Hello,I meet a problem:bash -x testBam2FastQ.sh and bash -x testMergeBam.sh failed on centos8_aarch64
aarch64:
[root@localhost test]# bash -x testMergeBam.sh
+ ERROR=false
+ ../bin/bam mergeBam --out results/mergeBam.bam --list testFiles/mergeBam.list --noph
Unrecognized option nophonehome
+ '[' 255 -ne 0 ']'
+ ERROR=true
+ diff results/mergeBam.bam expected/mergeBam.bam
diff: results/mergeBam.bam: No such file or directory
+ '[' 2 -ne 0 ']'
+ ERROR=true
+ ../bin/bam mergeBam -o results/mergeSam.sam -l testFiles/mergeSam.list --noph
Unrecognized option nophonehome
+ '[' 255 -ne 0 ']'
+ ERROR=true
+ diff results/mergeSam.sam expected/mergeSam.sam
diff: results/mergeSam.sam: No such file or directory
+ '[' 2 -ne 0 ']'
+ ERROR=true
+ ../bin/bam mergeBam -o results/mergeSam1.sam -i testFiles/sortedSam.sam -i testFiles/sortedSam1.sam --noph
Unrecognized option nophonehome
+ '[' 255 -ne 0 ']'
+ ERROR=true
+ diff results/mergeSam1.sam expected/mergeSam1.sam
diff: results/mergeSam1.sam: No such file or directory
+ '[' 2 -ne 0 ']'
+ ERROR=true
+ ../bin/bam mergeBam -o results/mergeSam2.sam -i testFiles/sortedSam1.sam -i testFiles/sortedSam.sam --noph
Unrecognized option nophonehome
+ '[' 255 -ne 0 ']'
+ ERROR=true
+ diff results/mergeSam2.sam expected/mergeSam2.sam
diff: results/mergeSam2.sam: No such file or directory
+ '[' 2 -ne 0 ']'
+ ERROR=true
+ ../bin/bam mergeBam -o results/mergeSam3.sam -i testFiles/sortedSam.sam -i testFiles/sortedSam.sam --noph
Unrecognized option nophonehome
+ '[' 255 -ne 0 ']'
+ ERROR=true
+ diff results/mergeSam3.sam expected/mergeSam3.sam
diff: results/mergeSam3.sam: No such file or directory
+ '[' 2 -ne 0 ']'
+ ERROR=true
+ ../bin/bam mergeBam -o results/mergeSam4.sam -i testFiles/sortedSam.sam -i testFiles/sortedSam2.sam --noph
+ '[' 255 -eq 0 ']'
+ '[' -e results/mergeSam4.sam ']'
+ diff results/mergeSam4.log expected/mergeSam4.log
1c1,11
< Unrecognized option nophonehome
---
> ERROR : Failed to add readgroup to header, duplicate, but non-identical RG ID, myID2
> prev: (@RG ID:myID2 SM:sample2 LB:library2
> )
> new: (@RG ID:myID2 SM:sample24 LB:library2
> )
> Exiting due to ERROR:
> ERROR: Failed to add readgroup to header, duplicate, but non-identical RG ID, myID2
> prev: (@RG ID:myID2 SM:sample2 LB:library2
> )
> new: (@RG ID:myID2 SM:sample24 LB:library2
> )
+ '[' 1 -ne 0 ']'
+ ERROR=true
+ ../bin/bam mergeBam -o results/mergeSamPI.sam -i testFiles/sortedSam.sam -i testFiles/sortedSamPI.sam --ignorePI --noph
Unrecognized option nophonehome
+ '[' 255 -ne 0 ']'
+ ERROR=true
+ diff results/mergeSamPI.sam expected/mergeSam3.sam
diff: results/mergeSamPI.sam: No such file or directory
+ '[' 2 -ne 0 ']'
+ ERROR=true
+ ../bin/bam mergeBam -o results/mergeSamPI4.sam -i testFiles/sortedSamPI.sam -i testFiles/sortedSam2.sam -I --noph
+ '[' 255 -eq 0 ']'
+ '[' -e results/mergeSamPI4.sam ']'
+ diff results/mergeSamPI4.log expected/mergeSam4PI.log
1c1,11
< Unrecognized option nophonehome
---
> ERROR : Failed to add readgroup to header, duplicate, but non-identical RG ID, myID2, even when ignoring PI
> prev: (@RG ID:myID2 SM:sample2 PI:500 LB:library2
> )
> new: (@RG ID:myID2 SM:sample24 LB:library2
> )
> Exiting due to ERROR:
> ERROR: Failed to add readgroup to header, duplicate, but non-identical RG ID, myID2, even when ignoring PI
