Unable to get to BAM file from SAM using samtools

<html> <head> <title> Unable to get to BAM file from SAM using samtools </title> <meta charset="UTF-8"> <meta name="viewport" content="width=device-width, initial-scale=1"> <link rel="icon" href="/static/forum_favicon.ico" type="image/x-icon"/> <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.2.1/jquery.min.js"></script> <script async src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-chtml.js" id="MathJax-script"></script> <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.2.1/jquery.min.js"></script> <script src="https://code.jquery.com/ui/1.12.1/jquery-ui.min.js"></script> <link disabled rel="stylesheet" href="//cdn.jsdelivr.net/gh/highlightjs/cdn-release@9.18.0/build/styles/default.min.css"> <script async src="//cdn.jsdelivr.net/gh/highlightjs/cdn-release@9.18.0/build/highlight.min.js"></script>  <script async src="https://www.googletagmanager.com/gtag/js?id=UA-101522-12"></script> <script> window.dataLayer = window.dataLayer || []; function gtag() { dataLayer.push(arguments); 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I intend to look at SNPs in DNA's coding portion to associate it with a resistant phenotype. For this, I used gsnap to map due to being SNP tolerant.</p> <p>My inquiry: I麓m having trouble getting from SAM to BAM. And this is the error I got:</p> <p><img alt="" src="/media/images/07438138-5864-4afc-9c2d-7a339636"></p> <p>I used samtools with this code:</p> <pre><code>samtools view -b -o HLR1_subsample.bam HLR1_subsample.sam </code></pre> <p>I麓ve repeated the mapping, I麓ve redo the instalation of samtools, checked the version of samtools, checked the version of gsnap. My version of samtools is samtools 1.19.2, GSNAP version 2024-11-20 called with args: gsnap.avx512.</p> <p>It keeps getting the error "positional data is too large for BAM format" as in the picture</p> <p>Second time posting a question. Not quite sure what it is truly needed to understand my question.</p> </span> </div> <span class="inplace-tags"> <a class="ptag" href="/tag/Samtools/"> Samtools </a> <a class="ptag" href="/tag/BAM/"> BAM </a> <a class="ptag" href="/tag/SAM/"> SAM </a> • 1.2k views </span> <time itemprop="dateCreated" datetime="2025-02-04"></time> <div class="actions top-level"> <a class="add-comment ui tiny label">ADD COMMENT</a> • <a itemprop="url" href="/p/9608666/#9608666">link</a> <span class="status muted user-info"> <span> 7 weeks ago by <a href="/u/144005/"> alejandro.mejiam1 </a> &utrif; 20 </span> </span> </div> <span class="diff-cont"></span> </div> <div class="comment-list"> <div class="indent" ><div> <a name="9608693"></a> <div class="post comment open" data-value="9608693"> <div class="body"> <div class="voting"> <button class="ui icon mini button" data-value="upvote" data-state="0"> <i class="thumbs up icon "></i> </button> <div class="score">0</div> <button class="ui icon mini button bookmark" data-value="bookmark" data-state="0"> <i class="bookmark icon "></i> </button> </div> <div class="content"> <div class="droppable inplace"> <div class="ui inverted dimmer"> <div class="ui text loader"> <div class="muted">Entering edit mode</div> </div> </div> <div class="magnify"> <p>Can you share the output of <code>samtools view -H</code> for a file where the bam conversion worked and one where the command failed?