[2024-01-24 15:10:49,199] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:49,201] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:49,201] [INFO] DQC Reference Directory: /var/lib/cwl/stg8b7cf949-a3a1-4c94-b300-6fa57afa7de0/dqc_reference
[2024-01-24 15:10:50,494] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:50,495] [INFO] Task started: Prodigal
[2024-01-24 15:10:50,495] [INFO] Running command: gunzip -c /var/lib/cwl/stg3fe7a714-f449-4565-9b94-543f0bf1fc58/GCF_002997955.1_ASM299795v1_genomic.fna.gz | prodigal -d GCF_002997955.1_ASM299795v1_genomic.fna/cds.fna -a GCF_002997955.1_ASM299795v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:52,780] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:52,780] [INFO] Task started: HMMsearch
[2024-01-24 15:10:52,780] [INFO] Running command: hmmsearch --tblout GCF_002997955.1_ASM299795v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8b7cf949-a3a1-4c94-b300-6fa57afa7de0/dqc_reference/reference_markers.hmm GCF_002997955.1_ASM299795v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:52,996] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:52,997] [INFO] Found 6/6 markers.
[2024-01-24 15:10:53,013] [INFO] Query marker FASTA was written to GCF_002997955.1_ASM299795v1_genomic.fna/markers.fasta
[2024-01-24 15:10:53,013] [INFO] Task started: Blastn
[2024-01-24 15:10:53,013] [INFO] Running command: blastn -query GCF_002997955.1_ASM299795v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b7cf949-a3a1-4c94-b300-6fa57afa7de0/dqc_reference/reference_markers.fasta -out GCF_002997955.1_ASM299795v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:53,664] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:53,668] [INFO] Selected 5 target genomes.
[2024-01-24 15:10:53,668] [INFO] Target genome list was writen to GCF_002997955.1_ASM299795v1_genomic.fna/target_genomes.txt
[2024-01-24 15:10:53,673] [INFO] Task started: fastANI
[2024-01-24 15:10:53,674] [INFO] Running command: fastANI --query /var/lib/cwl/stg3fe7a714-f449-4565-9b94-543f0bf1fc58/GCF_002997955.1_ASM299795v1_genomic.fna.gz --refList GCF_002997955.1_ASM299795v1_genomic.fna/target_genomes.txt --output GCF_002997955.1_ASM299795v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:10:54,866] [INFO] Task succeeded: fastANI
[2024-01-24 15:10:54,867] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8b7cf949-a3a1-4c94-b300-6fa57afa7de0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:10:54,867] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8b7cf949-a3a1-4c94-b300-6fa57afa7de0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:10:54,873] [INFO] Found 5 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 15:10:54,874] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:10:54,874] [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_002997955.1	83560	83560	type	True	100.0	357	357	95	conclusive
Chlamydia muridarum	strain=Nigg	GCA_002998035.1	83560	83560	type	True	99.9956	357	357	95	conclusive
Chlamydia muridarum	strain=Nigg	GCA_002997975.1	83560	83560	type	True	99.9954	357	357	95	conclusive
Chlamydia muridarum	strain=Nigg	GCA_002998015.1	83560	83560	type	True	99.9953	357	357	95	conclusive
Chlamydia muridarum	strain=Nigg	GCA_000174975.1	83560	83560	type	True	99.991	352	357	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 15:10:54,875] [INFO] DFAST Taxonomy check result was written to GCF_002997955.1_ASM299795v1_genomic.fna/tc_result.tsv
[2024-01-24 15:10:54,876] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:10:54,876] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:10:54,876] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8b7cf949-a3a1-4c94-b300-6fa57afa7de0/dqc_reference/checkm_data
[2024-01-24 15:10:54,877] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:10:54,896] [INFO] Task started: CheckM
[2024-01-24 15:10:54,896] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002997955.1_ASM299795v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002997955.1_ASM299795v1_genomic.fna/checkm_input GCF_002997955.1_ASM299795v1_genomic.fna/checkm_result
[2024-01-24 15:11:10,632] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:10,634] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:10,656] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:10,657] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:10,657] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002997955.1_ASM299795v1_genomic.fna/markers.fasta)
[2024-01-24 15:11:10,658] [INFO] Task started: Blastn
[2024-01-24 15:11:10,658] [INFO] Running command: blastn -query GCF_002997955.1_ASM299795v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b7cf949-a3a1-4c94-b300-6fa57afa7de0/dqc_reference/reference_markers_gtdb.fasta -out GCF_002997955.1_ASM299795v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:11,592] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:11,596] [INFO] Selected 11 target genomes.
[2024-01-24 15:11:11,596] [INFO] Target genome list was writen to GCF_002997955.1_ASM299795v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:11:11,610] [INFO] Task started: fastANI
[2024-01-24 15:11:11,610] [INFO] Running command: fastANI --query /var/lib/cwl/stg3fe7a714-f449-4565-9b94-543f0bf1fc58/GCF_002997955.1_ASM299795v1_genomic.fna.gz --refList GCF_002997955.1_ASM299795v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002997955.1_ASM299795v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:11:14,765] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:14,771] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:11:14,771] [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	99.992	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	82.5689	289	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	81.9548	280	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	80.6508	249	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 15:11:14,772] [INFO] GTDB search result was written to GCF_002997955.1_ASM299795v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:11:14,777] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:11:14,781] [INFO] DFAST_QC result json was written to GCF_002997955.1_ASM299795v1_genomic.fna/dqc_result.json
[2024-01-24 15:11:14,781] [INFO] DFAST_QC completed!
[2024-01-24 15:11:14,781] [INFO] Total running time: 0h0m26s