[2023-06-19 08:34:05,499] [INFO] DFAST_QC pipeline started.
[2023-06-19 08:34:05,502] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 08:34:05,502] [INFO] DQC Reference Directory: /var/lib/cwl/stg6b4a04f9-d9ba-4efc-8d34-c638a09ed39a/dqc_reference
[2023-06-19 08:34:06,703] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 08:34:06,704] [INFO] Task started: Prodigal
[2023-06-19 08:34:06,704] [INFO] Running command: gunzip -c /var/lib/cwl/stgc0070756-ac63-4d16-8651-bac9b74ebd08/GCA_018002875.1_ASM1800287v1_genomic.fna.gz | prodigal -d GCA_018002875.1_ASM1800287v1_genomic.fna/cds.fna -a GCA_018002875.1_ASM1800287v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 08:34:08,266] [INFO] Task succeeded: Prodigal
[2023-06-19 08:34:08,267] [INFO] Task started: HMMsearch
[2023-06-19 08:34:08,267] [INFO] Running command: hmmsearch --tblout GCA_018002875.1_ASM1800287v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6b4a04f9-d9ba-4efc-8d34-c638a09ed39a/dqc_reference/reference_markers.hmm GCA_018002875.1_ASM1800287v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 08:34:08,423] [INFO] Task succeeded: HMMsearch
[2023-06-19 08:34:08,425] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgc0070756-ac63-4d16-8651-bac9b74ebd08/GCA_018002875.1_ASM1800287v1_genomic.fna.gz]
[2023-06-19 08:34:08,440] [INFO] Query marker FASTA was written to GCA_018002875.1_ASM1800287v1_genomic.fna/markers.fasta
[2023-06-19 08:34:08,440] [INFO] Task started: Blastn
[2023-06-19 08:34:08,441] [INFO] Running command: blastn -query GCA_018002875.1_ASM1800287v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b4a04f9-d9ba-4efc-8d34-c638a09ed39a/dqc_reference/reference_markers.fasta -out GCA_018002875.1_ASM1800287v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:34:09,017] [INFO] Task succeeded: Blastn
[2023-06-19 08:34:09,023] [INFO] Selected 17 target genomes.
[2023-06-19 08:34:09,024] [INFO] Target genome list was writen to GCA_018002875.1_ASM1800287v1_genomic.fna/target_genomes.txt
[2023-06-19 08:34:09,028] [INFO] Task started: fastANI
[2023-06-19 08:34:09,028] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0070756-ac63-4d16-8651-bac9b74ebd08/GCA_018002875.1_ASM1800287v1_genomic.fna.gz --refList GCA_018002875.1_ASM1800287v1_genomic.fna/target_genomes.txt --output GCA_018002875.1_ASM1800287v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 08:34:19,802] [INFO] Task succeeded: fastANI
[2023-06-19 08:34:19,802] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6b4a04f9-d9ba-4efc-8d34-c638a09ed39a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 08:34:19,803] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6b4a04f9-d9ba-4efc-8d34-c638a09ed39a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 08:34:19,809] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2023-06-19 08:34:19,809] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-19 08:34:19,809] [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
Fluviibacter phosphoraccumulans	strain=SHINM1	GCA_016110345.1	1751046	1751046	type	True	98.3863	134	146	95	conclusive
--------------------------------------------------------------------------------
[2023-06-19 08:34:19,812] [INFO] DFAST Taxonomy check result was written to GCA_018002875.1_ASM1800287v1_genomic.fna/tc_result.tsv
[2023-06-19 08:34:19,813] [INFO] ===== Taxonomy check completed =====
[2023-06-19 08:34:19,813] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 08:34:19,813] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6b4a04f9-d9ba-4efc-8d34-c638a09ed39a/dqc_reference/checkm_data
[2023-06-19 08:34:19,814] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 08:34:19,827] [INFO] Task started: CheckM
[2023-06-19 08:34:19,828] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018002875.1_ASM1800287v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018002875.1_ASM1800287v1_genomic.fna/checkm_input GCA_018002875.1_ASM1800287v1_genomic.fna/checkm_result
[2023-06-19 08:34:32,704] [INFO] Task succeeded: CheckM
[2023-06-19 08:34:32,705] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 32.18%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 08:34:32,729] [INFO] ===== Completeness check finished =====
[2023-06-19 08:34:32,729] [INFO] ===== Start GTDB Search =====
[2023-06-19 08:34:32,730] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018002875.1_ASM1800287v1_genomic.fna/markers.fasta)
[2023-06-19 08:34:32,730] [INFO] Task started: Blastn
[2023-06-19 08:34:32,730] [INFO] Running command: blastn -query GCA_018002875.1_ASM1800287v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b4a04f9-d9ba-4efc-8d34-c638a09ed39a/dqc_reference/reference_markers_gtdb.fasta -out GCA_018002875.1_ASM1800287v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:34:33,489] [INFO] Task succeeded: Blastn
[2023-06-19 08:34:33,493] [INFO] Selected 11 target genomes.
[2023-06-19 08:34:33,493] [INFO] Target genome list was writen to GCA_018002875.1_ASM1800287v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 08:34:33,502] [INFO] Task started: fastANI
[2023-06-19 08:34:33,502] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0070756-ac63-4d16-8651-bac9b74ebd08/GCA_018002875.1_ASM1800287v1_genomic.fna.gz --refList GCA_018002875.1_ASM1800287v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018002875.1_ASM1800287v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 08:34:37,801] [INFO] Task succeeded: fastANI
[2023-06-19 08:34:37,807] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 08:34:37,807] [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_016110345.1	s__Fluviibacter phosphoraccumulans	98.3863	134	146	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Fluviibacter	95.0	99.06	98.97	0.90	0.90	3	conclusive
GCA_903870055.1	s__Fluviibacter sp903870055	84.6239	115	146	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Fluviibacter	95.0	99.89	99.89	0.98	0.98	2	-
GCA_018883265.1	s__Fluviibacter sp018883265	80.0242	77	146	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Fluviibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018883385.1	s__Fluviibacter sp018883385	80.0224	66	146	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Fluviibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 08:34:37,809] [INFO] GTDB search result was written to GCA_018002875.1_ASM1800287v1_genomic.fna/result_gtdb.tsv
[2023-06-19 08:34:37,810] [INFO] ===== GTDB Search completed =====
[2023-06-19 08:34:37,813] [INFO] DFAST_QC result json was written to GCA_018002875.1_ASM1800287v1_genomic.fna/dqc_result.json
[2023-06-19 08:34:37,813] [INFO] DFAST_QC completed!
[2023-06-19 08:34:37,814] [INFO] Total running time: 0h0m32s