why bcl2fastq always sleeping?

Question

[zm20074970]

Hi, everyone, I am using bcl2fastq v2.17 to change bcl files to fastq files, but after it processed several minutes, it would be static, the state is "S" when I typing "top" and will last two weeks without any error, and it only produced the fastq files in Lane 1, could someone give some advice, thanks very much!

The command is:

bcl2fastq-2.17.1.14/bin/bcl2fastq \
  -i Data/Intensities/BaseCalls/ \
  -R 151105_7001456_0617/ \
  --adapter-stringency 0.9 \
  --minimum-trimmed-read-length 35 \
  --mask-short-adapter-reads 22 \
  -r 2 \
  -p 2 \
  -d 2 \
  -w 2 \
  -o Unaligned \
  --sample-sheet SampleSheet.csv

The part of my SampleSheet.csv is:

[Settings]
ReverseComplement,0
Adapter,GATCGGAAGAGCACACGTCTGAACTCCAGTCAC
AdapterRead2,AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT

[Data]
Lane,Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_index_ID,index,Sample_Project,Description
1,150517F_1,,,,,ATCACG,150517,bovine_RNA
1,150517F_2,,,,,CGATGT,150517,bovine_RNA
1,150517F_3,,,,,TTAGGC,150517,bovine_RNA
1,150517F_4,,,,,TGACCA,150517,bovine_RNA
1,150517F_5,,,,,ACAGTG,150517,bovine_RNA
1,150517F_6,,,,,GCCAAT,150517,bovine_RNA
1,150517F_7,,,,,CAGATC,150517,bovine_RNA
1,150517F_8,,,,,ACTTGA,150517,bovine_RNA
1,150517F_9,,,,,GATCAG,150517,bovine_RNA
1,150517F_10,,,,,TAGCTT,150517,bovine_RNA
1,150517F_11,,,,,GGCTAC,150517,bovine_RNA
1,150517F_12,,,,,CTTGTA,150517,bovine_RNA
1,150517F_13,,,,,AGTCAA,150517,bovine_RNA
2,150517F_13_2,,,,,AGTCAA,150517,bovine_RNA
2,150517F_14,,,,,AGTTCC,150517,bovine_RNA
2,150517F_15,,,,,ATGTCA,150517,bovine_RNA
2,150517F_16,,,,,CCGTCC,150517,bovine_RNA
2,150517F_17,,,,,GTCCGC,150517,bovine_RNA
2,150517F_18,,,,,GTGAAA,150517,bovine_RNA
2,150517F_19,,,,,GTGGCC,150517,bovine_RNA
2,150517F_20,,,,,GTTTCG,150517,bovine_RNA
2,150517F_21,,,,,CGTACG,150517,bovine_RNA
2,150517F_22,,,,,GAGTGG,150517,bovine_RNA
2,150517F_23,,,,,ACTGAT,150517,bovine_RNA
2,150517F_24,,,,,ATTCCT,150517,bovine_RNA
2,150655B_CK,,,,,ATCACG,150655,Corbiculafluminea_RNA

[Jean-Karim Heriche]

A process goes into interruptible sleep state (S) when it waits for something (i.e it gets a blocking system calls). This usually happens with I/O operations like reading/writing to files or to a network or waiting for another process. You can get an idea of what a process is doing using strace:

> strace -p <process ID> -o strace_output.txt
and in another terminal:
> tail -f strace_output.txt