<p>I am very new to micro RNA analysis. I have been using H. sapiens, GRCh38 + major index as given in the Bowtie Website to align with my trimmed FASTQ file .
The command I am using to make very sensitive alignments with Bowtie2 is given below.</p>
<pre><code>module load  Bowtie2; 
bowtie2 --local -p 8 -q --phred33 -D 20 -R 3 -N 0 -L 8 \
    -i S,1,0.50 -x grch38_1kgmaj \
    -U /gpfs/ycga/scratch60/nicoli/ag2646/HumanmicroRNAbowtie_verysensitive_1.06.2021./3kPa_HDF_miRNA_1bbduk.fastq \
    -S /gpfs/ycga/scratch60/nicoli/ag2646/HumanmicroRNAbowtie_verysensitive_1.06.2021./3kPa_HDF_miRNA_1bbduk.sam
</code></pre>
<p>Then I am using:</p>
<pre><code>samtools sort -bS 3kPa_HDF_miRNA_1bbduk.sam &gt; 3kPa_HDF_miRNA_1bbduk.bam
</code></pre>
<p>to convert sam files into bam files.</p>
<p>However, I am hitting the error described below:</p>
<pre><code>[W::sam_read1_sam] Parse error at line 46371
</code></pre>
<p>When I grepped the specific line it shows:</p>
<pre><code>SRR8248790.46371        4       *       0       0       *       *       0       0       CCTGGATGATGATAAGCAAATGCTGACTGAACATGAAGGTCTTAATTAGCTCTAACTGACTAGATCGGAAGAGCAC   BBADAGEHIFHHIIIIIGGFIHIIIIIIIHHHHHIHHHEHEHEHFEHIIIEHIIIIIEHIIHIIIHGHHHIIII1C   YT:Z:UU
</code></pre>
<p>Any specific help troubleshooting this error will be very useful.</p>

CC BY-SA 4.0
2021-06-03T18:51:14.957Z
The `[W:` is just a warning. If the process errored out, there should be another actual error message that follows that warning.
Ram RS
CC BY-SA 4.0
2021-06-03T22:03:23.830Z
Is it the last line of the samfile? I wonder if the sam file could be truncated (like a missing newline or something).
Kamil S Jaron
CC BY-SA 4.0
2021-06-04T17:03:49.777Z
How did you "grep the line"? Is that actually line number 46371 of the file, or is that a random line that happens to contain the string `46371`?
terdon
CC BY-SA 4.0
2021-06-05T18:16:06.907Z
Is your `samtools sort` command actually a `samtools view` command? The `-bS` flag would not work with `samtools sort`: http://www.htslib.org/doc/samtools-sort.html. I tried it out of curiosity and got `samtools: invalid option -- b`.
Maximilian Press
CC BY-SA 4.0
2021-06-05T18:20:15.850Z
See similar situation here: https://www.biostars.org/p/169277/. Have you confirmed that bowtie2 finished without errors? Does your sam file look ok? how many lines does it have?
Maximilian Press
CC BY-SA 4.0
2021-06-09T20:37:14.020Z
My bowtie file alignment completed without truncation but only showed errros.
Aranyak Goswami
CC BY-SA 4.0
2021-06-30T05:53:37.033Z
Are you able to trace the same line in the raw fastq file (before trimming) with the same identifier?? If yes, what is the content of that line?
Lot_to_learn
CC BY-SA 4.0
2021-07-01T21:22:43.500Z
I have resolved all the errors. Thanks for all your help.
Aranyak Goswami
<samtools><genomics><format-conversion><bowtie2>
Conversion of SAM to BAM files
# Conversion of SAM to BAM files

(Asked by: username_0 on 2021-06-03)

I am very new to micro RNA analysis. I have been using H. sapiens, GRCh38 + major index as given in the Bowtie Website to align with my trimmed FASTQ file .
The command I am using to make very sensitive alignments with Bowtie2 is given below.
module load  Bowtie2; 
bowtie2 --local -p 8 -q --phred33 -D 20 -R 3 -N 0 -L 8 \
    -i S,1,0.50 -x grch38_1kgmaj \
    -U /gpfs/ycga/scratch60/nicoli/ag2646/HumanmicroRNAbowtie_verysensitive_1.06.2021./3kPa_HDF_miRNA_1bbduk.fastq \
    -S /gpfs/ycga/scratch60/nicoli/ag2646/HumanmicroRNAbowtie_verysensitive_1.06.2021./3kPa_HDF_miRNA_1bbduk.sam

Then I am using:
samtools sort -bS 3kPa_HDF_miRNA_1bbduk.sam > 3kPa_HDF_miRNA_1bbduk.bam

to convert sam files into bam files.
However, I am hitting the error described below:
[W::sam_read1_sam] Parse error at line 46371

When I grepped the specific line it shows:
SRR8248790.46371        4       *       0       0       *       *       0       0       CCTGGATGATGATAAGCAAATGCTGACTGAACATGAAGGTCTTAATTAGCTCTAACTGACTAGATCGGAAGAGCAC   BBADAGEHIFHHIIIIIGGFIHIIIIIIIHHHHHIHHHEHEHEHFEHIIIEHIIIIIEHIIHIIIHGHHHIIII1C   YT:Z:UU

Any specific help troubleshooting this error will be very useful.

**Tags:** samtools, genomics, format-conversion, bowtie2
> **Comments:**
> **username_1**: The `[W:` is just a warning. If the process errored out, there should be another actual error message that follows that warning.  
> **username_2**: Is it the last line of the samfile? I wonder if the sam file could be truncated (like a missing newline or something).  
> **username_3**: How did you "grep the line"? Is that actually line number 46371 of the file, or is that a random line that happens to contain the string `46371`?  
> **username_4**: Is your `samtools sort` command actually a `samtools view` command? The `-bS` flag would not work with `samtools sort`: http://www.htslib.org/doc/samtools-sort.html. I tried it out of curiosity and got `samtools: invalid option -- b`.  
> **username_4**: See similar situation here: https://www.biostars.org/p/169277/. Have you confirmed that bowtie2 finished without errors? Does your sam file look ok? how many lines does it have?  
> **username_0**: My bowtie file alignment completed without truncation but only showed errros.  
> **username_5**: Are you able to trace the same line in the raw fastq file (before trimming) with the same identifier?? If yes, what is the content of that line?  
> **username_0**: I have resolved all the errors. Thanks for all your help.  

---

## 0 answers

