[2024-01-24 11:44:23,004] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:23,006] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:23,006] [INFO] DQC Reference Directory: /var/lib/cwl/stg730f309c-2bcd-412e-aeb1-d85e8188ee55/dqc_reference
[2024-01-24 11:44:26,340] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:26,341] [INFO] Task started: Prodigal
[2024-01-24 11:44:26,341] [INFO] Running command: gunzip -c /var/lib/cwl/stgaee7a815-a684-474e-88b4-da501f2aacea/GCF_016583605.1_ASM1658360v1_genomic.fna.gz | prodigal -d GCF_016583605.1_ASM1658360v1_genomic.fna/cds.fna -a GCF_016583605.1_ASM1658360v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:33,462] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:33,463] [INFO] Task started: HMMsearch
[2024-01-24 11:44:33,463] [INFO] Running command: hmmsearch --tblout GCF_016583605.1_ASM1658360v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg730f309c-2bcd-412e-aeb1-d85e8188ee55/dqc_reference/reference_markers.hmm GCF_016583605.1_ASM1658360v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:33,721] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:33,723] [INFO] Found 6/6 markers.
[2024-01-24 11:44:33,749] [INFO] Query marker FASTA was written to GCF_016583605.1_ASM1658360v1_genomic.fna/markers.fasta
[2024-01-24 11:44:33,750] [INFO] Task started: Blastn
[2024-01-24 11:44:33,750] [INFO] Running command: blastn -query GCF_016583605.1_ASM1658360v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg730f309c-2bcd-412e-aeb1-d85e8188ee55/dqc_reference/reference_markers.fasta -out GCF_016583605.1_ASM1658360v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:34,459] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:34,463] [INFO] Selected 18 target genomes.
[2024-01-24 11:44:34,464] [INFO] Target genome list was writen to GCF_016583605.1_ASM1658360v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:34,488] [INFO] Task started: fastANI
[2024-01-24 11:44:34,488] [INFO] Running command: fastANI --query /var/lib/cwl/stgaee7a815-a684-474e-88b4-da501f2aacea/GCF_016583605.1_ASM1658360v1_genomic.fna.gz --refList GCF_016583605.1_ASM1658360v1_genomic.fna/target_genomes.txt --output GCF_016583605.1_ASM1658360v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:44,117] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:44,117] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg730f309c-2bcd-412e-aeb1-d85e8188ee55/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:44,117] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg730f309c-2bcd-412e-aeb1-d85e8188ee55/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:44,124] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:44:44,124] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:44,124] [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
Halorhodospira halochloris	strain=DSM 1059	GCA_016583605.1	1052	1052	type	True	100.0	891	892	95	conclusive
Halorhodospira halochloris	strain=DSM 1059	GCA_002356555.2	1052	1052	type	True	99.9937	892	892	95	conclusive
Halorhodospira abdelmalekii	strain=DSM 2110	GCA_016583625.1	421629	421629	type	True	78.2873	188	892	95	below_threshold
Halorhodospira halophila	strain=SL1	GCA_000015585.1	1053	1053	suspected-type	True	77.3463	149	892	95	below_threshold
Halorhodospira neutriphila	strain=DSM 15116	GCA_016584055.1	168379	168379	type	True	77.0753	106	892	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:44,132] [INFO] DFAST Taxonomy check result was written to GCF_016583605.1_ASM1658360v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:44,133] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:44,133] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:44,133] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg730f309c-2bcd-412e-aeb1-d85e8188ee55/dqc_reference/checkm_data
[2024-01-24 11:44:44,134] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:44,167] [INFO] Task started: CheckM
[2024-01-24 11:44:44,168] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016583605.1_ASM1658360v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016583605.1_ASM1658360v1_genomic.fna/checkm_input GCF_016583605.1_ASM1658360v1_genomic.fna/checkm_result
[2024-01-24 11:45:10,777] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:10,779] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:10,798] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:10,798] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:10,799] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016583605.1_ASM1658360v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:10,799] [INFO] Task started: Blastn
[2024-01-24 11:45:10,799] [INFO] Running command: blastn -query GCF_016583605.1_ASM1658360v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg730f309c-2bcd-412e-aeb1-d85e8188ee55/dqc_reference/reference_markers_gtdb.fasta -out GCF_016583605.1_ASM1658360v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:12,038] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:12,042] [INFO] Selected 22 target genomes.
[2024-01-24 11:45:12,042] [INFO] Target genome list was writen to GCF_016583605.1_ASM1658360v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:12,104] [INFO] Task started: fastANI
[2024-01-24 11:45:12,104] [INFO] Running command: fastANI --query /var/lib/cwl/stgaee7a815-a684-474e-88b4-da501f2aacea/GCF_016583605.1_ASM1658360v1_genomic.fna.gz --refList GCF_016583605.1_ASM1658360v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016583605.1_ASM1658360v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:22,537] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:22,548] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:22,548] [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
GCF_002356555.2	s__Halorhodospira halochloris	99.9937	892	892	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Halorhodospiraceae;g__Halorhodospira	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_016583625.1	s__Halorhodospira abdelmalekii	78.2668	189	892	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Halorhodospiraceae;g__Halorhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016653405.1	s__Halorhodospira halophila_A	77.9056	154	892	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Halorhodospiraceae;g__Halorhodospira	95.0	98.67	98.67	0.87	0.87	2	-
GCF_000015585.1	s__Halorhodospira halophila	77.3656	148	892	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Halorhodospiraceae;g__Halorhodospira	95.0	99.99	99.99	1.00	1.00	2	-
GCF_016584055.1	s__Halorhodospira neutriphila	77.0753	106	892	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Halorhodospiraceae;g__Halorhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003552625.1	s__Halorhodospira sp003552625	77.0097	104	892	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Halorhodospiraceae;g__Halorhodospira	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:22,549] [INFO] GTDB search result was written to GCF_016583605.1_ASM1658360v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:22,550] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:22,552] [INFO] DFAST_QC result json was written to GCF_016583605.1_ASM1658360v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:22,552] [INFO] DFAST_QC completed!
[2024-01-24 11:45:22,552] [INFO] Total running time: 0h0m60s