I'm trying the rnaseq pipeline with docker. At the fastq conversion step, the following error occurred. Would be grateful if you can advise. Thank you very much!
sudo docker run --rm -v $path_to_data:/data -t broadinstitute/gtex_rnaseq:V8 \
/bin/bash -c "/src/run_SamToFastq.py /data/$input_bam -p ${sample_id} -o /data"
[Nov 07 01:04:25] Starting SamToFastq
[Sat Nov 07 01:04:25 UTC 2020] picard.sam.SamToFastq INPUT=/data/HA10YLS.bam FASTQ=read1_pipe SECOND_END_FASTQ=read2_pip e UNPAIRED_FASTQ=read0_pipe INCLUDE_NON_PF_READS=true INCLUDE_NON_PRIMARY_ALIGNMENTS=false VALIDATION_STRINGENCY=SILENT OUTPUT_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 VERBOS ITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT _SECRETS=client_secrets.json
[Sat Nov 07 01:04:25 UTC 2020] Executing as root@cee0d84bfc96 on Linux 5.3.0-64-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_151-8u151-b12-0ubuntu0.16.04.2-b12; Picard version: 2.9.0-1-gf5b9f50-SNAPSHOT
INFO 2020-11-07 01:04:35 SamToFastq Processed 1,000,000 records. Elapsed time: 00:00:09s. Time for las t 1,000,000: 9s. Last read position: 1:27,415,567
INFO 2020-11-07 01:04:44 SamToFastq Processed 2,000,000 records. Elapsed time: 00:00:18s. Time for las t 1,000,000: 9s. Last read position: 1:43,164,794
INFO 2020-11-07 01:04:53 SamToFastq Processed 3,000,000 records. Elapsed time: 00:00:27s. Time for las t 1,000,000: 8s. Last read position: 1:91,716,929
INFO 2020-11-07 01:05:01 SamToFastq Processed 4,000,000 records. Elapsed time: 00:00:35s. Time for las t 1,000,000: 8s. Last read position: 1:117,624,489
INFO 2020-11-07 01:05:10 SamToFastq Processed 5,000,000 records. Elapsed time: 00:00:44s. Time for las t 1,000,000: 8s. Last read position: 1:153,855,959
INFO 2020-11-07 01:05:18 SamToFastq Processed 6,000,000 records. Elapsed time: 00:00:52s. Time for las t 1,000,000: 8s. Last read position: 1:178,824,140
INFO 2020-11-07 01:05:26 SamToFastq Processed 7,000,000 records. Elapsed time: 00:01:00s. Time for las t 1,000,000: 8s. Last read position: 1:205,087,027
INFO 2020-11-07 01:05:34 SamToFastq Processed 8,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 8s. Last read position: 1:244,318,744
INFO 2020-11-07 01:05:42 SamToFastq Processed 9,000,000 records. Elapsed time: 00:01:16s. Time for last 1,000,000: 7s. Last read position: 10:22,636,254
INFO 2020-11-07 01:05:50 SamToFastq Processed 10,000,000 records. Elapsed time: 00:01:24s. Time for last 1,000,000: 8s. Last read position: 10:68,338,518
INFO 2020-11-07 01:05:58 SamToFastq Processed 11,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 8s. Last read position: 10:96,535,790
INFO 2020-11-07 01:06:06 SamToFastq Processed 12,000,000 records. Elapsed time: 00:01:40s. Time for last 1,000,000: 8s. Last read position: 11:1,880,170
INFO 2020-11-07 01:06:10 SamToFastq Processed 13,000,000 records. Elapsed time: 00:01:44s. Time for last 1,000,000: 3s. Last read position: 11:5,225,474
INFO 2020-11-07 01:06:19 SamToFastq Processed 14,000,000 records. Elapsed time: 00:01:53s. Time for last 1,000,000: 8s. Last read position: 11:5,225,493
INFO 2020-11-07 01:06:33 SamToFastq Processed 15,000,000 records. Elapsed time: 00:02:07s. Time for last 1,000,000: 14s. Last read position: 11:5,225,528
INFO 2020-11-07 01:06:39 SamToFastq Processed 16,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 6s. Last read position: 11:5,225,556
INFO 2020-11-07 01:07:04 SamToFastq Processed 17,000,000 records. Elapsed time: 00:02:38s. Time for last 1,000,000: 25s. Last read position: 11:5,225,581
INFO 2020-11-07 01:07:57 SamToFastq Processed 18,000,000 records. Elapsed time: 00:03:31s. Time for last 1,000,000: 52s. Last read position: 11:5,225,589
INFO 2020-11-07 01:08:51 SamToFastq Processed 19,000,000 records. Elapsed time: 00:04:25s. Time for last 1,000,000: 53s. Last read position: 11:5,225,601
INFO 2020-11-07 01:10:25 SamToFastq Processed 20,000,000 records. Elapsed time: 00:05:59s. Time for last 1,000,000: 94s. Last read position: 11:5,225,620
