[2023-06-29 20:06:19,135] [INFO] DFAST_QC pipeline started.
[2023-06-29 20:06:19,137] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 20:06:19,137] [INFO] DQC Reference Directory: /var/lib/cwl/stgab284204-96a8-4ef7-a6a8-28ca25fade72/dqc_reference
[2023-06-29 20:06:20,449] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 20:06:20,450] [INFO] Task started: Prodigal
[2023-06-29 20:06:20,451] [INFO] Running command: gunzip -c /var/lib/cwl/stg65d6c6b4-9a20-47ed-bfb2-b5cd9abac72c/GCA_910577175.1_MGBC100288_genomic.fna.gz | prodigal -d GCA_910577175.1_MGBC100288_genomic.fna/cds.fna -a GCA_910577175.1_MGBC100288_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 20:06:27,995] [INFO] Task succeeded: Prodigal
[2023-06-29 20:06:27,996] [INFO] Task started: HMMsearch
[2023-06-29 20:06:27,996] [INFO] Running command: hmmsearch --tblout GCA_910577175.1_MGBC100288_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgab284204-96a8-4ef7-a6a8-28ca25fade72/dqc_reference/reference_markers.hmm GCA_910577175.1_MGBC100288_genomic.fna/protein.faa > /dev/null
[2023-06-29 20:06:28,272] [INFO] Task succeeded: HMMsearch
[2023-06-29 20:06:28,274] [INFO] Found 6/6 markers.
[2023-06-29 20:06:28,302] [INFO] Query marker FASTA was written to GCA_910577175.1_MGBC100288_genomic.fna/markers.fasta
[2023-06-29 20:06:28,302] [INFO] Task started: Blastn
[2023-06-29 20:06:28,302] [INFO] Running command: blastn -query GCA_910577175.1_MGBC100288_genomic.fna/markers.fasta -db /var/lib/cwl/stgab284204-96a8-4ef7-a6a8-28ca25fade72/dqc_reference/reference_markers.fasta -out GCA_910577175.1_MGBC100288_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:06:28,943] [INFO] Task succeeded: Blastn
[2023-06-29 20:06:28,950] [INFO] Selected 27 target genomes.
[2023-06-29 20:06:28,951] [INFO] Target genome list was writen to GCA_910577175.1_MGBC100288_genomic.fna/target_genomes.txt
[2023-06-29 20:06:28,953] [INFO] Task started: fastANI
[2023-06-29 20:06:28,953] [INFO] Running command: fastANI --query /var/lib/cwl/stg65d6c6b4-9a20-47ed-bfb2-b5cd9abac72c/GCA_910577175.1_MGBC100288_genomic.fna.gz --refList GCA_910577175.1_MGBC100288_genomic.fna/target_genomes.txt --output GCA_910577175.1_MGBC100288_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 20:06:44,569] [INFO] Task succeeded: fastANI
[2023-06-29 20:06:44,570] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgab284204-96a8-4ef7-a6a8-28ca25fade72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 20:06:44,570] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgab284204-96a8-4ef7-a6a8-28ca25fade72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 20:06:44,574] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 20:06:44,575] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 20:06:44,575] [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
Marvinbryantia formatexigens	strain=DSM 14469	GCA_025148285.1	168384	168384	type	True	76.7652	50	1031	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 20:06:44,577] [INFO] DFAST Taxonomy check result was written to GCA_910577175.1_MGBC100288_genomic.fna/tc_result.tsv
[2023-06-29 20:06:44,578] [INFO] ===== Taxonomy check completed =====
[2023-06-29 20:06:44,578] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 20:06:44,578] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgab284204-96a8-4ef7-a6a8-28ca25fade72/dqc_reference/checkm_data
[2023-06-29 20:06:44,579] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 20:06:44,618] [INFO] Task started: CheckM
[2023-06-29 20:06:44,618] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_910577175.1_MGBC100288_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_910577175.1_MGBC100288_genomic.fna/checkm_input GCA_910577175.1_MGBC100288_genomic.fna/checkm_result
[2023-06-29 20:07:13,199] [INFO] Task succeeded: CheckM
[2023-06-29 20:07:13,200] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 40.00%
--------------------------------------------------------------------------------
[2023-06-29 20:07:13,228] [INFO] ===== Completeness check finished =====
[2023-06-29 20:07:13,229] [INFO] ===== Start GTDB Search =====
[2023-06-29 20:07:13,229] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_910577175.1_MGBC100288_genomic.fna/markers.fasta)
[2023-06-29 20:07:13,229] [INFO] Task started: Blastn
[2023-06-29 20:07:13,230] [INFO] Running command: blastn -query GCA_910577175.1_MGBC100288_genomic.fna/markers.fasta -db /var/lib/cwl/stgab284204-96a8-4ef7-a6a8-28ca25fade72/dqc_reference/reference_markers_gtdb.fasta -out GCA_910577175.1_MGBC100288_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:07:14,300] [INFO] Task succeeded: Blastn
[2023-06-29 20:07:14,303] [INFO] Selected 15 target genomes.
[2023-06-29 20:07:14,304] [INFO] Target genome list was writen to GCA_910577175.1_MGBC100288_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 20:07:14,307] [INFO] Task started: fastANI
[2023-06-29 20:07:14,307] [INFO] Running command: fastANI --query /var/lib/cwl/stg65d6c6b4-9a20-47ed-bfb2-b5cd9abac72c/GCA_910577175.1_MGBC100288_genomic.fna.gz --refList GCA_910577175.1_MGBC100288_genomic.fna/target_genomes_gtdb.txt --output GCA_910577175.1_MGBC100288_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 20:07:23,284] [INFO] Task succeeded: fastANI
[2023-06-29 20:07:23,299] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 20:07:23,299] [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_910577175.1	s__SIG307 sp910577175	100.0	1029	1031	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__SIG307	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_910579465.1	s__SIG307 sp910579465	90.298	881	1031	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__SIG307	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017938405.1	s__SIG307 sp017938405	78.6188	249	1031	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__SIG307	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017503735.1	s__SIG307 sp017503735	78.3649	252	1031	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__SIG307	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017556805.1	s__SIG307 sp017556805	78.3373	251	1031	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__SIG307	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015057365.1	s__SIG307 sp015057365	78.0741	223	1031	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__SIG307	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017465475.1	s__SIG307 sp017465475	77.9375	231	1031	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__SIG307	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000403335.2	s__COE1 sp000403335	76.6087	50	1031	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1	95.0	98.29	97.29	0.83	0.75	4	-
GCA_009911175.1	s__Schaedlerella sp009911175	76.2426	50	1031	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	98.09	98.08	0.79	0.79	3	-
GCA_910587655.1	s__Agathobacter sp910587655	76.0771	57	1031	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 20:07:23,302] [INFO] GTDB search result was written to GCA_910577175.1_MGBC100288_genomic.fna/result_gtdb.tsv
[2023-06-29 20:07:23,302] [INFO] ===== GTDB Search completed =====
[2023-06-29 20:07:23,305] [INFO] DFAST_QC result json was written to GCA_910577175.1_MGBC100288_genomic.fna/dqc_result.json
[2023-06-29 20:07:23,306] [INFO] DFAST_QC completed!
[2023-06-29 20:07:23,306] [INFO] Total running time: 0h1m4s