No output file from Picard's MarkDuplicates

Hi,

I'm working on a pipeline which takes a BAM file and produces a layout file for viewing in software the team uses. I'm working on unix command line and have Java/1.8.0_60 installed. I've integrated MarkDuplicates into the pipeline and it works absolutely fine with small BAM files (~90kb) but when I try to run it with larger ones (~2gb) it doesn't produce an output file. I've tried running MarkDuplicates independently with the larger file and the same thing happens, no output, and no duplicates metrics file. Prior to MarkDuplicates in the pipeline is Samtools sort so the files should be in the correct sort order when they reach MarkDuplicates (both files already state in their header that they are sorted by coordinate anyway). This is my code (I've also tried it with the file names instead of the variables as I/O but no different):

java -jar picard.jar MarkDuplicates \
   I=${BASENAME_BAM_FILE} \
   O=${UNIQUE_BAM_FILE} \
   M=marked_dup_metrics.txt \
   REMOVE_DUPLICATES=TRUE \
   REMOVE_SEQUENCING_DUPLICATES=TRUE \
   PROGRAM_RECORD_ID=null 

I don't understand why it works for the small file but not the big one, people have said they've used it for BAM files of >10gb which is much bigger than my biggest. I've attached screen-grabs of the whole process for both the large file running independently (human-18hr) and the small one running in the pipeline (testdata). They are different but I'm struggling to understand what the problem is.
Any help would be greatly appreciated.

Thank you,
Rachel

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @RachelM42
    Hi Rachel,

    It looks like you are running into an error with the larger file. Have a look at this thread for some tips on troubleshooting.

    -Sheila

  • yuanwenyuanwen Member
    edited November 2017

    I got the same problem, and I validated my bam file before this step showing no error.

