[E::hts_open_format] Failed to open file "2_5_merged.sort.bam.tmp.1020.bam" : Too many open files 原脚本 samtools sort -o w.sort.bam w.merged.bam 排查原因:临时文件生成太多导致,改善方法就是增大临时文件可写入的大小来减少文件个数 $ samtools sort Usage: samtools sort [options...]...
此外,sambamba 还弥补了 samtools 无法对超过 512Mb 长度的染色体建立 bam 文件索引的缺陷,例如: $ samtools index -b test.sort.bam test.sort.bam.bai [E::hts_idx_check_range] Region 536870922..536871063 cannot be storedina bai index. Try using a csi index[E::sam_index] Read'E00548:269:H...
此外,sambamba 还弥补了 samtools 无法对超过 512Mb 长度的染色体建立 bam 文件索引的缺陷,例如: $ samtools index -b test.sort.bam test.sort.bam.bai [E::hts_idx_check_range] Region 536870922..536871063 cannot be stored in a bai index. Try using a csi index[E::sam_index] Read 'E00548:2...
$ samtools sort -@64 -o sort.bam alignments.sam [bam_sort_core] merging from 3392 files and 64 in-memory blocks... [E::hts_open_format] Failed to open file /tmp/sort.bam.RX8hvv.1020.bam samtools sort: fail to open "/projects/btl_scratch/sjackman/redcedar/tmp/sort.bam.RX8hvv.1...
(1M). Trying to run with -m too small can lead to the creation of a very large number of temporary files. This may make sort fail due to it exceeding limits on the number of files it can have open at the same time. Please check your -m parameter. It should be an integer ...
Ask away! Hello, My workflow seems to be failing as a result of what I think is a samtools error. Command: minimap2 -t 4 -ax splice -uf -p 1.0 "genome_index.mmi" "seqs.fastq.gz" | samtools view -Sb > "output.bam" 3499 samtools sort -@ 4 ...
When deciding how many molecules a set of UMIs represents, many approaches can be taken: We can ignore error possibilities and just perform exact matches: if two UMIs match, they are of the same molecule; if they mismatch, they are different molecules. ...
The first full variant calling run on our shiny new cluster has failed with this error: samtools sort: couldn't allocate memory for bam_mem It looks like the command that's failing is unset JAVA_HOME && /share/apps/rosalind/bcbio-nextgen/master/galaxy/../anaconda/bin/bwa mem -c 250 -...
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if (num_columns > sizeof(scanf_components)) { fprintf(stderr, "[amplicon] error: too many columns in line %d of %s.\n" "Found %d columns, but only up to %zu are expected.\n", line_count, infile, num_columns, sizeof(scanf_components) / sizeof(scanf_components[0])); ...