Thanks for the advice! I am currently working on nextflow wrapping of the script. Coming back to my problem, I am attaching an stdout snippet below:
Running FASTP
fastp --thread=50 --length_required=10 --qualified_quality_phred=32 --in1=/home/cluster/nath/run6/query/fastq/SRR10333577_1.fastq.gz --in2=/home/cluster/nath/run6/query/fastq/SRR10333577_2.fastq.gz --out1=SRR10333577_1_trimmed.fastq.gz --out2=SRR10333577_2_trimmed.fastq.gz --json=SRR10333577_1.json --html=SRR10333577_1.html
fastp v0.20.0, time used: 231 seconds
Running FASTQC
Started analysis of SRR10333577_1_trimmed.fastq.gz
Started analysis of SRR10333577_2_trimmed.fastq.gz
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Running HISAT2
Settings:
Output files: "index.*.ht2"
Line rate: 6 (line is 64 bytes)
Lines per side: 1 (side is 64 bytes)
Offset rate: 4 (one in 16)
FTable chars: 10
Strings: unpacked
Local offset rate: 3 (one in 8)
Local fTable chars: 6
Local sequence length: 57344
Local sequence overlap between two consecutive indexes: 1024
Endianness: little
Actual local endianness: little
Sanity checking: disabled
Assertions: disabled
Random seed: 0
Sizeofs: void*:8, int:4, long:8, size_t:8
Input files DNA, FASTA:
/home/cluster/nath/run6/query/ref_fa//ref.fa
Reading reference sizes
Time reading reference sizes: 00:00:25
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
Time to join reference sequences: 00:00:15
Time to read SNPs and splice sites: 00:00:00
Using parameters --bmax 582334929 --dcv 1024
Doing ahead-of-time memory usage test
Passed! Constructing with these parameters: --bmax 582334929 --dcv 1024
Constructing suffix-array element generator
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering GFM loop
I want all the stdout (including the echo points) to be saved to an external text file. I would be much obliged to get a detailed or semi-detailed idea on how to do that. Thanks!