831	831	suspected-type	True	77.5286	87	657	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 22:43:43,790] [INFO] DFAST Taxonomy check result was written to GCA_017430545.1_ASM1743054v1_genomic.fna/tc_result.tsv
[2023-06-28 22:43:43,791] [INFO] ===== Taxonomy check completed =====
[2023-06-28 22:43:43,791] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 22:43:43,791] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgca9d8180-ba23-425f-b39c-d9ca2085c727/dqc_reference/checkm_data
[2023-06-28 22:43:43,792] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 22:43:43,825] [INFO] Task started: CheckM
[2023-06-28 22:43:43,825] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017430545.1_ASM1743054v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017430545.1_ASM1743054v1_genomic.fna/checkm_input GCA_017430545.1_ASM1743054v1_genomic.fna/checkm_result
[2023-06-28 22:44:05,440] [INFO] Task succeeded: CheckM
[2023-06-28 22:44:05,441] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 42.71%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 22:44:05,464] [INFO] ===== Completeness check finished =====
[2023-06-28 22:44:05,465] [INFO] ===== Start GTDB Search =====
[2023-06-28 22:44:05,465] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017430545.1_ASM1743054v1_genomic.fna/markers.fasta)
[2023-06-28 22:44:05,465] [INFO] Task started: Blastn
[2023-06-28 22:44:05,466] [INFO] Running command: blastn -query GCA_017430545.1_ASM1743054v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca9d8180-ba23-425f-b39c-d9ca2085c727/dqc_reference/reference_markers_gtdb.fasta -out GCA_017430545.1_ASM1743054v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 22:44:06,316] [INFO] Task succeeded: Blastn
[2023-06-28 22:44:06,321] [INFO] Selected 8 target genomes.
[2023-06-28 22:44:06,321] [INFO] Target genome list was writen to GCA_017430545.1_ASM1743054v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 22:44:06,322] [INFO] Task started: fastANI
[2023-06-28 22:44:06,323] [INFO] Running command: fastANI --query /var/lib/cwl/stg2dd84a80-3e16-40d4-b3e1-43e86ea893d5/GCA_017430545.1_ASM1743054v1_genomic.fna.gz --refList GCA_017430545.1_ASM1743054v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017430545.1_ASM1743054v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 22:44:12,079] [INFO] Task succeeded: fastANI
[2023-06-28 22:44:12,094] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 22:44:12,095] [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_015056685.1	s__Butyrivibrio sp015056685	96.2339	556	657	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio	95.0	95.83	95.83	0.67	0.67	2	conclusive
GCF_000420825.1	s__Butyrivibrio sp000420825	94.5496	556	657	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108105.1	s__Butyrivibrio sp900108105	93.7981	559	657	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115735.1	s__Butyrivibrio proteoclasticus_B	90.7311	542	657	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017635265.1	s__Butyrivibrio sp017635265	84.9192	446	657	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103635.1	s__Butyrivibrio sp900103635	79.591	258	657	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio	95.0	95.99	95.99	0.85	0.85	2	-
GCF_900143205.1	s__Butyrivibrio hungatei	79.5404	267	657	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio	95.0	97.43	97.43	0.86	0.86	2	-
GCF_900102515.1	s__Butyrivibrio sp900102515	78.9979	224	657	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio	95.0	95.65	95.65	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2023-06-28 22:44:12,098] [INFO] GTDB search result was written to GCA_017430545.1_ASM1743054v1_genomic.fna/result_gtdb.tsv
[2023-06-28 22:44:12,099] [INFO] ===== GTDB Search completed =====
[2023-06-28 22:44:12,102] [INFO] DFAST_QC result json was written to GCA_017430545.1_ASM1743054v1_genomic.fna/dqc_result.json
[2023-06-28 22:44:12,102] [INFO] DFAST_QC completed!
[2023-06-28 22:44:12,102] [INFO] Total running time: 0h0m47s