</p> </div> <div class="actions "> <a class="add-comment ui tiny label">ADD REPLY</a> • <a itemprop="url" href="/p/9608666/#9608693">link</a> <span class="status muted user-info"> <span> 8 weeks ago by <a href="/u/22075/"> Arup Ghosh </a> <i class="ui muted bolt icon"></i> 3.3k </span> </span> </div> <span class="diff-cont"></span> </div> </div> </div> </div> </div> <div class="indent" ><div> <a name="9608702"></a> <div class="post comment open" data-value="9608702"> <div class="body"> <div class="voting"> <button class="ui icon mini button" data-value="upvote" data-state="0"> <i class="thumbs up icon "></i> </button> <div class="score">0</div> <button class="ui icon mini button bookmark" data-value="bookmark" data-state="0"> <i class="bookmark icon "></i> </button> </div> <div class="content"> <div class="droppable inplace"> <div class="ui inverted dimmer"> <div class="ui text loader"> <div class="muted">Entering edit mode</div> </div> </div> <div class="magnify"> <p>Sure thing:</p> <p>Failed <img alt="Failed" src="/media/images/928dfa48-bd0c-4732-9a26-ea3d731b"></p> <p>Worked <img alt="Worked" src="/media/images/437b9a5c-02d9-4628-b850-03e97e25"></p> <p>Is this enough?</p> </div> <div class="actions "> <a class="add-comment ui tiny label">ADD REPLY</a> • <a itemprop="url" href="/p/9608666/#9608702">link</a> <span class="status muted user-info"> <span> 8 weeks ago by <a href="/u/144005/"> alejandro.mejiam1 </a> &utrif; 20 </span> </span> </div> <span class="diff-cont"></span> </div> </div> </div> </div> </div> <div class="indent" ><div> <a name="9608703"></a> <div class="post comment open" data-value="9608703"> <div class="body"> <div class="voting"> <button class="ui icon mini button" data-value="upvote" data-state="0"> <i class="thumbs up icon "></i> </button> <div class="score">0</div> <button class="ui icon mini button bookmark" data-value="bookmark" data-state="0"> <i class="bookmark icon "></i> </button> </div> <div class="content"> <div class="droppable inplace"> <div class="ui inverted dimmer"> <div class="ui text loader"> <div class="muted">Entering edit mode</div> </div> </div> <div class="magnify"> <p>Please copy and paste text and then format (after selecting) as <code>code</code> using the <code>101010</code> button in edit window. Posting screenshots does not provide clear information about content.</p> <p>Do you have large datasets as in number of reads. Searches seem to indicate that other issue may be too many reads aligning to specific positions in your BAM file.</p> </div> <div class="actions "> <a class="add-comment ui tiny label">ADD REPLY</a> • <a itemprop="url" href="/p/9608666/#9608703">link</a> <span class="status muted user-info"> <span> 8 weeks ago by <a href="/u/18713/"> GenoMax </a> <i class="ui muted bolt icon"></i> 150k </span> </span> </div> <span class="diff-cont"></span> </div> </div> </div> </div> </div> <div class="indent" ><div> <a name="9608765"></a> <div class="post comment open" data-value="9608765"> <div class="body"> <div class="voting"> <button class="ui icon mini button" data-value="upvote" data-state="0"> <i class="thumbs up icon "></i> </button> <div class="score">0</div> <button class="ui icon mini button bookmark" data-value="bookmark" data-state="0"> <i class="bookmark icon "></i> </button> </div> <div class="content"> <div class="droppable inplace"> <div class="ui inverted dimmer"> <div class="ui text loader"> <div class="muted">Entering edit mode</div> </div> </div> <div class="magnify"> <p>Thank you for your suggestion. I paste the code as stated. I do not have a large data sets. Both of this data set have a size of 300000 reads.</p> <pre><code>#HPR1 -> worked (base) grupobcei@Artemisa:~/grupobcei/ewas/ewas_Acacias/03._ewas_mapped_subsample$ samtools view -H HPR1_subsample.sam @HD VN:1.0 SO:unsorted @PG ID:GSNAP PN:gsnap VN:2024-11-20 CL:gsnap.avx512 -d Aaegl5_index -D /mnt/disc2/grupobcei/ewas/index/Aaegl5_index/ --max-mismatches=0.10 -n 10 -Q --nofails -B 4 -t 30 --allow-pe-name-mismatch --format=sam HPR1_R1_subsample.fastq HPR1_R2_subsample.fastq @PG ID:samtools PN:samtools PP:GSNAP VN:1.19.2 CL:samtools view -H HPR1_subsample.sam @SQ SN:AaegL5_1 LN:310827022 @SQ SN:AaegL5_2 LN:474425716 @SQ SN:AaegL5_3 LN:409777670 @SQ SN:AaegL5_MT LN:16790 @SQ SN:NIGP01000004 LN:30735 #HLR1 -> Failed (base) grupobcei@Artemisa:~/grupobcei/ewas/ewas_Acacias/03._ewas_mapped_subsample$ samtools