> prev: (@RG ID:myID2 SM:sample2 PI:500 LB:library2
> )
> new: (@RG ID:myID2 SM:sample24 LB:library2
> )
+ '[' 1 -ne 0 ']'
+ ERROR=true
+ ../bin/bam mergeBam -o results/mergeSamPI1.sam -i testFiles/sortedSamPI1.sam -i testFiles/sortedSamPI.sam -I --noph
Unrecognized option nophonehome
+ '[' 255 -ne 0 ']'
+ ERROR=true
+ diff results/mergeSamPI1.sam expected/mergeSamPI1.sam
diff: results/mergeSamPI1.sam: No such file or directory
+ '[' 2 -ne 0 ']'
+ ERROR=true
+ ../bin/bam mergeBam -o results/mergeSamBeforePIfail.sam -i testFiles/sortedSamPI.sam -i testFiles/sortedSamPI2.sam -I --noph
+ '[' 255 -eq 0 ']'
+ '[' -e results/mergeSamBeforePIfail.sam ']'
+ diff results/mergeSamBeforePIfail.log expected/mergeSamPI_2.log
1c1,11
< Unrecognized option nophonehome
---
> ERROR : Failed to add readgroup to header, duplicate, but non-identical RG ID, myID2, even when ignoring PI
> prev: (@RG ID:myID2 SM:sample2 PI:500 LB:library2
> )
> new: (@RG ID:myID2 SM:sample22 PI:500 LB:library2
> )
> Exiting due to ERROR:
> ERROR: Failed to add readgroup to header, duplicate, but non-identical RG ID, myID2, even when ignoring PI
> prev: (@RG ID:myID2 SM:sample2 PI:500 LB:library2
> )
> new: (@RG ID:myID2 SM:sample22 PI:500 LB:library2
> )
+ '[' 1 -ne 0 ']'
+ ERROR=true
+ ../bin/bam mergeBam -o results/mergeSamAfterPIfail.sam -i testFiles/sortedSamPI.sam -i testFiles/sortedSamPI3.sam -I --noph
+ '[' 255 -eq 0 ']'
+ '[' -e results/mergeSamAfterPIfail.sam ']'
+ diff results/mergeSamAfterPIfail.log expected/mergeSamPI_3.log
1c1,11
< Unrecognized option nophonehome
---
> ERROR : Failed to add readgroup to header, duplicate, but non-identical RG ID, myID2, even when ignoring PI
> prev: (@RG ID:myID2 SM:sample2 PI:500 LB:library2
> )
> new: (@RG ID:myID2 SM:sample2 PI:500 LB:library22
> )
> Exiting due to ERROR:
> ERROR: Failed to add readgroup to header, duplicate, but non-identical RG ID, myID2, even when ignoring PI
> prev: (@RG ID:myID2 SM:sample2 PI:500 LB:library2
> )
> new: (@RG ID:myID2 SM:sample2 PI:500 LB:library22
> )
+ '[' 1 -ne 0 ']'
+ ERROR=true
+ ../bin/bam mergeBam -o results/mergeSamPIfail.sam -i testFiles/sortedSamPI.sam -i testFiles/sortedSamPI1.sam --noph
+ '[' 255 -eq 0 ']'
+ '[' -e results/mergeSamPIfail.sam ']'
+ diff results/mergeSamPIfail.log expected/mergeSamPIfail.log
1c1,11
< Unrecognized option nophonehome
---
> ERROR : Failed to add readgroup to header, duplicate, but non-identical RG ID, myID2
> prev: (@RG ID:myID2 SM:sample2 PI:500 LB:library2
> )
> new: (@RG ID:myID2 SM:sample2 PI:501 LB:library2
> )
> Exiting due to ERROR:
> ERROR: Failed to add readgroup to header, duplicate, but non-identical RG ID, myID2
> prev: (@RG ID:myID2 SM:sample2 PI:500 LB:library2
> )
> new: (@RG ID:myID2 SM:sample2 PI:501 LB:library2
> )
+ '[' 1 -ne 0 ']'
+ ERROR=true
+ ../bin/bam mergeBam -o results/mergeBamReg1List.sam -l testFiles/mergeBam.list --noph -r 1
Unrecognized option nophonehome
+ '[' 255 -ne 0 ']'
+ ERROR=true
+ diff results/mergeBamReg1List.sam expected/mergeBamReg1.sam
diff: results/mergeBamReg1List.sam: No such file or directory
+ '[' 2 -ne 0 ']'
+ ERROR=true
+ ../bin/bam mergeBam -o results/mergeBamReg1File.sam -l testFiles/mergeBam.list --noph -R testFiles/region1.txt
Unrecognized option nophonehome
