Open JianGuoZhou3 opened 2 years ago
Thanks for your support. Other datasets success, but this dataset did not work...
Whole-transcriptome RNA sequencing
Total RNA was extracted from unstained FFPE tumor samples by the All Prep-DNA/RNA-Micro Kit (Qiagen) following the
standard manufacturer’s protocol. Reverse transcription and second-strand cDNA synthesis were subsequently performed.
Barcoded RNA libraries were generated and captured by a customized whole-exome panel. All libraries were sequenced on
the Illumina NovaSeq 6000 platform with 2 × 150 bp paired-end reads. The mean sequencing coverage across all samples
was ∼100× (3.5 G). RNA-seq reads were mapped to the human reference genome GRCh37 using STAR[72]
(https://www.nature.com/articles/s41525-021-00169-w#ref-CR72), and gene expression was quantified using RSEM[73]
(https://www.nature.com/articles/s41525-021-00169-w#ref-CR73). Coding region reads were counted to calculate
fragments per kilobase of transcript per million mapped reads (FPKM) values at the gene level and log2-transformed before
analysis to avoid extremely skewed gene expression distributions.
Ref: https://www.nature.com/articles/s41525-021-00169-w#Sec9
Hi,
Please provide the output of the following command:
ls -ltr [/path/to/your/NCLscan/output/directory/]
Thanks, tw
HI @chiangtw please check this file! Best, JG nohup.out.txt
Hi @chiangtw @TreesLab @chenchiaying please check another cohort. Best, JG nohup.out1.txt
Hi,
For simplicity, is it possible to run NCLscan with only one sample at a time? And it would be very helpful to provide both the log messages and the file sizes of all output files from NCLscan.
You can use the following command to get the file sizes:
ls -ltr [/path/to/your/NCLscan/output/directory/] > file_sizes.txt
Thanks, tw
Hi,
For simplicity, is it possible to run NCLscan with only one sample at a time? And it would be very helpful to provide both the log messages and the file sizes of all output files from NCLscan.
You can use the following command to get the file sizes:
ls -ltr [/path/to/your/NCLscan/output/directory/] > file_sizes.txt
Thanks, tw
Hi @chiangtw Please check the file_sizes.txt of HRA000524 datasets' HRR179719. file_sizes.txt Thanks, JG.
Hi, i have met a similar problem
the filesizes are total 11415056 -rw-rw-r-- 1 logen logen 7099414220 4月 6 18:34 cpsf30_0h.main.bwa.bam -rw-rw-r-- 1 logen logen 833593837 4月 6 18:36 cpsf30_0h.main.bwa.unmapped.sam -rw-rw-r-- 1 logen logen 27324653 4月 6 18:36 cpsf30_0h.main.bwa.unmapped.sam.id -rw-rw-r-- 1 logen logen 243982013 4月 6 18:37 cpsf30_0h.main.bwa.unmapped_1.fastq -rw-rw-r-- 1 logen logen 243982013 4月 6 18:38 cpsf30_0h.main.bwa.unmapped_2.fastq -rw-rw-r-- 1 logen logen 301149143 4月 6 19:33 cpsf30_0h.main.sam -rw-rw-r-- 1 logen logen 136498545 4月 6 19:33 cpsf30_0h.main.unmapped.sam -rw-rw-r-- 1 logen logen 13700571 4月 6 19:33 cpsf30_0h.main.unmapped.sam.id -rw-rw-r-- 1 logen logen 122336081 4月 6 19:33 