view -H HLR1_subsample.sam @HD VN:1.0 SO:unsorted @PG ID:GSNAP PN:gsnap VN:2024-11-20 CL:gsnap.avx512 -d Aaegl5_index -D /mnt/disc2/grupobcei/ewas/index/Aaegl5_index/ --max-mismatches=0.10 -n 10 -Q --nofails -B 4 -t 30 --allow-pe-name-mismatch --format=sam HLR1_R1_subsample.fastq HLR1_R2_subsample.fastq @PG ID:samtools PN:samtools PP:GSNAP VN:1.19.2 CL:samtools view -H HLR1_subsample.sam @SQ SN:AaegL5_1 LN:310827022 @SQ SN:AaegL5_2 LN:474425716 @SQ SN:AaegL5_3 LN:409777670 @SQ SN:AaegL5_MT LN:16790 @SQ SN:NIGP01000004 LN:30735 </code></pre> </div> <div class="actions "> <a class="add-comment ui tiny label">ADD REPLY</a> • <a itemprop="url" href="/p/9608666/#9608765">link</a> <span class="status muted user-info"> updated 8 weeks ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/18713/"> <span itemprop="name">GenoMax</span> </a> <i class="ui muted bolt icon"></i> 150k • written 8 weeks ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/144005/"> <span itemprop="name">alejandro.mejiam1</span> </a> &utrif; 20 </span> </div> <span class="diff-cont"></span> </div> </div> </div> </div> </div> <div class="indent" ><div> <a name="9608766"></a> <div class="post comment open" data-value="9608766"> <div class="body"> <div class="voting"> <button class="ui icon mini button" data-value="upvote" data-state="0"> <i class="thumbs up icon "></i> </button> <div class="score">0</div> <button class="ui icon mini button bookmark" data-value="bookmark" data-state="0"> <i class="bookmark icon "></i> </button> </div> <div class="content"> <div class="droppable inplace"> <div class="ui inverted dimmer"> <div class="ui text loader"> <div class="muted">Entering edit mode</div> </div> </div> <div class="magnify"> <p>Do the files that fail always fail or work if resubmitted again?</p> <p>Why are you using this option? If your paired-end reads are out of sync your alignments are going to be incorrect.</p> <blockquote><p>--allow-pe-name-mismatch</p> </blockquote> </div> <div class="actions "> <a class="add-comment ui tiny label">ADD REPLY</a> • <a itemprop="url" href="/p/9608666/#9608766">link</a> <span class="status muted user-info"> <span> 8 weeks ago by <a href="/u/18713/"> GenoMax </a> <i class="ui muted bolt icon"></i> 150k </span> </span> </div> <span class="diff-cont"></span> </div> </div> </div> </div> </div> <div class="indent" ><div> <a name="9608840"></a> <div class="post comment open" data-value="9608840"> <div class="body"> <div class="voting"> <button class="ui icon mini button" data-value="upvote" data-state="0"> <i class="thumbs up icon "></i> </button> <div class="score">0</div> <button class="ui icon mini button bookmark" data-value="bookmark" data-state="0"> <i class="bookmark icon "></i> </button> </div> <div class="content"> <div class="droppable inplace"> <div class="ui inverted dimmer"> <div class="ui text loader"> <div class="muted">Entering edit mode</div> </div> </div> <div class="magnify"> <p>Yes. They fail or work when resubmitted consistently.</p> <p>We allowed certain level of mismatch with this option. However, I麓ve re run the alignments withouth that option and they kept failing to change from sam to bam.</p> <pre><code> (base) grupobcei@Artemisa:~/grupobcei/ewas/ewas_Acacias/02.1_ewas_trimmed_subsample$ samtools view -H HLR1_wo_mismatch.sam samtools: /home/administrador/programas/miniconda3/bin/../lib/libtinfow.so.6: no version information available (required by samtools) samtools: /home/administrador/programas/miniconda3/bin/../lib/libncursesw.so.6: no version information available (required by samtools) samtools: /home/administrador/programas/miniconda3/bin/../lib/libncursesw.so.6: no version information available (required by samtools) @HD VN:1.0 SO:unsorted @PG ID:GSNAP PN:gsnap VN:2024-11-20 CL:gsnap.avx512 -d Aaegl5_index -D /mnt/disc2/grupobcei/ewas/index/Aaegl5_index/ --max-mismatches=0.10 -n 