<p>I have started using snakemake 6.5.2 to align fastq files with reference file. I have pasted the error below in this question. How to allocate memory in the snakefile and read the header from samfile, '-'. This is the snakefile (wrapper for running alignment):</p>
<pre><code> rule bwa_mem2_mem:
        input:
            reads=[&quot;/scicore/home/cichon/GROUP/test_workflow/samples/{sample}.1.fq&quot;, &quot;/scicore/home/cichon/GROUP/test_workflow/samples/{sample}.2.fq&quot;]
        output:
            &quot;/scicore/home/cichon/GROUP/test_workflow/output/{sample}.bam&quot;
        log:
            &quot;/scicore/home/cichon/GROUP/test_workflow/output/{sample}.log&quot;
        params:
            index=&quot;/scicore/home/cichon/GROUP/test_workflow/data/gch38.fa&quot;,
            extra=r&quot;-R '@RG\tID:{sample}\tSM:{sample}'&quot;,
            sort=&quot;none&quot;,             # Can be 'none', 'samtools' or 'picard'.
            sort_order=&quot;coordinate&quot;, # Can be 'coordinate' (default) or 'queryname'.
            sort_extra=&quot;&quot;     

        threads: 8
        wrapper:
            &quot;0.77.0/bio/bwa-mem2/mem&quot;
</code></pre>
<p>I used this command to execute the above snakemake file:</p>
<pre><code>snakemake --use-conda --snakefile Snakefile --cores -p /scicore/home/cichon/GROUP/test_workflow/output/DE98NGSUKBD117612_1.bam /scicore/home/cichon/GROUP/test_workflow/output/DE71NGSUKBD117613_3.bam
</code></pre>
<p>Error from log file:</p>
<pre><code>Looking to launch executable &quot;/scicore/home/cichon/GROUP/test_workflow/.snakemake/conda/0ecf6ba401c70d7501c73bb1c733a060/bin/bwa-mem2.avx&quot;, simd = .avx
Launching executable &quot;/scicore/home/cichon/GROUP/test_workflow/.snakemake/conda/0ecf6ba401c70d7501c73bb1c733a060/bin/bwa-mem2.avx&quot;
-----------------------------
Executing in AVX mode!!
-----------------------------
* SA compression enabled with xfactor: 8
* Ref file: /scicore/home/cichon/GROUP/test_workflow/data/gch38.fa
* Entering FMI_search
* Index file found. Loading index from /scicore/home/cichon/GROUP/test_workflow/data/gch38.fa.bwt.2bit.64
* Reference seq len for bi-index = 6544178411
* sentinel-index: 2782712944
* Count:
0,  1
1,  1914743810
2,  3272089206
3,  4629434602
4,  6544178411

* Reading other elements of the index from files /scicore/home/cichon/GROUP/test_workflow/data/gch38.fa
* Index prefix: /scicore/home/cichon/GROUP/test_workflow/data/gch38.fa
* Read 0 ALT contigs
[fread] Cannot allocate memory
[main_samview] fail to read the header from &quot;-&quot;.
</code></pre>
<p>Thanks</p>
<p>Priya</p>

CC BY-SA 4.0
2021-08-25T12:57:57.090Z
Please don't close the question. I am the one posted the question in Biostars as I didn't get a clear answer, I have posted it here again . Thanks
Atom
CC BY-SA 4.0
2021-08-26T12:10:17.640Z
Clearly, this seems a problem with memory allocation. You should tell us what you tried from the suggestions of Biostars so we can help you in your problem.
user324810
<ngs><snakemake><python><workflow-management>
BWA-MEM2 alignment-Snakemake
# BWA-MEM2 alignment-Snakemake

(Asked by: username_0 on 2021-08-25)

I have started using snakemake 6.5.2 to align fastq files with reference file. I have pasted the error below in this question. How to allocate memory in the snakefile and read the header from samfile, '-'. This is the snakefile (wrapper for running alignment):
 rule bwa_mem2_mem:
        input:
            reads=["/scicore/home/cichon/GROUP/test_workflow/samples/{sample}.1.fq", "/scicore/home/cichon/GROUP/test_workflow/samples/{sample}.2.fq"]
        output:
            "/scicore/home/cichon/GROUP/test_workflow/output/{sample}.bam"
        log:
            "/scicore/home/cichon/GROUP/test_workflow/output/{sample}.log"
        params:
            index="/scicore/home/cichon/GROUP/test_workflow/data/gch38.fa",
            extra=r"-R '@RG\tID:{sample}\tSM:{sample}'",
            sort="none",             # Can be 'none', 'samtools' or 'picard'.
            sort_order="coordinate", # Can be 'coordinate' (default) or 'queryname'.
            sort_extra=""     

        threads: 8
        wrapper:
            "0.77.0/bio/bwa-mem2/mem"

I used this command to execute the above snakemake file:
snakemake --use-conda --snakefile Snakefile --cores -p /scicore/home/cichon/GROUP/test_workflow/output/DE98NGSUKBD117612_1.bam /scicore/home/cichon/GROUP/test_workflow/output/DE71NGSUKBD117613_3.bam

Error from log file:
Looking to launch executable "/scicore/home/cichon/GROUP/test_workflow/.snakemake/conda/0ecf6ba401c70d7501c73bb1c733a060/bin/bwa-mem2.avx", simd = .avx
Launching executable "/scicore/home/cichon/GROUP/test_workflow/.snakemake/conda/0ecf6ba401c70d7501c73bb1c733a060/bin/bwa-mem2.avx"
-----------------------------
Executing in AVX mode!!
-----------------------------
* SA compression enabled with xfactor: 8
* Ref file: /scicore/home/cichon/GROUP/test_workflow/data/gch38.fa
* Entering FMI_search
* Index file found. Loading index from /scicore/home/cichon/GROUP/test_workflow/data/gch38.fa.bwt.2bit.64
* Reference seq len for bi-index = 6544178411
* sentinel-index: 2782712944
* Count:
0,  1
1,  1914743810
2,  3272089206
3,  4629434602
4,  6544178411

* Reading other elements of the index from files /scicore/home/cichon/GROUP/test_workflow/data/gch38.fa
* Index prefix: /scicore/home/cichon/GROUP/test_workflow/data/gch38.fa
* Read 0 ALT contigs
[fread] Cannot allocate memory
[main_samview] fail to read the header from "-".

Thanks
Priya

**Tags:** ngs, snakemake, python, workflow-management
> **Comments:**
> **username_0**: Please don't close the question. I am the one posted the question in Biostars as I didn't get a clear answer, I have posted it here again . Thanks  
> **username_1**: Clearly, this seems a problem with memory allocation. You should tell us what you tried from the suggestions of Biostars so we can help you in your problem.  

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## 0 answers

