Problem with grep on multiple files and not getting desired output

I am using the below command on a file to extract few lines based on chr# ( different chromosome numbers). This is just a single file am working on. i have 8 such files and for each file I have to do this for chr(1to 22 and then chrX and chrY) , am not using any loop, I did it invidually , but if you see that I want the header to be intact for each of my output. If I execute individually I get the header in the output but if am running but if I run the script for all the 8 files together which is like 8*24 commands in a script one after another, the output does not have any header. Can you tell me why is this happening? #!/bin/sh # #$ -N DOC_gatk_chr #$ -cwd #$ -e err_DOC_gatk_chr.txt #$ -o out_DOC_gatk_chr.txt #$ -S /bin/sh #$ -M vivek.das@ieo.eu #$ -m bea #$ -l h_vmem=25G more S_313_IPS_S7995.coverage.sample_interval_summary | head -n1; more S_313_IPS_S7995.coverage.sample_interval_summary | grep "chr1" > S_313_IPS_S7995.chr1.coverage more S_313_IPS_S7995.coverage.sample_interval_summary | head -n1; more S_313_IPS_S7995.coverage.sample_interval_summary | grep "chr2" > S_313_IPS_S7995.chr2.coverage more S_313_IPS_S7995.coverage.sample_interval_summary | head -n1; more S_313_IPS_S7995.coverage.sample_interval_summary | grep "chr3" > S_313_IPS_S7995.chr3.coverage more S_313_IPS_S7995.coverage.sample_interval_summary | head -n1; more S_313_IPS_S7995.coverage.sample_interval_summary | grep "chr4" > S_313_IPS_S7995.chr4.coverage more S_313_IPS_S7995.coverage.sample_interval_summary | head -n1; more S_313_IPS_S7995.coverage.sample_interval_summary | grep "chr5" > S_313_IPS_S7995.chr5.coverage more S_313_IPS_S7995.coverage.sample_interval_summary | head -n1; more S_313_IPS_S7995.coverage.sample_interval_summary | grep "chr6" > S_313_IPS_S7995.chr6.coverage more S_313_IPS_S7995.coverage.sample_interval_summary | head -n1; more S_313_IPS_S7995.coverage.sample_interval_summary | grep "chr7" > S_313_IPS_S7995.chr7.coverage more S_313_IPS_S7995.coverage.sample_interval_summary | head -n1; more S_313_IPS_S7995.coverage.sample_interval_summary | grep "chr8" > S_313_IPS_S7995.chr8.coverage more S_313_IPS_S7995.coverage.sample_interval_summary | head -n1; more S_313_IPS_S7995.coverage.sample_interval_summary | grep "chr9" > S_313_IPS_S7995.chr9.coverage Am running it as a job with qsub so the structure of the script looks like above. It works if I execute the commands individually but if I run them like this , the header does not get printed in the output file, the ';' is not recognized it seems. I tried to ran it with both qsub filename.sh and sh filename.sh. I found that with sh filename.sh the header gets printed in the console. So definitely the command before';' semi-colon is not being written in the file. How can I get rid of this problem. Desired output: Target total_coverage average_coverage IPS_S7995_total_cvg IPS_S7995_mean_cvg IPS_S7995_granular_Q1 IPS_S7995_granular_median IPS_S7995_granular_Q3 IPS_S7995_%_above_15 chr2:41460-41683 14271 63.71 14271 63.71 56 67 79 100.0 chr2:45338-46352 123888 122.06 123888 122.06 79 123 147 94.6 chr2:218731-218983 11653 46.06 11653 46.06 36 50 55 100.0 chr2:224825-225012 12319 65.53 12319 65.53 57 68 76 100.0 chr2:229912-230090 20983 117.22 20983 117.22 93 120 147 100.0 chr2:230947-231137 22386 117.20 22386 117.20 100 120 139 100.0 chr2:233074-233258 11710 63.30 11710 63.30 54 66 73 100.0 chr2:234086-234300 22952 106.75 22952 106.75 91 113 126 100.0 chr2:242747-242922 20496 116.45 20496 116.45 93 124 142 100.0 chr2:243469-243671 27074 133.37 27074 133.37 126 138 148 100.0 But output am getting is below without the header chr2:41460-41683 14271 63.71 14271 63.71 56 67 79 100.0 chr2:45338-46352 123888 122.06 123888 122.06 79 123 147 94.6 chr2:218731-218983 11653 46.06 11653 46.06 36 50 55 100.0 chr2:224825-225012 12319 65.53 12319 65.53 57 68 76 100.0 chr2:229912-230090 20983 117.22 20983 117.22 93 120 147 100.0 chr2:230947-231137 22386 117.20 22386 117.20 100 120 139 100.0 chr2:233074-233258 11710 63.30 11710 63.30 54 66 73 100.0 chr2:234086-234300 22952 106.75 22952 106.75 91 113 126 100.0 chr2:242747-242922 20496 116.45 20496 116.45 93 124 142 100.0 chr2:243469-243671 27074 133.37 27074 133.37 126 138 148 100.0