INFO 2020-11-07 01:12:17 SamToFastq Processed 21,000,000 records. Elapsed time: 00:07:51s. Time for last 1,000,000: 112s. Last read position: 11:5,225,647
INFO 2020-11-07 01:13:46 SamToFastq Processed 22,000,000 records. Elapsed time: 00:09:20s. Time for last 1,000,000: 89s. Last read position: 11:5,225,657
INFO 2020-11-07 01:15:05 SamToFastq Processed 23,000,000 records. Elapsed time: 00:10:39s. Time for last 1,000,000: 78s. Last read position: 11:5,225,669
INFO 2020-11-07 01:16:50 SamToFastq Processed 24,000,000 records. Elapsed time: 00:12:24s. Time for last 1,000,000: 104s. Last read position: 11:5,225,672
INFO 2020-11-07 01:31:59 SamToFastq Processed 25,000,000 records. Elapsed time: 00:27:33s. Time for last 1,000,000: 909s. Last read position: 11:5,225,692
INFO 2020-11-07 01:35:20 SamToFastq Processed 26,000,000 records. Elapsed time: 00:30:54s. Time for last 1,000,000: 200s. Last read position: 11:5,225,705
INFO 2020-11-07 01:36:50 SamToFastq Processed 27,000,000 records. Elapsed time: 00:32:24s. Time for last 1,000,000: 90s. Last read position: 11:5,226,586
INFO 2020-11-07 01:37:15 SamToFastq Processed 28,000,000 records. Elapsed time: 00:32:49s. Time for last 1,000,000: 24s. Last read position: 11:5,226,603
INFO 2020-11-07 01:37:36 SamToFastq Processed 29,000,000 records. Elapsed time: 00:33:10s. Time for last 1,000,000: 21s. Last read position: 11:5,226,620
INFO 2020-11-07 01:37:46 SamToFastq Processed 30,000,000 records. Elapsed time: 00:33:20s. Time for last 1,000,000: 9s. Last read position: 11:5,226,633
INFO 2020-11-07 01:38:08 SamToFastq Processed 31,000,000 records. Elapsed time: 00:33:42s. Time for last 1,000,000: 22s. Last read position: 11:5,226,647
INFO 2020-11-07 01:39:22 SamToFastq Processed 32,000,000 records. Elapsed time: 00:34:56s. Time for last 1,000,000: 73s. Last read position: 11:5,226,662
INFO 2020-11-07 01:40:54 SamToFastq Processed 33,000,000 records. Elapsed time: 00:36:28s. Time for last 1,000,000: 92s. Last read position: 11:5,226,687
INFO 2020-11-07 01:42:27 SamToFastq Processed 34,000,000 records. Elapsed time: 00:38:01s. Time for last 1,000,000: 93s. Last read position: 11:5,226,721
INFO 2020-11-07 01:43:57 SamToFastq Processed 35,000,000 records. Elapsed time: 00:39:31s. Time for last 1,000,000: 89s. Last read position: 11:5,226,753
INFO 2020-11-07 01:44:12 SamToFastq Processed 36,000,000 records. Elapsed time: 00:39:46s. Time for last 1,000,000: 15s. Last read position: 11:5,226,771
INFO 2020-11-07 01:44:28 SamToFastq Processed 37,000,000 records. Elapsed time: 00:40:02s. Time for last 1,000,000: 15s. Last read position: 11:5,226,774
INFO 2020-11-07 01:44:49 SamToFastq Processed 38,000,000 records. Elapsed time: 00:40:23s. Time for last 1,000,000: 21s. Last read position: 11:5,226,776
INFO 2020-11-07 01:45:01 SamToFastq Processed 39,000,000 records. Elapsed time: 00:40:35s. Time for last 1,000,000: 11s. Last read position: 11:10,766,183
INFO 2020-11-07 01:45:09 SamToFastq Processed 40,000,000 records. Elapsed time: 00:40:43s. Time for last 1,000,000: 8s. Last read position: 11:62,522,604
INFO 2020-11-07 01:45:17 SamToFastq Processed 41,000,000 records. Elapsed time: 00:40:51s. Time for last 1,000,000: 8s. Last read position: 11:65,502,777
INFO 2020-11-07 01:45:26 SamToFastq Processed 42,000,000 records. Elapsed time: 00:41:00s. Time for last 1,000,000: 8s. Last read position: 11:76,990,676
INFO 2020-11-07 01:45:34 SamToFastq Processed 43,000,000 records. Elapsed time: 00:41:08s. Time for last 1,000,000: 8s. Last read position: 11:121,496,986
INFO 2020-11-07 01:45:42 SamToFastq Processed 44,000,000 records. Elapsed time: 00:41:16s. Time for last 1,000,000: 8s. Last read position: 12:10,704,125
INFO 2020-11-07 01:45:50 SamToFastq Processed 45,000,000 records. Elapsed time: 00:41:24s. Time for last 1,000,000: 8s. Last read position: 12:50,461,337
INFO 2020-11-07 01:45:58 SamToFastq Processed 46,000,000 records. Elapsed time: 00:41:32s. Time for last 1,000,000: 8s. Last read position: 12:71,840,291