    My code and output are:
    $ java -jar picard.jar MarkDuplicates I=TA10437_sorted_Header.bam O=TA10437_marked_duplicates.bam M=TA10437_marked_dup_metrics.txt
    11:10:28.138 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Users/yuanwenguo/Desktop/Tools/picard/picard.jar!/com/intel/gkl/native/libgkl_compression.dylib
    [Wed Nov 15 11:10:28 CST 2017] MarkDuplicates INPUT=[TA10437_sorted_Header.bam] OUTPUT=TA10437_marked_duplicates.bam METRICS_FILE=TA10437_marked_dup_metrics.txt MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 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 USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
    [Wed Nov 15 11:10:28 CST 2017] Executing as [email protected] on Mac OS X 10.12.6 x86_64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_111-b14; Deflater: Intel; Inflater: Intel; Picard version: 2.15.0-SNAPSHOT
    INFO 2017-11-15 11:10:28 MarkDuplicates Start of doWork freeMemory: 60138376; totalMemory: 64487424; maxMemory: 954728448
    INFO 2017-11-15 11:10:28 MarkDuplicates Reading input file and constructing read end information.
    INFO 2017-11-15 11:10:28 MarkDuplicates Will retain up to 3459161 data points before spilling to disk.
    INFO 2017-11-15 11:10:36 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 6s. Last read position: contig298680_1-1576:606
    INFO 2017-11-15 11:10:36 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
    INFO 2017-11-15 11:10:42 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 5s. Last read position: contig13456_1-3123:1,745
    INFO 2017-11-15 11:10:42 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
    INFO 2017-11-15 11:10:47 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 5s. Last read position: contig35003_516-1841:768
    INFO 2017-11-15 11:10:47 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
    INFO 2017-11-15 11:10:55 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 7s. Last read position: contig23676_368-1071:227
    INFO 2017-11-15 11:10:55 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
    INFO 2017-11-15 11:11:00 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 5s. Last read position: contig3149097_1-512:163
    INFO 2017-11-15 11:11:00 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
    INFO 2017-11-15 11:11:06 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 5s. Last read position: contig103519_1-1985:1,134
    INFO 2017-11-15 11:11:06 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
    INFO 2017-11-15 11:11:12 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 6s. Last read position: contig04421_1-5006:1,124
    INFO 2017-11-15 11:11:12 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
    INFO 2017-11-15 11:11:18 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 5s. Last read position: contig497688_1-1387:1,089
    INFO 2017-11-15 11:11:18 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
    INFO 2017-11-15 11:11:22 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:52s. Time for last 1,000,000: 4s. Last read position: contig202579_1-1929:1,029
    INFO 2017-11-15 11:11:22 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
    INFO 2017-11-15 11:11:27 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 5s. Last read position: contig1915676_576-711:35
    INFO 2017-11-15 11:11:27 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
    INFO 2017-11-15 11:11:35 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 7s. Last read position: contig1697097_1-372:1
    INFO 2017-11-15 11:11:35 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
    INFO 2017-11-15 11:11:40 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:01:10s. Time for last 1,000,000: 5s. Last read position: contig01914_5001-5863:716
    INFO 2017-11-15 11:11:40 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
    INFO 2017-11-15 11:11:44 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 4s. Last read position: contig1649529_337-781:226
    INFO 2017-11-15 11:11:44 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
    INFO 2017-11-15 11:11:52 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:01:22s. Time for last 1,000,000: 7s. Last read position: contig47680_1-1246:738
    INFO 2017-11-15 11:11:52 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
    INFO 2017-11-15 11:11:57 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:01:27s. Time for last 1,000,000: 4s. Last read position: contig114561_1-2294:1,488
    INFO 2017-11-15 11:11:57 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
    INFO 2017-11-15 11:12:02 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 4s. Last read position: contig196153_486-1946:259
    INFO 2017-11-15 11:12:02 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
    INFO 2017-11-15 11:12:08 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:01:38s. Time for last 1,000,000: 5s. Last read position: contig472903_1-1412:1,146
    INFO 2017-11-15 11:12:08 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
    INFO 2017-11-15 11:12:15 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 6s. Last read position: contig148274_268-448:72
    INFO 2017-11-15 11:12:15 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
    INFO 2017-11-15 11:12:20 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:01:50s. Time for last 1,000,000: 5s. Last read position: contig06468_2267-2485:12
    INFO 2017-11-15 11:12:20 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
    INFO 2017-11-15 11:12:25 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:01:55s. Time for last 1,000,000: 4s. Last read position: contig28222_1-3346:784
    INFO 2017-11-15 11:12:25 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
    INFO 2017-11-15 11:12:32 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:02:02s. Time for last 1,000,000: 6s. Last read position: contig418732_652-1484:797
    INFO 2017-11-15 11:12:32 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
    INFO 2017-11-15 11:12:37 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:02:07s. Time for last 1,000,000: 5s. Last read position: contig37078_543-1953:1,074
    INFO 2017-11-15 11:12:37 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
    INFO 2017-11-15 11:12:42 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:02:11s. Time for last 1,000,000: 4s. Last read position: contig36130_1679-3100:188
    INFO 2017-11-15 11:12:42 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
    INFO 2017-11-15 11:12:46 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:02:16s. Time for last 1,000,000: 4s. Last read position: contig72487_1-2627:236
    INFO 2017-11-15 11:12:46 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
    INFO 2017-11-15 11:12:53 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:02:23s. Time for last 1,000,000: 6s. Last read position: contig48822_1-1838:388
    INFO 2017-11-15 11:12:53 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
    INFO 2017-11-15 11:12:58 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:02:28s. Time for last 1,000,000: 4s. Last read position: contig127681_1-2237:1,047
    INFO 2017-11-15 11:12:58 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
