sortmerna output

E:\Gut MTX>sortmerna -ref rRNA_database\smr_v4.3_default_db.fasta -reads reads_fastq\SRR5947903\SRR5947903_1.fastq -reads reads_fastq\SRR5947903\SRR5947903_2.fastq -fastx -other -paired_out -threads 8
[process:1393] === Options processing starts ... ===
Found value: sortmerna
Found flag: -ref
Found value: rRNA_database\smr_v4.3_default_db.fasta of previous flag: -ref
Found flag: -reads
Found value: reads_fastq\SRR5947903\SRR5947903_1.fastq of previous flag: -reads
Found flag: -reads
Found value: reads_fastq\SRR5947903\SRR5947903_2.fastq of previous flag: -reads
Found flag: -fastx
Previous flag: -fastx is Boolean. Setting to True
Found flag: -other
Previous flag: -other is Boolean. Setting to True
Found flag: -paired_out
Previous flag: -paired_out is Boolean. Setting to True
Found flag: -threads
Found value: 8 of previous flag: -threads
[process:1483] Processing option: fastx with value:
[process:1483] Processing option: other with value:
[opt_other:268] other was specified without argument. Will use default Directory and Prefix for the non-aligned output.
[process:1483] Processing option: paired_out with value:
[process:1483] Processing option: reads with value: reads_fastq\SRR5947903\SRR5947903_1.fastq
[opt_reads:98] Processing reads file [1] out of total [2] files
[process:1483] Processing option: reads with value: reads_fastq\SRR5947903\SRR5947903_2.fastq
[opt_reads:98] Processing reads file [2] out of total [2] files
[process:1483] Processing option: ref with value: rRNA_database\smr_v4.3_default_db.fasta
[opt_ref:158] Processing reference [1] out of total [1] references
[opt_ref:206] File "E:\\Gut MTX\\rRNA_database\\smr_v4.3_default_db.fasta" exists and is readable
[process:1483] Processing option: threads with value: 8
[process:1503] === Options processing done ===
[process:1506] Alignment type: [best:1 num_alignments:1 min_lis:2 seeds:2]
[validate_kvdbdir:1242] 'workdir' option was not provided. Using USERDIR to set the working directory: ""
[validate_kvdbdir:1248] Key-value DB location "C:\\Users\\rosko\\sortmerna\\run\\kvdb"
[validate_idxdir:1214] Using index directory: "C:\\Users\\rosko\\sortmerna\\run\\idx"
[validate_idxdir:1230] IDX directory: "C:\\Users\\rosko\\sortmerna\\run\\idx" exists and is not empty
[validate_readb_dir:1306] Using split reads directory : "C:\\Users\\rosko\\sortmerna\\run\\readb"
[validate_readb_dir:1322] split reads directory : "C:\\Users\\rosko\\sortmerna\\run\\readb" exists and is not empty
[main:62] Running command:
sortmerna -ref rRNA_database\smr_v4.3_default_db.fasta -reads reads_fastq\SRR5947903\SRR5947903_1.fastq -reads reads_fastq\SRR5947903\SRR5947903_2.fastq -fastx -other -paired_out -threads 8
[Index:102] Found 4 non-empty index files. Skipping indexing.
[init:108] Readfeed init started
[define_format:881] file: "reads_fastq/SRR5947903/SRR5947903_1.fastq" is FASTQ flat ASCII
[define_format:881] file: "reads_fastq/SRR5947903/SRR5947903_2.fastq" is FASTQ flat ASCII
[count_reads:915] started count  ...
[next:322] EOF REV reached. Total reads: 7189805
[count_reads:945] done count. Elapsed time: 47.0337 sec. Total reads: 14379611
[init_split_files:967] added file: C:/Users/rosko/sortmerna/run/readb/fwd_0.fq
[init_split_files:967] added file: C:/Users/rosko/sortmerna/run/readb/rev_0.fq
[init_split_files:967] added file: C:/Users/rosko/sortmerna/run/readb/fwd_1.fq
[init_split_files:967] added file: C:/Users/rosko/sortmerna/run/readb/rev_1.fq
[init_split_files:967] added file: C:/Users/rosko/sortmerna/run/readb/fwd_2.fq
[init_split_files:967] added file: C:/Users/rosko/sortmerna/run/readb/rev_2.fq
[init_split_files:967] added file: C:/Users/rosko/sortmerna/run/readb/fwd_3.fq
[init_split_files:967] added file: C:/Users/rosko/sortmerna/run/readb/rev_3.fq
[init_split_files:967] added file: C:/Users/rosko/sortmerna/run/readb/fwd_4.fq
[init_split_files:967] added file: C:/Users/rosko/sortmerna/run/readb/rev_4.fq
[init_split_files:967] added file: C:/Users/rosko/sortmerna/run/readb/fwd_5.fq
[init_split_files:967] added file: C:/Users/rosko/sortmerna/run/readb/rev_5.fq
[init_split_files:967] added file: C:/Users/rosko/sortmerna/run/readb/fwd_6.fq
[init_split_files:967] added file: C:/Users/rosko/sortmerna/run/readb/rev_6.fq
[init_split_files:967] added file: C:/Users/rosko/sortmerna/run/readb/fwd_7.fq
[init_split_files:967] added file: C:/Users/rosko/sortmerna/run/readb/rev_7.fq
[is_split_ready:726] found existing readfeed descriptor C:/Users/rosko/sortmerna/run/readb/readfeed
[split:605] start splitting. Using number of splits equals number of processing threads: 8
[clean:1098] found descriptor C:/Users/rosko/sortmerna/run/readb/readfeed
[clean:1142] removing split file: C:/Users/rosko/sortmerna/run/readb/fwd_0.fq
[clean:1142] removing split file: C:/Users/rosko/sortmerna/run/readb/rev_0.fq
[clean:1142] removing split file: C:/Users/rosko/sortmerna/run/readb/fwd_1.fq
[clean:1142] removing split file: C:/Users/rosko/sortmerna/run/readb/rev_1.fq
[clean:1142] removing split file: C:/Users/rosko/sortmerna/run/readb/fwd_2.fq
[clean:1142] removing split file: C:/Users/rosko/sortmerna/run/readb/rev_2.fq
[clean:1142] removing split file: C:/Users/rosko/sortmerna/run/readb/fwd_3.fq
[clean:1142] removing split file: C:/Users/rosko/sortmerna/run/readb/rev_3.fq
[clean:1142] removing split file: C:/Users/rosko/sortmerna/run/readb/fwd_4.fq
[clean:1142] removing split file: C:/Users/rosko/sortmerna/run/readb/rev_4.fq
[clean:1142] removing split file: C:/Users/rosko/sortmerna/run/readb/fwd_5.fq
[clean:1142] removing split file: C:/Users/rosko/sortmerna/run/readb/rev_5.fq
[clean:1142] removing split file: C:/Users/rosko/sortmerna/run/readb/fwd_6.fq
[clean:1142] removing split file: C:/Users/rosko/sortmerna/run/readb/rev_6.fq
[clean:1142] removing split file: C:/Users/rosko/sortmerna/run/readb/fwd_7.fq
[clean:1142] removing split file: C:/Users/rosko/sortmerna/run/readb/rev_7.fq
[next:322] EOF REV reached. Total reads: 7189805