10 -Q --nofails -B 4 -t 30 --format=sam HLR1_R1_subsample.fastq HLR1_R2_subsample.fastq @PG ID:samtools PN:samtools PP:GSNAP VN:1.19.2 CL:samtools view -H HLR1_wo_mismatch.sam @SQ SN:AaegL5_1 LN:310827022 @SQ SN:AaegL5_2 LN:474425716 @SQ SN:AaegL5_3 LN:409777670 @SQ SN:AaegL5_MT LN:16790 @SQ SN:NIGP01000004 LN:30735 @SQ SN:NIGP01000005 LN:39846 @SQ SN:NIGP01000006 LN:33725 (base) grupobcei@Artemisa:~/grupobcei/ewas/ewas_Acacias/02.1_ewas_trimmed_subsample$ samtools view -b -o HLR1_wo_mismatch.bam HLR1_wo_mismatch.sam samtools: /home/administrador/programas/miniconda3/bin/../lib/libtinfow.so.6: no version information available (required by samtools) samtools: /home/administrador/programas/miniconda3/bin/../lib/libncursesw.so.6: no version information available (required by samtools) samtools: /home/administrador/programas/miniconda3/bin/../lib/libncursesw.so.6: no version information available (required by samtools) [E::bam_write1] Positional data is too large for BAM format samtools view: writing to "HLR1_wo_mismatch.bam" failed </code></pre> </div> <div class="actions "> <a class="add-comment ui tiny label">ADD REPLY</a> • <a itemprop="url" href="/p/9608666/#9608840">link</a> <span class="status muted user-info"> updated 8 weeks ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/18713/"> <span itemprop="name">GenoMax</span> </a> <i class="ui muted bolt icon"></i> 150k • written 8 weeks ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/144005/"> <span itemprop="name">alejandro.mejiam1</span> </a> &utrif; 20 </span> </div> <span class="diff-cont"></span> </div> </div> </div> </div> </div> <div class="indent" ><div> <a name="9608841"></a> <div class="post comment open" data-value="9608841"> <div class="body"> <div class="voting"> <button class="ui icon mini button" data-value="upvote" data-state="0"> <i class="thumbs up icon "></i> </button> <div class="score">0</div> <button class="ui icon mini button bookmark" data-value="bookmark" data-state="0"> <i class="bookmark icon "></i> </button> </div> <div class="content"> <div class="droppable inplace"> <div class="ui inverted dimmer"> <div class="ui text loader"> <div class="muted">Entering edit mode</div> </div> </div> <div class="magnify"> <blockquote><p>However, I麓ve re run the alignments withouth that option and they kept failing to change from sam to bam.</p> </blockquote> <p>Did you scan/trim your paired end data files independently? If you did then the reads are likely out of sync. If that is the case you need to go back to the original files and scan/trim the paired end files together to make sure that does not happen.</p> <p>Results you have from out of sync paired-end data are going to have discordant alignments for part of the data.</p> </div> <div class="actions "> <a class="add-comment ui tiny label">ADD REPLY</a> • <a itemprop="url" href="/p/9608666/#9608841">link</a> <span class="status muted user-info"> <span> 8 weeks ago by <a href="/u/18713/"> GenoMax </a> <i class="ui muted bolt icon"></i> 150k </span> </span> </div> <span class="diff-cont"></span> </div> </div> </div> </div> </div> <div class="indent" ><div> <a name="9608930"></a> <div class="post comment open" data-value="9608930"> <div class="body"> <div class="voting"> <button class="ui icon mini button" data-value="upvote" data-state="0"> <i class="thumbs up icon "></i> </button> <div class="score">0</div> <button class="ui icon mini button bookmark" data-value="bookmark" data-state="0"> <i class="bookmark icon "></i> </button> </div> <div class="content"> <div class="droppable inplace"> <div class="ui inverted dimmer"> <div class="ui text loader"> <div class="muted">Entering edit mode</div> </div> </div> <div class="magnify"> <p>I麓ve had run cutadapt</p> <pre><code>cutadapt -a AGATCGGAAGAGC -A AGATCGGAAGAGC -g GCTCTTCCGATCT -G GCTCTTCCGATCT -a AGATGTGTATAAGAGACAG -A AGATGTGTATAAGAGACAG -g CTGTCTCTTATACACATCT -G CTGTCTCTTATACACATCT -q 30,30 --minimum-length 80 -o HLR1_R1.fastq -p HLR1_R2.fastq HLR1_R1_001.fastq.gz HLR1_R2_001.fastq.gz </code></pre> <p>Using this code, so they shouldn麓t be out of sync.