Unconfigured Ad

Collapse
X
 
  • Filter
  • Time
  • Show
Clear All
new posts
  • Genom
    Junior Member
    • Jan 2022
    • 7

    #16
    BWA 2 files fasq to 1 fil sam

    I am creating a sam file, with 2 fastq files, using bwa
    I apply the following command

    bwa mem -t 2 GRCh38.primary_assembly.genome.fa.gz V350019555_L03_B5GHUMqcnrRAABA-556_1.fq.gz
    V350019555_L03_B5GHUMqcnrRAABA-556_2.fq.gz
    > V350019555_L03_B5GHUMqcnrRAABA-556.sam


    The alignment begins to be generated, but after 15 hours, the following appears, and it generates a 0-bit sam file


    V350019555L3C006R0051051033 16 chr21 9651911 29 150M * TGTTTTCTCTTTTTACAGCAAGGACAGTTTATTAAACACACTGTTTTAAACCTTATTTTTTCTCTAAATAATATTTCATATAAGTCAATATGTAGACTTTATGTATTTTTAAAATGAAGACATAGCATTCCATTGAACTTAGACAAAAAT EFFFFFFEGFFFFGEFF9FEFFFFGGFCFFFFGFFFFFFDFFFFFFFFFFFFFGAFFFCGBFDF@G@FGFFGFGFFFFGFFFFGFGFCFFFFFFFDGFGFGFFGFFFFFAFFFFFFEFFFFFFFFFFGDFFFF@FG8FF?FFFFFFGFFF NM:i:1 MD:Z:23G126 AS:i:145 XS:i:131 XA:Z:chr4,+189704487,150M,4;
    [main] Version: 0.7.17-r1188
    [main] CMD: bwa mem -t 2 GRCh38.primary_assembly.genome.fa.gz V350019555_L03_B5GHUMqcnrRAABA-556_1.fq.gz
    [main] Real time: 26995.284 sec; CPU: 33394.341 sec
    zsh: command not found: V350019555_L03_B5GHUMqcnrRAABA-556_2.fq.gz





    I have previously analyzed the files with fasqc, and they seem correct


    What is happening, what should I do?

    Comment

    • GenoMax
      Senior Member
      • Feb 2008
      • 7142

      #17
      @Genom: As answered on Biostars you need to have all command line options on one line. If command needs to span multiple lines then a \ is needed at the end of incomplete lines.

      Comment

      Latest Articles

      Collapse

      • SEQadmin2
        Advanced Sequencing Platforms Tackle Neuroscience’s Toughest Genomics Problems
        by SEQadmin2



        Genomics studies in neuroscience face a special challenge due to the brain’s complexity and scarcity of samples. Mapping changes in cell type and state using conventional next-generation sequencing methods remains challenging. Advances in technologies like single-cell sequencing, spatial transcriptomics, and long-read sequencing have opened the door to deeper studies of the brain and diseases like Alzheimer’s, amyotrophic lateral sclerosis (ALS), and schizophrenia.
        ...
        07-09-2026, 11:10 AM
      • SEQadmin2
        Cancer Drug Resistance: The Lingering Barrier to Rising Survival
        by SEQadmin2



        Cancer survival rates have significantly increased in the last few decades in the United States, reaching a combined 70% 5-year survival rate by 2021. Behind this number, there are years of research to find new therapies, drug targets, and early detection methods. But there is one core challenge that keeps slowing down these advances, and it’s about drug resistance.

        There is no single reason why many patients don’t respond to treatment as expected. Cancer is...
        07-08-2026, 05:17 AM
      • GATTACAT
        Reply to Nine Things a Sample Prep Scientist Thinks About Before Sequencing
        by GATTACAT
        Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.
        07-01-2026, 11:43 AM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by SEQadmin2, 07-13-2026, 10:26 AM
      0 responses
      20 views
      0 reactions
      Last Post SEQadmin2  
      Started by SEQadmin2, 07-09-2026, 10:04 AM
      0 responses
      32 views
      0 reactions
      Last Post SEQadmin2  
      Started by SEQadmin2, 07-08-2026, 10:08 AM
      0 responses
      20 views
      0 reactions
      Last Post SEQadmin2  
      Started by SEQadmin2, 07-07-2026, 11:05 AM
      0 responses
      34 views
      0 reactions
      Last Post SEQadmin2  
      Working...