cpsf30_0h.main.unmapped_1.fastq -rw-rw-r-- 1 logen logen 122336081 4月 6 19:33 cpsf30_0h.main.unmapped_2.fastq -rw-rw-r-- 1 logen logen 107499109 4月 6 19:34 cpsf30_0h.main.unmapped.fa -rw-rw-r-- 1 logen logen 107499109 4月 6 19:34 cpsf30_0h.unmapped.fa -rw-rw-r-- 1 logen logen 282143365 4月 6 19:45 cpsf30_0h.rG.psl -rw-rw-r-- 1 logen logen 0 4月 6 19:45 cpsf30_0h.un.psl -rw-rw-r-- 1 logen logen 282143365 4月 6 19:45 cpsf30_0h.rG.non_un.psl -rw-rw-r-- 1 logen logen 21258825 4月 6 19:45 cpsf30_0h.chi0.bed -rw-rw-r-- 1 logen logen 35733415 4月 6 19:45 cpsf30_0h.unmapped.2.fa -rw-rw-r-- 1 logen logen 42764808 4月 6 19:49 cpsf30_0h.coding.2.psl -rw-rw-r-- 1 logen logen 203472 4月 6 19:49 cpsf30_0h.lncRNA.2.psl -rw-rw-r-- 1 logen logen 0 4月 6 19:50 cpsf30_0h.chrM.2.psl -rw-rw-r-- 1 logen logen 16117 4月 6 19:50 cpsf30_0h.colinear.psl -rw-rw-r-- 1 logen logen 21238911 4月 6 19:50 cpsf30_0h.chi.bed -rw-rw-r-- 1 logen logen 1208387 4月 6 19:50 cpsf30_0h.preJS.bed -rw-rw-r-- 1 logen logen 1146828 4月 6 19:50 cpsf30_0h.preJS.info -rw-rw-r-- 1 logen logen 1144729 4月 6 19:50 cpsf30_0h.preJS.info2 -rw-rw-r-- 1 logen logen 488714 4月 6 19:50 cpsf30_0h.JS.info_1 -rw-rw-r-- 1 logen logen 705918 4月 6 19:50 cpsf30_0h.JS.info_2 -rw-rw-r-- 1 logen logen 60031 4月 6 19:50 cpsf30_0h.JS.info -rw-rw-r-- 1 logen logen 51785 4月 6 19:50 cpsf30_0h.JS.cleaned.info -rw-rw-r-- 1 logen logen 2880629 4月 6 19:50 cpsf30_0h.preJS.seq -rw-rw-r-- 1 logen logen 2878530 4月 6 19:50 cpsf30_0h.preJS.seq2 -rw-rw-r-- 1 logen logen 1101790 4月 6 19:50 cpsf30_0h.JS.seq_1 -rw-rw-r-- 1 logen logen 1776738 4月 6 19:50 cpsf30_0h.JS.seq_2 -rw-rw-r-- 1 logen logen 182401 4月 6 19:50 cpsf30_0h.JS.seq12 -rw-rw-r-- 1 logen logen 157328 4月 6 19:50 cpsf30_0h.JS.seq -rw-rw-r-- 1 logen logen 157786 4月 6 19:50 cpsf30_0h.JS.fa -rwxr--r-- 1 logen logen 1683393 4月 6 19:50 cpsf30_0h.JS.ndx -rw-rw-r-- 1 logen logen 135280811 4月 6 19:51 cpsf30_0h.main_1.JS.sam -rw-rw-r-- 1 logen logen 135283178 4月 6 19:53 cpsf30_0h.main_2.JS.sam -rw-rw-r-- 1 logen logen 270563989 4月 6 19:53 all.cpsf30_0h.JS.sam -rw-rw-r-- 1 logen logen 9731 4月 6 19:53 all.cpsf30_0h.JS.Parsered.sam -rw-rw-r-- 1 logen logen 343 4月 6 19:53 tmp.info -rw-rw-r-- 1 logen logen 273 4月 6 19:53 cpsf30_0h.info -rw-rw-r-- 1 logen logen 1048 4月 6 19:53 cpsf30_0h.JS.clear.fa -rw-rw-r-- 1 logen logen 55491 4月 6 19:53 cpsf30_0h.JS.GRCh37.psl -rw-rw-r-- 1 logen logen 205 4月 6 19:53 cpsf30_0h.JS.GRCh37.2.psl -rw-rw-r-- 1 logen logen 38 4月 6 19:53 cpsf30_0h.linearJS -rw-rw-r-- 1 logen logen 255 4月 6 19:53 cpsf30_0h.tmp.info -rw-rw-r-- 1 logen logen 115 4月 6 19:53 cpsf30_0h.tmp2.info -rw-rw-r-- 1 logen logen 77 4月 6 19:53 cpsf30_0h.2.info -rw-rw-r-- 1 logen logen 688 4月 6 19:53 cpsf30_0h.2.info.fa -rw-rw-r-- 1 logen logen 7122 4月 6 19:53 cpsf30_0h.2.info.GRCh37.psl -rw-rw-r-- 1 logen logen 380 4月 6 19:53 cpsf30_0h.2.chi.bed -rw-rw-r-- 1 logen logen 804 4月 6 19:53 temp.list -rw-rw-r-- 1 logen logen 558 4月 6 19:53 cpsf30_0h.chi2.bed -rw-rw-r-- 1 