[2023-06-29 20:55:26,253] [INFO] DFAST_QC pipeline started.
[2023-06-29 20:55:26,256] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 20:55:26,256] [INFO] DQC Reference Directory: /var/lib/cwl/stg0809b6c0-a160-4349-98e6-cd14019dd5f8/dqc_reference
[2023-06-29 20:55:27,537] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 20:55:27,538] [INFO] Task started: Prodigal
[2023-06-29 20:55:27,538] [INFO] Running command: gunzip -c /var/lib/cwl/stgfb4f5b97-bc36-4dd4-a20d-bf0538d2e75c/GCA_016784585.1_ASM1678458v1_genomic.fna.gz | prodigal -d GCA_016784585.1_ASM1678458v1_genomic.fna/cds.fna -a GCA_016784585.1_ASM1678458v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 20:55:31,221] [INFO] Task succeeded: Prodigal
[2023-06-29 20:55:31,222] [INFO] Task started: HMMsearch
[2023-06-29 20:55:31,222] [INFO] Running command: hmmsearch --tblout GCA_016784585.1_ASM1678458v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0809b6c0-a160-4349-98e6-cd14019dd5f8/dqc_reference/reference_markers.hmm GCA_016784585.1_ASM1678458v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 20:55:31,422] [INFO] Task succeeded: HMMsearch
[2023-06-29 20:55:31,423] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgfb4f5b97-bc36-4dd4-a20d-bf0538d2e75c/GCA_016784585.1_ASM1678458v1_genomic.fna.gz]
[2023-06-29 20:55:31,442] [INFO] Query marker FASTA was written to GCA_016784585.1_ASM1678458v1_genomic.fna/markers.fasta
[2023-06-29 20:55:31,443] [INFO] Task started: Blastn
[2023-06-29 20:55:31,443] [INFO] Running command: blastn -query GCA_016784585.1_ASM1678458v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0809b6c0-a160-4349-98e6-cd14019dd5f8/dqc_reference/reference_markers.fasta -out GCA_016784585.1_ASM1678458v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:55:31,979] [INFO] Task succeeded: Blastn
[2023-06-29 20:55:31,983] [INFO] Selected 11 target genomes.
[2023-06-29 20:55:31,983] [INFO] Target genome list was writen to GCA_016784585.1_ASM1678458v1_genomic.fna/target_genomes.txt
[2023-06-29 20:55:31,984] [INFO] Task started: fastANI
[2023-06-29 20:55:31,985] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb4f5b97-bc36-4dd4-a20d-bf0538d2e75c/GCA_016784585.1_ASM1678458v1_genomic.fna.gz --refList GCA_016784585.1_ASM1678458v1_genomic.fna/target_genomes.txt --output GCA_016784585.1_ASM1678458v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 20:55:43,113] [INFO] Task succeeded: fastANI
[2023-06-29 20:55:43,114] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0809b6c0-a160-4349-98e6-cd14019dd5f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 20:55:43,114] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0809b6c0-a160-4349-98e6-cd14019dd5f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 20:55:43,119] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 20:55:43,120] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 20:55:43,120] [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
Tichowtungia aerotolerans	strain=S-5007	GCA_009905215.1	2697043	2697043	type	True	78.8424	191	430	95	below_threshold
Pontiella desulfatans	strain=F1(T)	GCA_900890425.1	2750659	2750659	type	True	77.4887	88	430	95	below_threshold
Pontiella sulfatireligans	strain=F21(T)	GCA_900890705.1	2750658	2750658	type	True	76.7542	88	430	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 20:55:43,122] [INFO] DFAST Taxonomy check result was written to GCA_016784585.1_ASM1678458v1_genomic.fna/tc_result.tsv
[2023-06-29 20:55:43,123] [INFO] ===== Taxonomy check completed =====
[2023-06-29 20:55:43,123] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 20:55:43,123] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0809b6c0-a160-4349-98e6-cd14019dd5f8/dqc_reference/checkm_data
[2023-06-29 20:55:43,124] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 20:55:43,141] [INFO] Task started: CheckM
[2023-06-29 20:55:43,142] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016784585.1_ASM1678458v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016784585.1_ASM1678458v1_genomic.fna/checkm_input GCA_016784585.1_ASM1678458v1_genomic.fna/checkm_result
[2023-06-29 20:56:01,516] [INFO] Task succeeded: CheckM
[2023-06-29 20:56:01,517] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 55.73%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 20:56:01,534] [INFO] ===== Completeness check finished =====
[2023-06-29 20:56:01,534] [INFO] ===== Start GTDB Search =====
[2023-06-29 20:56:01,535] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016784585.1_ASM1678458v1_genomic.fna/markers.fasta)
[2023-06-29 20:56:01,535] [INFO] Task started: Blastn
[2023-06-29 20:56:01,535] [INFO] Running command: blastn -query GCA_016784585.1_ASM1678458v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0809b6c0-a160-4349-98e6-cd14019dd5f8/dqc_reference/reference_markers_gtdb.fasta -out GCA_016784585.1_ASM1678458v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:56:02,064] [INFO] Task succeeded: Blastn
[2023-06-29 20:56:02,067] [INFO] Selected 9 target genomes.
[2023-06-29 20:56:02,067] [INFO] Target genome list was writen to GCA_016784585.1_ASM1678458v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 20:56:02,074] [INFO] Task started: fastANI
[2023-06-29 20:56:02,075] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb4f5b97-bc36-4dd4-a20d-bf0538d2e75c/GCA_016784585.1_ASM1678458v1_genomic.fna.gz --refList GCA_016784585.1_ASM1678458v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016784585.1_ASM1678458v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 20:56:07,920] [INFO] Task succeeded: fastANI
[2023-06-29 20:56:07,928] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 20:56:07,929] [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_014381785.1	s__UBA5540 sp014381785	88.2304	313	430	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__Kiritimatiellales;f__Pontiellaceae;g__UBA5540	95.0	99.87	99.87	0.92	0.92	2	-
GCA_016342445.1	s__UBA5540 sp016342445	79.9017	192	430	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__Kiritimatiellales;f__Pontiellaceae;g__UBA5540	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009905215.1	s__UBA5540 sp009905215	78.8636	189	430	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__Kiritimatiellales;f__Pontiellaceae;g__UBA5540	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903831085.1	s__UBA5540 sp903831085	77.5407	126	430	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__Kiritimatiellales;f__Pontiellaceae;g__UBA5540	95.0	99.88	99.84	0.97	0.96	4	-
GCF_900890425.1	s__Pontiella desulfatans	77.4887	88	430	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__Kiritimatiellales;f__Pontiellaceae;g__Pontiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903826865.1	s__UBA5540 sp903826865	77.185	119	430	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__Kiritimatiellales;f__Pontiellaceae;g__UBA5540	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013141415.1	s__UBA5540 sp013141415	77.0024	114	430	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__Kiritimatiellales;f__Pontiellaceae;g__UBA5540	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900890705.1	s__Pontiella sulfatireligans	76.7774	87	430	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__Kiritimatiellales;f__Pontiellaceae;g__Pontiella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 20:56:07,931] [INFO] GTDB search result was written to GCA_016784585.1_ASM1678458v1_genomic.fna/result_gtdb.tsv
[2023-06-29 20:56:07,931] [INFO] ===== GTDB Search completed =====
[2023-06-29 20:56:07,934] [INFO] DFAST_QC result json was written to GCA_016784585.1_ASM1678458v1_genomic.fna/dqc_result.json
[2023-06-29 20:56:07,935] [INFO] DFAST_QC completed!
[2023-06-29 20:56:07,935] [INFO] Total running time: 0h0m42s