some samtools command does not use -@ parameter

[songlyzz]

Hi，
tianxiong
Recently，I used your software and when I run the test command that I found there is something wrong with samtools below above：

------ Start pipeline ------
bam file not specified, map raw reads tp genome via bwa mem Wed Jun 28 15:27:25 CST 2023
transform sam to sorted bam and index it Wed Jun 28 15:27:27 CST 2023
get concordant-uniq-split reads Wed Jun 28 15:27:30 CST 2023
[M::bam2fq_mainloop] processed 0 reads
check fragment length Wed Jun 28 15:27:32 CST 2023
insert size set to 95 quantile: 458
get mate seq of the uniq-unpaired Wed Jun 28 15:27:33 CST 2023
fastq: invalid option -- '@'
Usage: samtools fastq [options...] <in.bam>
Options:
-0 FILE write paired reads flagged both or neither READ1 and READ2 to FILE
-1 FILE write paired reads flagged READ1 to FILE
-2 FILE write paired reads flagged READ2 to FILE
-f INT only include reads with all bits set in INT set in FLAG [0]
-F INT only include reads with none of the bits set in INT set in FLAG [0]
-n don't append /1 and /2 to the read name
-O output quality in the OQ tag if present
-s FILE write singleton reads to FILE [assume single-end]
-t copy RG, BC and QT tags to the FASTQ header line
-v INT default quality score if not given in file [1]
--input-fmt-option OPT[=VAL]
Specify a single input file format option in the form
of OPTION or OPTION=VALUE
--reference FILE
Reference sequence FASTA FILE [null]
map paired split uniqMappers and unpaired uniqMappers to transposons Wed Jun 28 15:27:34 CST 2023
merge fragments in genome and transposon Wed Jun 28 15:27:34 CST 2023
mytest.t is empty
merge support reads in the same direction within 458 - Wed Jun 28 15:27:35 CST 2023
expr: syntax error
/TEMP2/bin/TEMP2_insertion.sh: line 208: [: -lt: unary operator expected
sort: cannot read: mytest.supportReads/*.bed: No such file or directory

It is that samtools fastq and index now did not use the parameter -@ so it can not run，hope you can advise this mistake.

[songlyzz]

Meanwhile, If I want to run hg38 genome, I don't find the TE fasta file and TE bed file, and when I use the rmsk file download from (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/rmsk.txt.gz) ,I find it is different with the rmsk.bed with each column mean. It would be great if you were able to provide reference files in the github.

[tianxiongbb]

Hi, only recent version of samtools support multithread (the -@ parameter) in some of its modules. Please re-install your samtools and make sure its version is >=1.9. You can make a conda environment to avoid conflict with your current samtools.