[2024-01-24 12:45:10,388] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:45:10,390] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:45:10,390] [INFO] DQC Reference Directory: /var/lib/cwl/stg6c19edd9-b4c5-4a8f-8fb7-e15069c9d68b/dqc_reference
[2024-01-24 12:45:13,088] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:45:13,089] [INFO] Task started: Prodigal
[2024-01-24 12:45:13,089] [INFO] Running command: gunzip -c /var/lib/cwl/stg1547cdd8-a688-45b7-8832-18d83f483e86/GCF_028869115.1_ASM2886911v1_genomic.fna.gz | prodigal -d GCF_028869115.1_ASM2886911v1_genomic.fna/cds.fna -a GCF_028869115.1_ASM2886911v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:22,150] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:22,151] [INFO] Task started: HMMsearch
[2024-01-24 12:45:22,151] [INFO] Running command: hmmsearch --tblout GCF_028869115.1_ASM2886911v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6c19edd9-b4c5-4a8f-8fb7-e15069c9d68b/dqc_reference/reference_markers.hmm GCF_028869115.1_ASM2886911v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:22,417] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:22,419] [INFO] Found 6/6 markers.
[2024-01-24 12:45:22,455] [INFO] Query marker FASTA was written to GCF_028869115.1_ASM2886911v1_genomic.fna/markers.fasta
[2024-01-24 12:45:22,456] [INFO] Task started: Blastn
[2024-01-24 12:45:22,456] [INFO] Running command: blastn -query GCF_028869115.1_ASM2886911v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c19edd9-b4c5-4a8f-8fb7-e15069c9d68b/dqc_reference/reference_markers.fasta -out GCF_028869115.1_ASM2886911v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:23,141] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:23,145] [INFO] Selected 22 target genomes.
[2024-01-24 12:45:23,146] [INFO] Target genome list was writen to GCF_028869115.1_ASM2886911v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:23,963] [INFO] Task started: fastANI
[2024-01-24 12:45:23,964] [INFO] Running command: fastANI --query /var/lib/cwl/stg1547cdd8-a688-45b7-8832-18d83f483e86/GCF_028869115.1_ASM2886911v1_genomic.fna.gz --refList GCF_028869115.1_ASM2886911v1_genomic.fna/target_genomes.txt --output GCF_028869115.1_ASM2886911v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:36,160] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:36,161] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6c19edd9-b4c5-4a8f-8fb7-e15069c9d68b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:36,161] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6c19edd9-b4c5-4a8f-8fb7-e15069c9d68b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:36,169] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:45:36,169] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:36,169] [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
Pseudemcibacter aquimaris	strain=Y4	GCA_020748165.1	2857064	2857064	type	True	99.9834	1104	1123	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 12:45:36,171] [INFO] DFAST Taxonomy check result was written to GCF_028869115.1_ASM2886911v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:36,175] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:36,175] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:36,175] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6c19edd9-b4c5-4a8f-8fb7-e15069c9d68b/dqc_reference/checkm_data
[2024-01-24 12:45:36,177] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:36,234] [INFO] Task started: CheckM
[2024-01-24 12:45:36,234] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028869115.1_ASM2886911v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028869115.1_ASM2886911v1_genomic.fna/checkm_input GCF_028869115.1_ASM2886911v1_genomic.fna/checkm_result
[2024-01-24 12:46:08,489] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:08,491] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:08,516] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:08,516] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:08,517] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028869115.1_ASM2886911v1_genomic.fna/markers.fasta)
[2024-01-24 12:46:08,517] [INFO] Task started: Blastn
[2024-01-24 12:46:08,517] [INFO] Running command: blastn -query GCF_028869115.1_ASM2886911v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c19edd9-b4c5-4a8f-8fb7-e15069c9d68b/dqc_reference/reference_markers_gtdb.fasta -out GCF_028869115.1_ASM2886911v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:09,562] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:09,567] [INFO] Selected 22 target genomes.
[2024-01-24 12:46:09,567] [INFO] Target genome list was writen to GCF_028869115.1_ASM2886911v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:09,627] [INFO] Task started: fastANI
[2024-01-24 12:46:09,627] [INFO] Running command: fastANI --query /var/lib/cwl/stg1547cdd8-a688-45b7-8832-18d83f483e86/GCF_028869115.1_ASM2886911v1_genomic.fna.gz --refList GCF_028869115.1_ASM2886911v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028869115.1_ASM2886911v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:21,049] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:21,055] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:46:21,056] [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_002390425.1	s__UBA4441 sp002390425	78.6434	297	1123	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Emcibacteraceae;g__UBA4441	95.0	99.08	99.08	0.89	0.89	2	-
GCA_018660225.1	s__UBA4441 sp018660225	77.2523	241	1123	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Emcibacteraceae;g__UBA4441	95.0	99.68	99.64	0.89	0.88	3	-
GCA_016763335.1	s__UBA4441 sp016763335	76.9972	192	1123	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Emcibacteraceae;g__UBA4441	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018675425.1	s__UBA4441 sp018675425	76.9725	79	1123	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Emcibacteraceae;g__UBA4441	95.0	99.54	99.14	0.91	0.86	6	-
GCA_018699075.1	s__UBA4441 sp018699075	76.8522	175	1123	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Emcibacteraceae;g__UBA4441	95.0	99.25	99.25	0.75	0.75	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:21,057] [INFO] GTDB search result was written to GCF_028869115.1_ASM2886911v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:21,058] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:21,060] [INFO] DFAST_QC result json was written to GCF_028869115.1_ASM2886911v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:21,061] [INFO] DFAST_QC completed!
[2024-01-24 12:46:21,061] [INFO] Total running time: 0h1m11s