</p> </div> <div class="actions "> <a class="add-comment ui tiny label">ADD REPLY</a> • <a itemprop="url" href="/p/9608666/#9608930">link</a> <span class="status muted user-info"> <span> 8 weeks ago by <a href="/u/144005/"> alejandro.mejiam1 </a> &utrif; 20 </span> </span> </div> <span class="diff-cont"></span> </div> </div> </div> </div> </div> <div class="indent" ><div> <a name="9608943"></a> <div class="post comment open" data-value="9608943"> <div class="body"> <div class="voting"> <button class="ui icon mini button" data-value="upvote" data-state="0"> <i class="thumbs up icon "></i> </button> <div class="score">0</div> <button class="ui icon mini button bookmark" data-value="bookmark" data-state="0"> <i class="bookmark icon "></i> </button> </div> <div class="content"> <div class="droppable inplace"> <div class="ui inverted dimmer"> <div class="ui text loader"> <div class="muted">Entering edit mode</div> </div> </div> <div class="magnify"> <blockquote><p>-o HLR1_R1.fastq -p HLR1_R2.fastq HLR1_R1_001.fastq.gz HLR1_R2_001.fastq.gz</p> </blockquote> <p><s>This does not appear to be correct. Are you able to provide multiple input files at the same to to <code>cutadapt</code> (will have to look that up). In any case you have 3 files which is not balanced.</s></p><s> <p>Edit: You can't directly provide multiple files of pairs as input to cutadapt. <code>-o</code> also specifies output. So It looks like if you ran the command line exactly as above then the results are not correct.</s></p> </s> </div> <div class="actions "> <a class="add-comment ui tiny label">ADD REPLY</a> • <a itemprop="url" href="/p/9608666/#9608943">link</a> <span class="status muted user-info"> <span> 8 weeks ago by <a href="/u/18713/"> GenoMax </a> <i class="ui muted bolt icon"></i> 150k </span> </span> </div> <span class="diff-cont"></span> </div> </div> </div> </div> </div> <div class="indent" ><div> <a name="9608997"></a> <div class="post comment open" data-value="9608997"> <div class="body"> <div class="voting"> <button class="ui icon mini button" data-value="upvote" data-state="0"> <i class="thumbs up icon "></i> </button> <div class="score">0</div> <button class="ui icon mini button bookmark" data-value="bookmark" data-state="0"> <i class="bookmark icon "></i> </button> </div> <div class="content"> <div class="droppable inplace"> <div class="ui inverted dimmer"> <div class="ui text loader"> <div class="muted">Entering edit mode</div> </div> </div> <div class="magnify"> <p>I麓ve actually done this with other samples and with some of them the actual SAM to BAM step can be done. Additionally, I looked for it in the manual, and in the option paired adapters <a href="https://cutadapt.readthedocs.io/en/stable/guide.html#pair-adapters" rel="nofollow">cutadapt manual - pair adapters</a> it is correct to use <code>-o</code> and <code>-p</code> to produce an output of paired reads.</p> <p>So I麓m still clueless about this problem.</p> </div> <div class="actions "> <a class="add-comment ui tiny label">ADD REPLY</a> • <a itemprop="url" href="/p/9608666/#9608997">link</a> <span class="status muted user-info"> <span> 8 weeks ago by <a href="/u/144005/"> alejandro.mejiam1 </a> &utrif; 20 </span> </span> </div> <span class="diff-cont"></span> </div> </div> </div> </div> </div> <div class="indent" ><div> <a name="9608998"></a> <div class="post comment open" data-value="9608998"> <div class="body"> <div class="voting"> <button class="ui icon mini button" data-value="upvote" data-state="0"> <i class="thumbs up icon "></i> </button> <div class="score">0</div> <button class="ui icon mini button bookmark" data-value="bookmark" data-state="0"> <i class="bookmark icon "></i> </button> </div> <div class="content"> <div class="droppable inplace"> <div class="ui inverted dimmer"> <div class="ui text loader"> <div class="muted">Entering edit mode</div> </div> </div> <div class="magnify"> <p>That is a confusing way to provide input options (am not a <code>cutadapt</code> user) but you are right. I will scratch my comment above.