[2023-06-19 09:00:15,634] [INFO] DFAST_QC pipeline started.
[2023-06-19 09:00:15,640] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 09:00:15,640] [INFO] DQC Reference Directory: /var/lib/cwl/stgc4908480-87d7-4c23-86a0-1c7c08e734ea/dqc_reference
[2023-06-19 09:00:16,857] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 09:00:16,860] [INFO] Task started: Prodigal
[2023-06-19 09:00:16,860] [INFO] Running command: gunzip -c /var/lib/cwl/stg5bc2df52-3532-4b89-869d-8fc94162ac2b/GCA_018652035.1_ASM1865203v1_genomic.fna.gz | prodigal -d GCA_018652035.1_ASM1865203v1_genomic.fna/cds.fna -a GCA_018652035.1_ASM1865203v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 09:00:19,003] [INFO] Task succeeded: Prodigal
[2023-06-19 09:00:19,004] [INFO] Task started: HMMsearch
[2023-06-19 09:00:19,004] [INFO] Running command: hmmsearch --tblout GCA_018652035.1_ASM1865203v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc4908480-87d7-4c23-86a0-1c7c08e734ea/dqc_reference/reference_markers.hmm GCA_018652035.1_ASM1865203v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 09:00:19,229] [INFO] Task succeeded: HMMsearch
[2023-06-19 09:00:19,231] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5bc2df52-3532-4b89-869d-8fc94162ac2b/GCA_018652035.1_ASM1865203v1_genomic.fna.gz]
[2023-06-19 09:00:19,254] [INFO] Query marker FASTA was written to GCA_018652035.1_ASM1865203v1_genomic.fna/markers.fasta
[2023-06-19 09:00:19,255] [INFO] Task started: Blastn
[2023-06-19 09:00:19,255] [INFO] Running command: blastn -query GCA_018652035.1_ASM1865203v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc4908480-87d7-4c23-86a0-1c7c08e734ea/dqc_reference/reference_markers.fasta -out GCA_018652035.1_ASM1865203v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 09:00:19,845] [INFO] Task succeeded: Blastn
[2023-06-19 09:00:19,852] [INFO] Selected 22 target genomes.
[2023-06-19 09:00:19,852] [INFO] Target genome list was writen to GCA_018652035.1_ASM1865203v1_genomic.fna/target_genomes.txt
[2023-06-19 09:00:19,855] [INFO] Task started: fastANI
[2023-06-19 09:00:19,855] [INFO] Running command: fastANI --query /var/lib/cwl/stg5bc2df52-3532-4b89-869d-8fc94162ac2b/GCA_018652035.1_ASM1865203v1_genomic.fna.gz --refList GCA_018652035.1_ASM1865203v1_genomic.fna/target_genomes.txt --output GCA_018652035.1_ASM1865203v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 09:00:29,552] [INFO] Task succeeded: fastANI
[2023-06-19 09:00:29,553] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc4908480-87d7-4c23-86a0-1c7c08e734ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 09:00:29,553] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc4908480-87d7-4c23-86a0-1c7c08e734ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 09:00:29,556] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 09:00:29,557] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 09:00:29,557] [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
Candidatus Pseudothioglobus singularis	strain=PS1	GCA_001281385.1	1427364	1427364	type	True	78.8896	178	344	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 09:00:29,559] [INFO] DFAST Taxonomy check result was written to GCA_018652035.1_ASM1865203v1_genomic.fna/tc_result.tsv
[2023-06-19 09:00:29,561] [INFO] ===== Taxonomy check completed =====
[2023-06-19 09:00:29,561] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 09:00:29,561] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc4908480-87d7-4c23-86a0-1c7c08e734ea/dqc_reference/checkm_data
[2023-06-19 09:00:29,563] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 09:00:29,585] [INFO] Task started: CheckM
[2023-06-19 09:00:29,585] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018652035.1_ASM1865203v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018652035.1_ASM1865203v1_genomic.fna/checkm_input GCA_018652035.1_ASM1865203v1_genomic.fna/checkm_result
[2023-06-19 09:00:44,984] [INFO] Task succeeded: CheckM
[2023-06-19 09:00:44,985] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 5.56%
Strain heterogeneity: 25.00%
--------------------------------------------------------------------------------
[2023-06-19 09:00:45,017] [INFO] ===== Completeness check finished =====
[2023-06-19 09:00:45,017] [INFO] ===== Start GTDB Search =====
[2023-06-19 09:00:45,017] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018652035.1_ASM1865203v1_genomic.fna/markers.fasta)
[2023-06-19 09:00:45,017] [INFO] Task started: Blastn
[2023-06-19 09:00:45,018] [INFO] Running command: blastn -query GCA_018652035.1_ASM1865203v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc4908480-87d7-4c23-86a0-1c7c08e734ea/dqc_reference/reference_markers_gtdb.fasta -out GCA_018652035.1_ASM1865203v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 09:00:45,898] [INFO] Task succeeded: Blastn
[2023-06-19 09:00:45,903] [INFO] Selected 9 target genomes.
[2023-06-19 09:00:45,904] [INFO] Target genome list was writen to GCA_018652035.1_ASM1865203v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 09:00:45,909] [INFO] Task started: fastANI
[2023-06-19 09:00:45,910] [INFO] Running command: fastANI --query /var/lib/cwl/stg5bc2df52-3532-4b89-869d-8fc94162ac2b/GCA_018652035.1_ASM1865203v1_genomic.fna.gz --refList GCA_018652035.1_ASM1865203v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018652035.1_ASM1865203v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 09:00:48,131] [INFO] Task succeeded: fastANI
[2023-06-19 09:00:48,141] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 09:00:48,142] [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_014384565.1	s__Pseudothioglobus aerophilus	98.9713	289	344	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	99.14	98.97	0.83	0.77	11	conclusive
GCA_905182815.1	s__Pseudothioglobus sp905182815	94.8406	256	344	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905618925.1	s__Pseudothioglobus sp905618925	89.2022	215	344	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	95.58	95.58	0.66	0.66	2	-
GCA_905614365.1	s__Pseudothioglobus sp905614365	88.4157	212	344	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	96.68	96.27	0.61	0.56	4	-
GCA_905612405.1	s__Pseudothioglobus sp905612405	87.4156	196	344	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905620445.1	s__Pseudothioglobus sp905620445	86.2889	161	344	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003326015.1	s__Pseudothioglobus singularis_A	80.0847	197	344	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002698045.1	s__Pseudothioglobus sp002698045	78.5224	87	344	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	95.47	95.47	0.68	0.68	2	-
GCA_902513495.1	s__Pseudothioglobus sp902513495	78.3043	104	344	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	97.65	97.05	0.53	0.51	3	-
--------------------------------------------------------------------------------
[2023-06-19 09:00:48,143] [INFO] GTDB search result was written to GCA_018652035.1_ASM1865203v1_genomic.fna/result_gtdb.tsv
[2023-06-19 09:00:48,144] [INFO] ===== GTDB Search completed =====
[2023-06-19 09:00:48,147] [INFO] DFAST_QC result json was written to GCA_018652035.1_ASM1865203v1_genomic.fna/dqc_result.json
[2023-06-19 09:00:48,147] [INFO] DFAST_QC completed!
[2023-06-19 09:00:48,147] [INFO] Total running time: 0h0m33s