Samtools give this error

Question

[Kash]

Hi all,

I am trying to align some fastq files to a reference genome. I am very new to this work. When I run this code it gives the following error. I do not understand the reason for this.

CODE ->

/home/kkdesi01/samtools-1.3.1/samtools sort /scratch/global/kkdesi01/NGS_Class/animals/Twilight/WGS/bwaDir/SRR1055837.bam -T /scratch/global/kkdesi01/NGS_Class\
/animals/Twilight/WGS/bwaDir/SRR1055837.sorted -o scratch/global/kkdesi01/NGS_Class/animals/Twilight/WGS/bwaDir/SRR1055837.sorted.bam

/home/kkdesi01/samtools-1.3.1/samtools index /scratch/global/kkdesi01/NGS_Class/animals/Twilight/WGS/bwaDir/SRR1055837.sorted.bam

ERROR message ->

[E::hts_open_format] fail to open file 'scratch/global/kkdesi01/NGS_Class/animals/Twilight/WGS/bwaDir/SRR1055837.sorted.bam'
[bam_merge_core2] failed to create "scratch/global/kkdesi01/NGS_Class/animals/Twilight/WGS/bwaDir/SRR1055837.sorted.bam": No such file or directory
[E::hts_open_format] fail to open file '/scratch/global/kkdesi01/NGS_Class/animals/Twilight/WGS/bwaDir/SRR1055837.sorted.bam'
samtools index: failed to open "/scratch/global/kkdesi01/NGS_Class/animals/Twilight/WGS/bwaDir/SRR1055837.sorted.bam": No such file or directory

Can some one please help me to resolve this. I am using SAmtools 1.3.1 Thank you in advance

Kalpi

[Kash]

Now I get this message in the error file.

[bam_sort_core] merging from 303 files...

And my bwaDie looks like this. 
total 224241792
-rw------- 1 kkdesi01 unixuser 138463147124 Jun 18 11:27 SRR1055837.sam
-rw------- 1 kkdesi01 unixuser  51312872276 Jun 18 14:13 SRR1055837.bam
-rw------- 1 kkdesi01 unixuser  39839305515 Jul  1 21:04 SRR1055837.sorted.bam
-rw------- 1 kkdesi01 unixuser      8023696 Jul  1 21:15 SRR1055837.sorted.bam.bai

Can someone please tell me what does this error means. Is it actually an error? Am I done with sorting? Thank you inadvance.

Kalpi

[GenoMax]

Looks like you are all done :-)

Go on to the next step of your analysis.

[Kash]

Yayy Thank you :D Does it give an error file even it runs correctly.

Answer 1

[GenoMax]

You are missing a leading / in the -o directive on your samtools command. Following should work. You should not need the -T since you are already working in that same directory.

/home/kkdesi01/samtools-1.3.1/samtools sort /scratch/global/kkdesi01/NGS_Class/animals/Twilight/WGS/bwaDir/SRR1055837.bam  -o /scratch/global/kkdesi01/NGS_Class/animals/Twilight/WGS/bwaDir/SRR1055837.sorted.bam

The index command looks fine. Once the sorted file gets produced indexing will work.

[Kash]

Thank you very much. It is running now. Will you please tell me how I can learn these things. Are there any books or tutorials? I really want to know these things better.

Kalpi

[GenoMax]

Follow this tutorial to acquire unix/command line skills. Only way to become good at this is to practice :-)

[Kash]

Yes I will start there. Thank you