</p> <p>At this point nothing else that comes to mind then. If you are willing you could instead try <code>fastp</code> or <code>bbduk.sh</code> from BBMap suite as an alternate option on one of the sample file pair that is failing and see if it helps.</p> </div> <div class="actions "> <a class="add-comment ui tiny label">ADD REPLY</a> • <a itemprop="url" href="/p/9608666/#9608998">link</a> <span class="status muted user-info"> <span> 8 weeks ago by <a href="/u/18713/"> GenoMax </a> <i class="ui muted bolt icon"></i> 150k </span> </span> </div> <span class="diff-cont"></span> </div> </div> </div> </div> </div> <div class="indent" ><div> <a name="9609081"></a> <div class="post comment open" data-value="9609081"> <div class="body"> <div class="voting"> <button class="ui icon mini button" data-value="upvote" data-state="0"> <i class="thumbs up icon "></i> </button> <div class="score">0</div> <button class="ui icon mini button bookmark" data-value="bookmark" data-state="0"> <i class="bookmark icon "></i> </button> </div> <div class="content"> <div class="droppable inplace"> <div class="ui inverted dimmer"> <div class="ui text loader"> <div class="muted">Entering edit mode</div> </div> </div> <div class="magnify"> <p>I麓m asking for help to other professors at my University. Will reply if I find some way around it. Thank you for your help.</p> </div> <div class="actions "> <a class="add-comment ui tiny label">ADD REPLY</a> • <a itemprop="url" href="/p/9608666/#9609081">link</a> <span class="status muted user-info"> <span> 7 weeks ago by <a href="/u/144005/"> alejandro.mejiam1 </a> &utrif; 20 </span> </span> </div> <span class="diff-cont"></span> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> <div class="ui vertical segment"> <a name="9608667"></a> <div class="post view open" data-value="9608667"> <div class="body" itemprop="suggestedAnswer" itemscope itemtype="https://schema.org/Answer" > <div class="voting"> <button class="ui icon button" data-value="upvote" data-state="0"><i class="thumbs up icon"></i> </button> <div class="score" itemprop="upvoteCount">1</div> <button class="ui icon button" data-value="bookmark" data-state="0"><i class="bookmark icon"></i> </button> </div> <div class="content"> <div class="droppable inplace"> <div class="ui inverted dimmer"> <div class="ui text loader"> <div class="muted">Entering edit mode</div> </div> </div> <div class="wrap magnify"> <div class="user_box tablet right"> <div> <a class="" href="/u/25721/"> <img class="ui centered circular image" src="https://secure.gravatar.com/avatar/f08050345f8a0ff11e9bbaab4a1c4212?s=80&d=retro&f=y"> </a> </div> <div class="muted"> <div>9 weeks ago</div> <div><a href="/u/25721/">ATpoint</a> <i class="ui muted bolt icon"></i> 87k </div> </div> </div> <span itemprop="text"> <p>Please get used to googling the main error message: <a href="https://github.com/samtools/samtools/issues/1669" rel="nofollow">https://github.com/samtools/samtools/issues/1669</a></p> </span> </div> <time itemprop="dateCreated" datetime="2025-02-04"></time> <div class="actions "> <a class="add-comment ui tiny label">ADD COMMENT</a> • <a itemprop="url" href="/p/9608666/#9608667">link</a> <span class="status muted user-info"> <span> 9 weeks ago by <a href="/u/25721/"> ATpoint </a> <i class="ui muted bolt icon"></i> 87k </span> </span> </div> <span class="diff-cont"></span> </div> <div class="comment-list"> <div class="indent" ><div> <a name="9608683"></a> <div class="post comment