INFO 2020-11-07 01:46:06 SamToFastq Processed 47,000,000 records. Elapsed time: 00:41:40s. Time for last 1,000,000: 8s. Last read position: 12:112,314,456
INFO 2020-11-07 01:46:14 SamToFastq Processed 48,000,000 records. Elapsed time: 00:41:48s. Time for last 1,000,000: 8s. Last read position: 13:28,198,124
INFO 2020-11-07 01:46:22 SamToFastq Processed 49,000,000 records. Elapsed time: 00:41:56s. Time for last 1,000,000: 8s. Last read position: 13:77,191,780
INFO 2020-11-07 01:46:30 SamToFastq Processed 50,000,000 records. Elapsed time: 00:42:04s. Time for last 1,000,000: 8s. Last read position: 14:35,400,666
INFO 2020-11-07 01:46:35 SamToFastq Processed 51,000,000 records. Elapsed time: 00:42:09s. Time for last 1,000,000: 4s. Last read position: 14:49,586,632
INFO 2020-11-07 01:46:49 SamToFastq Processed 52,000,000 records. Elapsed time: 00:42:23s. Time for last 1,000,000: 14s. Last read position: 14:49,586,718
INFO 2020-11-07 01:46:55 SamToFastq Processed 53,000,000 records. Elapsed time: 00:42:29s. Time for last 1,000,000: 6s. Last read position: 14:49,862,578
INFO 2020-11-07 01:47:08 SamToFastq Processed 54,000,000 records. Elapsed time: 00:42:42s. Time for last 1,000,000: 13s. Last read position: 14:49,862,687
INFO 2020-11-07 01:47:18 SamToFastq Processed 55,000,000 records. Elapsed time: 00:42:52s. Time for last 1,000,000: 9s. Last read position: 14:71,390,545
INFO 2020-11-07 01:47:26 SamToFastq Processed 56,000,000 records. Elapsed time: 00:43:00s. Time for last 1,000,000: 8s. Last read position: 14:105,644,571
INFO 2020-11-07 01:47:34 SamToFastq Processed 57,000,000 records. Elapsed time: 00:43:08s. Time for last 1,000,000: 8s. Last read position: 15:56,700,946
INFO 2020-11-07 01:47:42 SamToFastq Processed 58,000,000 records. Elapsed time: 00:43:16s. Time for last 1,000,000: 8s. Last read position: 15:82,372,502
INFO 2020-11-07 01:47:49 SamToFastq Processed 59,000,000 records. Elapsed time: 00:43:23s. Time for last 1,000,000: 7s. Last read position: 16:172,890
INFO 2020-11-07 01:48:07 SamToFastq Processed 60,000,000 records. Elapsed time: 00:43:41s. Time for last 1,000,000: 17s. Last read position: 16:172,896
INFO 2020-11-07 01:48:14 SamToFastq Processed 61,000,000 records. Elapsed time: 00:43:48s. Time for last 1,000,000: 7s. Last read position: 16:172,901
INFO 2020-11-07 01:48:23 SamToFastq Processed 62,000,000 records. Elapsed time: 00:43:57s. Time for last 1,000,000: 8s. Last read position: 16:172,908
INFO 2020-11-07 01:50:46 SamToFastq Processed 63,000,000 records. Elapsed time: 00:46:20s. Time for last 1,000,000: 142s. Last read position: 16:172,939
[Sat Nov 07 02:03:15 UTC 2020] picard.sam.SamToFastq done. Elapsed time: 58.83 minutes.
Runtime.totalMemory()=4898947072
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded
at htsjdk.samtools.BAMRecordCodec.decode(BAMRecordCodec.java:198)
at htsjdk.samtools.BAMFileReader$BAMFileIterator.getNextRecord(BAMFileReader.java:813)
at htsjdk.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:787)
at htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:781)
at htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:751)
at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:569)
at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:543)
at picard.sam.SamToFastq.doWork(SamToFastq.java:174)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:205)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:94)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:104)
Traceback (most recent call last):
File "/src/run_SamToFastq.py", line 52, in
+' VALIDATION_STRINGENCY=SILENT FASTQ=read1_pipe SECOND_END_FASTQ=read2_pipe UNPAIRED_FASTQ=read0_pipe', shell=True)
File "/usr/lib/python3.5/subprocess.py", line 581, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'java -jar -Xmx8g /opt/picard-tools/picard.jar SamToFastq INPUT=/data/HA10YLS.bam INCLUDE_NON_PF_READS=true INCLUDE_NON_PRIMARY_ALIGNMENTS=false VALIDATION_STRINGENCY=SILENT FASTQ=read1_pipe SECOND_END_FASTQ=read2_pipe UNPAIRED_FASTQ=read0_pipe' returned non-zero exit status 1