+ '[' 255 -ne 0 ']'
+ ERROR=true
+ diff results/mergeBamReg1File.sam expected/mergeBamReg1.sam
diff: results/mergeBamReg1File.sam: No such file or directory
+ '[' 2 -ne 0 ']'
+ ERROR=true
+ ../bin/bam mergeBam -o results/mergeBamReg13List.sam -l testFiles/mergeBam.list --noph -r 1,3
Unrecognized option nophonehome
+ '[' 255 -ne 0 ']'
+ ERROR=true
+ diff results/mergeBamReg13List.sam expected/mergeBamReg13.sam
diff: results/mergeBamReg13List.sam: No such file or directory
+ '[' 2 -ne 0 ']'
+ ERROR=true
+ ../bin/bam mergeBam -o results/mergeBamReg13File.sam -l testFiles/mergeBam.list --noph -R testFiles/region13.txt
Unrecognized option nophonehome
+ '[' 255 -ne 0 ']'
+ ERROR=true
+ diff results/mergeBamReg13File.sam expected/mergeBamReg13.sam
diff: results/mergeBamReg13File.sam: No such file or directory
+ '[' 2 -ne 0 ']'
+ ERROR=true
+ ../bin/bam mergeBam -o results/mergeBamReg1P3List.sam -l testFiles/mergeBam.list --noph -r 1:75-1011,1:1750-1750,3
Unrecognized option nophonehome
+ '[' 255 -ne 0 ']'
+ ERROR=true
+ diff results/mergeBamReg1P3List.sam expected/mergeBamReg1P3.sam
diff: results/mergeBamReg1P3List.sam: No such file or directory
+ '[' 2 -ne 0 ']'
+ ERROR=true
+ ../bin/bam mergeBam -o results/mergeBamReg1P3File.sam -l testFiles/mergeBam.list --noph -R testFiles/region1P3.txt
Unrecognized option nophonehome
+ '[' 255 -ne 0 ']'
+ ERROR=true
+ diff results/mergeBamReg1P3File.sam expected/mergeBamReg1P3.sam
diff: results/mergeBamReg1P3File.sam: No such file or directory
+ '[' 2 -ne 0 ']'
+ ERROR=true
+ ../bin/bam mergeBam -o results/mergeBamReg1PList.sam -l testFiles/mergeBam.list --noph -r 1:1014
Unrecognized option nophonehome
+ '[' 255 -ne 0 ']'
+ ERROR=true
+ diff results/mergeBamReg1PList.sam expected/mergeBamReg1P.sam
diff: results/mergeBamReg1PList.sam: No such file or directory
+ '[' 2 -ne 0 ']'
+ ERROR=true
+ ../bin/bam mergeBam -o results/mergeBamReg1PFile.sam -l testFiles/mergeBam.list --noph -R testFiles/region1P.txt
Unrecognized option nophonehome
+ '[' 255 -ne 0 ']'
+ ERROR=true
+ diff results/mergeBamReg1PFile.sam expected/mergeBamReg1P.sam
diff: results/mergeBamReg1PFile.sam: No such file or directory
+ '[' 2 -ne 0 ']'
+ ERROR=true
+ ../bin/bam mergeBam -o results/mergeErr.sam -l testFiles/mergeBam.list --noph -r 1:1r-5
Unrecognized option nophonehome
+ '[' 255 -eq 0 ']'
+ diff results/mergeErr1.err expected/mergeErr1.err
0a1,4
>
> FATAL ERROR -
> Error: Invalid region string, '1:1r-5', the start position, '1r', is not an integer >= 1.
>
+ '[' 1 -ne 0 ']'
+ ERROR=true
+ ../bin/bam mergeBam -o results/mergeBamReg1File.sam -l testFiles/mergeBam.list --noph -R testFiles/region1err.txt
Unrecognized option nophonehome
+ '[' 255 -eq 0 ']'
+ diff results/mergeErr2.err expected/mergeErr2.err
0a1,4
>
> FATAL ERROR -
> Error: Invalid region string, '1:4-5k', the end position, '5k', is not an integer >= 1.
>
+ '[' 1 -ne 0 ']'
+ ERROR=true
+ true == true
+ echo 'Failed testMergeBam.sh'
Failed testMergeBam.sh
+ exit 1
However, the two test files on ccentos8_x86_64 have passed. Why is this the case? Is aarch64 not supported?
Hello,I meet a problem:bash -x testBam2FastQ.sh and bash -x testMergeBam.sh failed on centos8_aarch64
However, the two test files on ccentos8_x86_64 have passed. Why is this the case? Is aarch64 not supported?