[2024-01-24 13:12:38,374] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:38,377] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:38,377] [INFO] DQC Reference Directory: /var/lib/cwl/stgfc9e621d-9ea0-4251-91bc-7e44a19fdd42/dqc_reference
[2024-01-24 13:12:39,905] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:39,906] [INFO] Task started: Prodigal
[2024-01-24 13:12:39,907] [INFO] Running command: gunzip -c /var/lib/cwl/stg9b14bd31-bc0f-4625-bee7-83a1d2ac984d/GCF_002998115.1_ASM299811v1_genomic.fna.gz | prodigal -d GCF_002998115.1_ASM299811v1_genomic.fna/cds.fna -a GCF_002998115.1_ASM299811v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:12:42,188] [INFO] Task succeeded: Prodigal
[2024-01-24 13:12:42,189] [INFO] Task started: HMMsearch
[2024-01-24 13:12:42,189] [INFO] Running command: hmmsearch --tblout GCF_002998115.1_ASM299811v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfc9e621d-9ea0-4251-91bc-7e44a19fdd42/dqc_reference/reference_markers.hmm GCF_002998115.1_ASM299811v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:12:42,420] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:12:42,421] [INFO] Found 6/6 markers.
[2024-01-24 13:12:42,437] [INFO] Query marker FASTA was written to GCF_002998115.1_ASM299811v1_genomic.fna/markers.fasta
[2024-01-24 13:12:42,437] [INFO] Task started: Blastn
[2024-01-24 13:12:42,437] [INFO] Running command: blastn -query GCF_002998115.1_ASM299811v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc9e621d-9ea0-4251-91bc-7e44a19fdd42/dqc_reference/reference_markers.fasta -out GCF_002998115.1_ASM299811v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:12:43,022] [INFO] Task succeeded: Blastn
[2024-01-24 13:12:43,025] [INFO] Selected 5 target genomes.
[2024-01-24 13:12:43,026] [INFO] Target genome list was writen to GCF_002998115.1_ASM299811v1_genomic.fna/target_genomes.txt
[2024-01-24 13:12:43,058] [INFO] Task started: fastANI
[2024-01-24 13:12:43,058] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b14bd31-bc0f-4625-bee7-83a1d2ac984d/GCF_002998115.1_ASM299811v1_genomic.fna.gz --refList GCF_002998115.1_ASM299811v1_genomic.fna/target_genomes.txt --output GCF_002998115.1_ASM299811v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:12:44,227] [INFO] Task succeeded: fastANI
[2024-01-24 13:12:44,228] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfc9e621d-9ea0-4251-91bc-7e44a19fdd42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:12:44,228] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfc9e621d-9ea0-4251-91bc-7e44a19fdd42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:12:44,235] [INFO] Found 5 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 13:12:44,235] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:12:44,235] [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
Chlamydia muridarum	strain=Nigg	GCA_002998035.1	83560	83560	type	True	99.9981	357	357	95	conclusive
Chlamydia muridarum	strain=Nigg	GCA_002997975.1	83560	83560	type	True	99.9979	357	357	95	conclusive
Chlamydia muridarum	strain=Nigg	GCA_002998015.1	83560	83560	type	True	99.9978	357	357	95	conclusive
Chlamydia muridarum	strain=Nigg	GCA_002997955.1	83560	83560	type	True	99.9942	357	357	95	conclusive
Chlamydia muridarum	strain=Nigg	GCA_000174975.1	83560	83560	type	True	99.9936	352	357	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:12:44,237] [INFO] DFAST Taxonomy check result was written to GCF_002998115.1_ASM299811v1_genomic.fna/tc_result.tsv
[2024-01-24 13:12:44,237] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:12:44,238] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:12:44,238] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfc9e621d-9ea0-4251-91bc-7e44a19fdd42/dqc_reference/checkm_data
[2024-01-24 13:12:44,239] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:12:44,253] [INFO] Task started: CheckM
[2024-01-24 13:12:44,254] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002998115.1_ASM299811v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002998115.1_ASM299811v1_genomic.fna/checkm_input GCF_002998115.1_ASM299811v1_genomic.fna/checkm_result
[2024-01-24 13:12:59,411] [INFO] Task succeeded: CheckM
[2024-01-24 13:12:59,413] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:12:59,458] [INFO] ===== Completeness check finished =====
[2024-01-24 13:12:59,458] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:12:59,459] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002998115.1_ASM299811v1_genomic.fna/markers.fasta)
[2024-01-24 13:12:59,459] [INFO] Task started: Blastn
[2024-01-24 13:12:59,460] [INFO] Running command: blastn -query GCF_002998115.1_ASM299811v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc9e621d-9ea0-4251-91bc-7e44a19fdd42/dqc_reference/reference_markers_gtdb.fasta -out GCF_002998115.1_ASM299811v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:00,418] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:00,422] [INFO] Selected 11 target genomes.
[2024-01-24 13:13:00,422] [INFO] Target genome list was writen to GCF_002998115.1_ASM299811v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:13:00,444] [INFO] Task started: fastANI
[2024-01-24 13:13:00,444] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b14bd31-bc0f-4625-bee7-83a1d2ac984d/GCF_002998115.1_ASM299811v1_genomic.fna.gz --refList GCF_002998115.1_ASM299811v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002998115.1_ASM299811v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:13:03,954] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:03,960] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:13:03,960] [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_000006685.1	s__Chlamydia muridarum	99.9946	356	357	d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Chlamydiaceae;g__Chlamydia	95.0	99.96	98.97	1.00	0.98	29	conclusive
GCF_900169085.1	s__Chlamydia suis	82.6135	286	357	d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Chlamydiaceae;g__Chlamydia	95.0	98.47	97.62	0.99	0.97	33	-
GCF_000012125.1	s__Chlamydia trachomatis	81.9244	281	357	d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Chlamydiaceae;g__Chlamydia	95.0	99.35	98.96	0.99	0.82	178	-
GCA_017472245.1	s__Chlamydia sp017472245	80.606	248	357	d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Chlamydiaceae;g__Chlamydia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:13:03,963] [INFO] GTDB search result was written to GCF_002998115.1_ASM299811v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:13:03,964] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:13:03,966] [INFO] DFAST_QC result json was written to GCF_002998115.1_ASM299811v1_genomic.fna/dqc_result.json
[2024-01-24 13:13:03,967] [INFO] DFAST_QC completed!
[2024-01-24 13:13:03,967] [INFO] Total running time: 0h0m26s