[2024-01-24 12:22:14,059] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:14,067] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:14,067] [INFO] DQC Reference Directory: /var/lib/cwl/stgcc3485bf-7a5f-460e-8e77-cc32363a8c2b/dqc_reference
[2024-01-24 12:22:15,625] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:15,625] [INFO] Task started: Prodigal
[2024-01-24 12:22:15,626] [INFO] Running command: gunzip -c /var/lib/cwl/stg3ccd40a3-834a-4ae1-bea7-60b5605b43f7/GCF_000218875.1_ASM21887v1_genomic.fna.gz | prodigal -d GCF_000218875.1_ASM21887v1_genomic.fna/cds.fna -a GCF_000218875.1_ASM21887v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:20,669] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:20,670] [INFO] Task started: HMMsearch
[2024-01-24 12:22:20,670] [INFO] Running command: hmmsearch --tblout GCF_000218875.1_ASM21887v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcc3485bf-7a5f-460e-8e77-cc32363a8c2b/dqc_reference/reference_markers.hmm GCF_000218875.1_ASM21887v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:20,951] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:20,952] [INFO] Found 6/6 markers.
[2024-01-24 12:22:20,973] [INFO] Query marker FASTA was written to GCF_000218875.1_ASM21887v1_genomic.fna/markers.fasta
[2024-01-24 12:22:20,973] [INFO] Task started: Blastn
[2024-01-24 12:22:20,973] [INFO] Running command: blastn -query GCF_000218875.1_ASM21887v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcc3485bf-7a5f-460e-8e77-cc32363a8c2b/dqc_reference/reference_markers.fasta -out GCF_000218875.1_ASM21887v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:21,633] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:21,637] [INFO] Selected 20 target genomes.
[2024-01-24 12:22:21,638] [INFO] Target genome list was writen to GCF_000218875.1_ASM21887v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:21,683] [INFO] Task started: fastANI
[2024-01-24 12:22:21,683] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ccd40a3-834a-4ae1-bea7-60b5605b43f7/GCF_000218875.1_ASM21887v1_genomic.fna.gz --refList GCF_000218875.1_ASM21887v1_genomic.fna/target_genomes.txt --output GCF_000218875.1_ASM21887v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:33,144] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:33,144] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcc3485bf-7a5f-460e-8e77-cc32363a8c2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:33,145] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcc3485bf-7a5f-460e-8e77-cc32363a8c2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:33,149] [INFO] Found 2 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:22:33,149] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:33,149] [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
Zymomonas mobilis subsp. pomaceae	strain=ATCC 29192	GCA_000218875.1	120044	542	type	True	100.0	683	686	95	conclusive
Zymomonas mobilis subsp. pomaceae	strain=NBRC 13757	GCA_006539385.1	120044	542	type	True	99.9767	658	686	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 12:22:33,151] [INFO] DFAST Taxonomy check result was written to GCF_000218875.1_ASM21887v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:33,151] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:33,151] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:33,152] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcc3485bf-7a5f-460e-8e77-cc32363a8c2b/dqc_reference/checkm_data
[2024-01-24 12:22:33,153] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:33,183] [INFO] Task started: CheckM
[2024-01-24 12:22:33,184] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000218875.1_ASM21887v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000218875.1_ASM21887v1_genomic.fna/checkm_input GCF_000218875.1_ASM21887v1_genomic.fna/checkm_result
[2024-01-24 12:22:55,762] [INFO] Task succeeded: CheckM
[2024-01-24 12:22:55,763] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:22:55,784] [INFO] ===== Completeness check finished =====
[2024-01-24 12:22:55,785] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:22:55,785] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000218875.1_ASM21887v1_genomic.fna/markers.fasta)
[2024-01-24 12:22:55,786] [INFO] Task started: Blastn
[2024-01-24 12:22:55,786] [INFO] Running command: blastn -query GCF_000218875.1_ASM21887v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcc3485bf-7a5f-460e-8e77-cc32363a8c2b/dqc_reference/reference_markers_gtdb.fasta -out GCF_000218875.1_ASM21887v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:56,863] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:56,869] [INFO] Selected 18 target genomes.
[2024-01-24 12:22:56,869] [INFO] Target genome list was writen to GCF_000218875.1_ASM21887v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:22:56,885] [INFO] Task started: fastANI
[2024-01-24 12:22:56,885] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ccd40a3-834a-4ae1-bea7-60b5605b43f7/GCF_000218875.1_ASM21887v1_genomic.fna.gz --refList GCF_000218875.1_ASM21887v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000218875.1_ASM21887v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:05,585] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:05,589] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:05,590] [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_000218875.1	s__Zymomonas pomaceae	100.0	683	686	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Zymomonas	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_006715975.1	s__Zymomonas mobilis_B	79.4869	283	686	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Zymomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000175255.2	s__Zymomonas mobilis	79.2224	284	686	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Zymomonas	95.0	98.43	96.89	0.96	0.93	26	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:05,591] [INFO] GTDB search result was written to GCF_000218875.1_ASM21887v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:05,592] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:05,595] [INFO] DFAST_QC result json was written to GCF_000218875.1_ASM21887v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:05,595] [INFO] DFAST_QC completed!
[2024-01-24 12:23:05,595] [INFO] Total running time: 0h0m52s