open" data-value="9608683"> <div class="body"> <div class="voting"> <button class="ui icon mini button" data-value="upvote" data-state="0"> <i class="thumbs up icon "></i> </button> <div class="score">0</div> <button class="ui icon mini button bookmark" data-value="bookmark" data-state="0"> <i class="bookmark icon "></i> </button> </div> <div class="content"> <div class="droppable inplace"> <div class="ui inverted dimmer"> <div class="ui text loader"> <div class="muted">Entering edit mode</div> </div> </div> <div class="magnify"> <p>Ok. I understand the error. However, some of my samples did pass from SAM to BAM, how is this possible? I mean, all the chromosome have the same size in the reference genome, how can it be different when I sequenced them? I think I麓m missing the point here.</p> <p>Thanks</p> </div> <div class="actions "> <a class="add-comment ui tiny label">ADD REPLY</a> • <a itemprop="url" href="/p/9608666/#9608683">link</a> <span class="status muted user-info"> <span> 8 weeks ago by <a href="/u/144005/"> alejandro.mejiam1 </a> &utrif; 20 </span> </span> </div> <span class="diff-cont"></span> </div> </div> </div> </div> </div> <div class="indent" ><div> <a name="9608687"></a> <div class="post comment open" data-value="9608687"> <div class="body"> <div class="voting"> <button class="ui icon mini button" data-value="upvote" data-state="0"> <i class="thumbs up icon "></i> </button> <div class="score">0</div> <button class="ui icon mini button bookmark" data-value="bookmark" data-state="0"> <i class="bookmark icon "></i> </button> </div> <div class="content"> <div class="droppable inplace"> <div class="ui inverted dimmer"> <div class="ui text loader"> <div class="muted">Entering edit mode</div> </div> </div> <div class="magnify"> <blockquote><p>I mean, all the chromosome have the same size in the reference genome,</p> </blockquote> <p>The chromosomes are not the same size (see <a href="https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_002204515.2/" rel="nofollow">https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_002204515.2/</a> ) . If you have them as same size you did something incorrect. They are not over 2 Gbp each so not sure why you are getting that error.</p> <p><img alt="aedes" src="/media/images/325e0bd5-5dce-45db-ab05-cc56b456"></p> </div> <div class="actions "> <a class="add-comment ui tiny label">ADD REPLY</a> • <a itemprop="url" href="/p/9608666/#9608687">link</a> <span class="status muted user-info"> <span> 8 weeks ago by <a href="/u/18713/"> GenoMax </a> <i class="ui muted bolt icon"></i> 150k </span> </span> </div> <span class="diff-cont"></span> </div> </div> </div> </div> </div> <div class="indent" ><div> <a name="9608690"></a> <div class="post comment open" data-value="9608690"> <div class="body"> <div class="voting"> <button class="ui icon mini button" data-value="upvote" data-state="0"> <i class="thumbs up icon "></i> </button> <div class="score">0</div> <button class="ui icon mini button bookmark" data-value="bookmark" data-state="0"> <i class="bookmark icon "></i> </button> </div> <div class="content"> <div class="droppable inplace"> <div class="ui inverted dimmer"> <div class="ui text loader"> <div class="muted">Entering edit mode</div> </div> </div> <div class="magnify"> <p>I think OP means that they align different samples to always the same reference and some pass while others don't, hence the conflict is why sometimes the reference appears too large and sometimes it is not. I have no answer unfortuinately.