running picard FastqToSam but the output file is 0 byte

Question

[elaineyang622]

my code is :

java -jar ~/tools/picard/picard-2.8.2.jar FastqToSam \

F1=../S0_L004_R1_001.fastq.gz \

F2=../S0_L004_R2_001.fastq.gz \

 O=fastq_to_bam.bam \

SM=S0_L004

in the log file ,I can't find any error,but fastq_to_bam.bam is 0 byte.

The contents of the log file are as follows：

[Tue Apr 24 15:26:28 CST 2018] picard.sam.FastqToSam FASTQ=../S0_L004_R1_001.fastq.gz FASTQ2=../S0_L004_R2_001.fastq.gz OUTPUT=fastq_to_bam.bam SAMPLE_NAME=S0_L004    USE_SEQUENTIAL_FASTQS=false READ_GROUP_NAME=A SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json

[Tue Apr 24 15:26:28 CST 2018] Executing as lijie@node6 on Linux 2.6.32-504.el6.x86_64 amd64; 

Java HotSpot(TM) 64-Bit Server VM 1.8.0_77-b03; Picard version: 2.8.2-SNAPSHOT
INFO    2018-04-24 15:26:29     FastqToSam      Auto-detected quality format as: Standard.

INFO    2018-04-24 15:26:39     FastqToSam      Processed     1,000,000 records.  Elapsed time: 00:00:09s.  Time for last 1,000,000:    9s.  Last read position:  * / *

INFO    2018-04-24 15:26:50     FastqToSam      Processed     2,000,000 records.  Elapsed time: 00:00:21s.  Time for last 1,000,000:   11s.  Last read position:  * / *

......
......
......

So， what's wrong?

[WouterDeCoster]

I see you are tagging "alignment" but FastqToSam is not an aligner. What are you trying to achieve?

[Pierre Lindenbaum]

we just see the first lines of the logs , what the final message ?

[elaineyang622]

I just want to translate the fastq file into .bam ,and the fastq file is raw data,I'm not align to ref_genome

[Pierre Lindenbaum]

we just see the first lines of the logs , what the final message ?

[efwissel]

I'm having the same error and my final message is below, the file created is 0 bytes.

INFO    2018-06-05 11:21:03     FastqToSam      Processed    63,000,000 records.  Elapsed time: 00:09:24s.  Time for last 1,000,000:    8s.  Last read position: */*
INFO    2018-06-05 11:21:12     FastqToSam      Processed    64,000,000 records.  Elapsed time: 00:09:33s.  Time for last 1,000,000:    8s.  Last read position: */*
INFO    2018-06-05 11:21:20     FastqToSam      Processed    65,000,000 records.  Elapsed time: 00:09:41s.  Time for last 1,000,000:    8s.  Last read position: */*
INFO    2018-06-05 11:21:29     FastqToSam      Processed    66,000,000 records.  Elapsed time: 00:09:50s.  Time for last 1,000,000:    8s.  Last read position: */*
INFO    2018-06-05 11:21:31     FastqToSam      Processed 33075319 fastq reads
INFO    2018-06-05 11:21:32     SortingCollection       Creating merging iterator from 133 files
[Tue Jun 05 11:36:34 EDT 2018] picard.sam.FastqToSam done. Elapsed time: 24.95 minutes.
Runtime.totalMemory()=2076049408

EDIT: I'm also getting these error codes, maybe they are related? I'm using a wrapper to submit all my jobs at once for about 100 files. I think the problem is with the input files, but I don't know if it's with the file themselves or because I am accessing files a directory above the script.

Exception in thread "main" htsjdk.samtools.SAMException: Sequence header must start with @: ^_^@^@^@^@^@^@^Ct}�n��^R����^A.tU�������^L_^F�`����/�زD�y�m[���LFF��8q�����^?ǧ^]��>����������������^Fg��wk���1�k�[��c��^Z~�� at line 1 in fastq /pine/scr/w/i/wissel/hmd_srr/data/BAM/../ERR209255_2.fastq.gz.1
    at htsjdk.samtools.fastq.FastqReader.readNextRecord(FastqReader.java:110)
    at htsjdk.samtools.fastq.FastqReader.<init>(FastqReader.java:94)
    at htsjdk.samtools.fastq.FastqReader.<init>(FastqReader.java:77)
    at picard.sam.FastqToSam.fileToFastqReader(FastqToSam.java:426)
    at picard.sam.FastqToSam.doWork(FastqToSam.java:317)
    at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:282)
    at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103)
    at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113)