logen logen 378 4月 6 19:53 cpsf30_0h.chi3.bed -rw-rw-r-- 1 logen logen 389 4月 6 19:53 cpsf30_0h.PreJS2.bed -rw-rw-r-- 1 logen logen 384 4月 6 19:53 cpsf30_0h.PreJS2.info -rw-rw-r-- 1 logen logen 342 4月 6 19:53 cpsf30_0h.PreJS2.info2 -rw-rw-r-- 1 logen logen 207 4月 6 19:53 cpsf30_0h.JS2.info_1 -rw-rw-r-- 1 logen logen 151 4月 6 19:53 cpsf30_0h.JS2.info_2 -rw-rw-r-- 1 logen logen 263 4月 6 19:53 cpsf30_0h.JS2.info -rw-rw-r-- 1 logen logen 263 4月 6 19:53 cpsf30_0h.JS2.cleaned.info -rw-rw-r-- 1 logen logen 180 4月 6 19:53 cpsf30_0h.JS2.preIdx -rw-rw-r-- 1 logen logen 267 4月 6 19:53 cpsf30_0h.JS1.preIdx -rw-rw-r-- 1 logen logen 261 4月 6 19:53 cpsf30_0h.JS1.Idx -rw-rw-r-- 1 logen logen 180 4月 6 19:53 cpsf30_0h.JS2.Idx -rw-rw-r-- 1 logen logen 3422 4月 6 19:53 cpsf30_0h.PreJS2.seq -rw-rw-r-- 1 logen logen 3380 4月 6 19:53 cpsf30_0h.PreJS2.seq2 -rw-rw-r-- 1 logen logen 1689 4月 6 19:53 cpsf30_0h.JS2.seq_1 -rw-rw-r-- 1 logen logen 1689 4月 6 19:53 cpsf30_0h.JS2.seq_2 -rw-rw-r-- 1 logen logen 3283 4月 6 19:53 cpsf30_0h.JS2.seq -rw-rw-r-- 1 logen logen 3285 4月 6 19:53 cpsf30_0h.JS2.prefa -rw-rw-r-- 1 logen logen 3337 4月 6 19:53 cpsf30_0h.JS2.fa -rwxr--r-- 1 logen logen 1063520 4月 6 19:53 cpsf30_0h.JS2.ndx -rw-rw-r-- 1 logen logen 271518275 4月 6 19:55 cpsf30_0h.main.JS2.sam -rw-rw-r-- 1 logen logen 0 4月 6 19:55 all.cpsf30_0h.1.sam -rw-rw-r-- 1 logen logen 0 4月 6 19:55 all.cpsf30_0h.1.result -rw-rw-r-- 1 logen logen 271518275 4月 6 19:55 all.cpsf30_0h.JS2.sam -rw-rw-r-- 1 logen logen 0 4月 6 19:55 cpsf30_0h.ncl.sam -rw-rw-r-- 1 logen logen 0 4月 6 19:55 all.cpsf30_0h.result -rw-rw-r-- 1 logen logen 263 4月 6 19:55 cpsf30_0h.JS2.result.info -rw-rw-r-- 1 logen logen 184 4月 6 19:55 cpsf30_0h.result.info -rw-rw-r-- 1 logen logen 180 4月 6 19:55 cpsf30_0h.2b.info -rw-rw-r-- 1 logen logen 0 4月 6 19:55 cpsf30_0h.4.info -rw-rw-r-- 1 logen logen 0 4月 6 19:55 cpsf30_0h.3.info -rw-rw-r-- 1 logen logen 0 4月 6 19:55 cpsf30_0h.preResult -rw-rw-r-- 1 logen logen 0 4月 6 19:55 cpsf30_0h.main_1.um3.fastq -rw-rw-r-- 1 logen logen 0 4月 6 19:55 cpsf30_0h.main_2.um3.fastq -rw-rw-r-- 1 logen logen 0 4月 6 19:55 cpsf30_0h.main.um3.fa -rw-rw-r-- 1 logen logen 0 4月 6 19:55 all.cpsf30_0h.um3.fa -rw-rw-r-- 1 logen logen 0 4月 6 19:55 all.cpsf30_0h.um3.colinear.psl -rw-rw-r-- 1 logen logen 271518275 4月 6 19:55 cpsf30_0h.main.JS2b.sam -rw-rw-r-- 1 logen logen 0 4月 6 19:55 all.cpsf30_0h.1b.sam -rw-rw-r-- 1 logen logen 0 4月 6 19:55 all.cpsf30_0h.1b.result -rw-rw-r-- 1 logen logen 271518275 4月 6 19:55 all.cpsf30_0h.JS2b.sam -rw-rw-r-- 1 logen logen 0 4月 6 19:55 cpsf30_0h.result.sam -rw-rw-r-- 1 logen logen 0 4月 6 19:55 all.cpsf30_0h.b.result -rw-rw-r-- 1 logen logen 0 4月 6 19:55 cpsf30_0h.3b.info -rw-rw-r-- 1 logen logen 0 4月 6 19:55 cpsf30_0h.result.tmp -rw-rw-r-- 1 logen logen 0 4月 6 19:55 cpsf30_0h.4b.info
@chiangtw Failed to HRA000524 dataset (https://ngdc.cncb.ac.cn/gsa-human/browse/HRA000524) I'm not sure this error belongs to bulk RNAseq or this NCLsan?