</p> </div> <div class="actions "> <a class="add-comment ui tiny label">ADD REPLY</a> • <a itemprop="url" href="/p/9608666/#9608690">link</a> <span class="status muted user-info"> <span> 8 weeks ago by <a href="/u/25721/"> ATpoint </a> <i class="ui muted bolt icon"></i> 87k </span> </span> </div> <span class="diff-cont"></span> </div> </div> </div> </div> </div> <div class="indent" ><div> <a name="9608701"></a> <div class="post comment open" data-value="9608701"> <div class="body"> <div class="voting"> <button class="ui icon mini button" data-value="upvote" data-state="0"> <i class="thumbs up icon "></i> </button> <div class="score">0</div> <button class="ui icon mini button bookmark" data-value="bookmark" data-state="0"> <i class="bookmark icon "></i> </button> </div> <div class="content"> <div class="droppable inplace"> <div class="ui inverted dimmer"> <div class="ui text loader"> <div class="muted">Entering edit mode</div> </div> </div> <div class="magnify"> <p>Exactly. Sorry if it is not clear enough.</p> </div> <div class="actions "> <a class="add-comment ui tiny label">ADD REPLY</a> • <a itemprop="url" href="/p/9608666/#9608701">link</a> <span class="status muted user-info"> <span> 8 weeks ago by <a href="/u/144005/"> alejandro.mejiam1 </a> &utrif; 20 </span> </span> </div> <span class="diff-cont"></span> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </span> <div class="ui info message"> <p><a class="ui small label" href="/accounts/login/"> <i class="sign in icon"></i>Login</a> before adding your answer.</p> </div> <script> $(document).ready(function () { $('#subscribe').dropdown(); drag_and_drop(); $('.ui.dropdown').dropdown(); //var users = "**MISSING**".split(','); autocomplete_users(); //init_pagedown(); $(this).on('click', '#inplace .save', function () { event.preventDefault(); var post = $(this).closest('.post'); edit_post(post); }); $(this).on('click', '#inplace .create', function () { event.preventDefault(); create_comment(); }); $(this).on('click', '.edit-button', function (event) { event.preventDefault(); inplace_form($(this)); }); $(this).on('click', ".add-comment", function () { inplace_form($(this), true); }); }); </script> </div> <div class="four wide column sidefeed"> <div class="ui large wrap-text" id="sidebar"> <div class="ui large wrap-text" id="sidebar"> <div class="title">Similar Posts</div> <div class="ui basic segment similar" id="similar"> <div id="similar-feed" post_uid="9608666"></div> <div class="ui inverted dimmer"> <div class="content"> <div class="ui text loader"> <div class="muted">Loading Similar Posts</div> </div> </div> </div> </div> </div> </div> </div> </div> <div id="traffic">Traffic: 1782 users visited in the last hour</div> </div> <div class="ui three center aligned column stackable tiny grid"> <div class=" left aligned column" style="padding-right: 13%"> <b>Content</b> <a href="/#search-anchor">Search</a><br> <a href="/user/list/">Users</a><br> <a href="/t/">Tags</a><br> <a href="/b/list/">Badges</a> </div> <div class="left aligned column" style="padding-right: 12%"> <b>Help</b> <a href="/info/about/">About</a><br> <a href="/info/faq/">FAQ</a><br> </div> <div class=" left aligned column"> <b>Access</b> <a href="/info/rss/">RSS</a><br> <a href="/info/api/">API</a><br> <a href="#">Stats</a> </div> </div> <div class="ui divider"></div> <div class="ui vertical center aligned basic segment"> <p>Use of this site constitutes acceptance of our <a href="/info/policy/">User Agreement and Privacy Policy</a>.</p> <div class="smaller muted"> Powered by the <a href="https://github.com/ialbert/biostar-central" class="ui image"> <img src="/static/images/badge-forum.svg"></a> version 2.3.6 </div> </div> <div align="center"> <script type="text/javascript" src="//rf.revolvermaps.com/0/0/0.js?i=5j83en1rmbf&d=2&p=2&b=0&w=293&g=2&f=arial&fs=12&r=0&c0=362b05&c1=375363&c2=000000&ic0=0&ic1=0" async="async"></script> </div> <div align="center" style="margin-top:1ex"> <script type="text/javascript" src="//rh.revolvermaps.com/0/0/6.js?i=7pci0h9z8v6&m=0&s=300&c=ff0000&cr1=ffffff&f=arial& amp;l=0" async="async"></script> </div> </div> </body> </html>

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Unable to get to BAM file from SAM using samtools