    INFO 2017-11-15 11:13:02 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:02:32s. Time for last 1,000,000: 4s. Last read position: contig60690_1-1085:643
    INFO 2017-11-15 11:13:02 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
    INFO 2017-11-15 11:13:09 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:02:39s. Time for last 1,000,000: 6s. Last read position: contig375651_1-1465:50
    INFO 2017-11-15 11:13:09 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
    INFO 2017-11-15 11:13:14 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:02:44s. Time for last 1,000,000: 4s. Last read position: contig2268451_1-647:380
    INFO 2017-11-15 11:13:14 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
    INFO 2017-11-15 11:13:18 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:02:48s. Time for last 1,000,000: 4s. Last read position: contig257365_1-1645:43
    INFO 2017-11-15 11:13:18 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
    INFO 2017-11-15 11:13:23 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:02:52s. Time for last 1,000,000: 4s. Last read position: contig1427124_121-700:295
    INFO 2017-11-15 11:13:23 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
    INFO 2017-11-15 11:13:29 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:02:59s. Time for last 1,000,000: 6s. Last read position: contig2491761_1-605:280
    INFO 2017-11-15 11:13:29 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
    INFO 2017-11-15 11:13:35 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:03:05s. Time for last 1,000,000: 5s. Last read position: contig02341_1-339:4
    INFO 2017-11-15 11:13:35 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
    INFO 2017-11-15 11:13:39 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:03:09s. Time for last 1,000,000: 4s. Last read position: contig2578868_14-591:425
    INFO 2017-11-15 11:13:39 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
    INFO 2017-11-15 11:13:47 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:03:16s. Time for last 1,000,000: 7s. Last read position: contig529444_1-1215:383
    INFO 2017-11-15 11:13:47 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
    INFO 2017-11-15 11:13:52 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:03:22s. Time for last 1,000,000: 5s. Last read position: contig16390_1077-2254:283
    INFO 2017-11-15 11:13:52 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
    INFO 2017-11-15 11:13:57 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:03:27s. Time for last 1,000,000: 4s. Last read position: contig15323_1293-3009:1,544
    INFO 2017-11-15 11:13:57 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
    INFO 2017-11-15 11:14:02 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:03:31s. Time for last 1,000,000: 4s. Last read position: contig553400_30-141:1
    INFO 2017-11-15 11:14:02 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
    INFO 2017-11-15 11:14:10 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:03:40s. Time for last 1,000,000: 8s. Last read position: contig28169_158-269:50
    INFO 2017-11-15 11:14:10 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
    INFO 2017-11-15 11:14:16 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:03:46s. Time for last 1,000,000: 6s. Last read position: contig108212_679-1661:875
    INFO 2017-11-15 11:14:16 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
    INFO 2017-11-15 11:14:20 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:03:50s. Time for last 1,000,000: 4s. Last read position: contig404940_356-1319:249
    INFO 2017-11-15 11:14:20 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
    INFO 2017-11-15 11:14:27 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:03:57s. Time for last 1,000,000: 7s. Last read position: contig3477157_1-474:135
    INFO 2017-11-15 11:14:27 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
    INFO 2017-11-15 11:14:32 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:04:02s. Time for last 1,000,000: 4s. Last read position: contig456357_844-1279:87
    INFO 2017-11-15 11:14:32 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
    INFO 2017-11-15 11:14:36 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:04:06s. Time for last 1,000,000: 4s. Last read position: contig47389_1-2409:464
    INFO 2017-11-15 11:14:36 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
    INFO 2017-11-15 11:14:44 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:04:14s. Time for last 1,000,000: 7s. Last read position: contig146928_4-566:218
    INFO 2017-11-15 11:14:44 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
    INFO 2017-11-15 11:14:49 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:04:19s. Time for last 1,000,000: 4s. Last read position: contig102141_140-1755:790
    INFO 2017-11-15 11:14:49 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
    INFO 2017-11-15 11:14:54 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:04:24s. Time for last 1,000,000: 5s. Last read position: contig1137654_654-824:91
    INFO 2017-11-15 11:14:54 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
    INFO 2017-11-15 11:14:59 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:04:29s. Time for last 1,000,000: 4s. Last read position: contig136365_1-293:51
    INFO 2017-11-15 11:14:59 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
    INFO 2017-11-15 11:15:07 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:04:37s. Time for last 1,000,000: 7s. Last read position: contig444281_118-1185:801
    INFO 2017-11-15 11:15:07 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
    INFO 2017-11-15 11:15:11 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:04:41s. Time for last 1,000,000: 4s. Last read position: contig1082578_1-852:364
    INFO 2017-11-15 11:15:11 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
    INFO 2017-11-15 11:15:11 MarkDuplicates Read 50098586 records. 0 pairs never matched.
    INFO 2017-11-15 11:15:13 MarkDuplicates After buildSortedReadEndLists freeMemory: 706367352; totalMemory: 767033344; maxMemory: 954728448
    INFO 2017-11-15 11:15:13 MarkDuplicates Will retain up to 29835264 duplicate indices before spilling to disk.
    INFO 2017-11-15 11:15:13 MarkDuplicates Traversing read pair information and detecting duplicates.
    INFO 2017-11-15 11:15:13 MarkDuplicates Traversing fragment information and detecting duplicates.
    INFO 2017-11-15 11:15:36 MarkDuplicates Sorting list of duplicate records.
    INFO 2017-11-15 11:15:38 MarkDuplicates After generateDuplicateIndexes freeMemory: 482698576; totalMemory: 768081920; maxMemory: 954728448
    INFO 2017-11-15 11:15:38 MarkDuplicates Marking 27448356 records as duplicates.
    INFO 2017-11-15 11:15:38 MarkDuplicates Found 0 optical duplicate clusters.
    INFO 2017-11-15 11:15:40 MarkDuplicates Reads are assumed to be ordered by: unsorted
    [Wed Nov 15 11:15:40 CST 2017] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 5.20 minutes.
    Runtime.totalMemory()=731906048
    To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
    Exception in thread "main" picard.PicardException: This program requires input that are either coordinate or query sorted. Found unsorted
    at picard.sam.markduplicates.MarkDuplicates.doWork(MarkDuplicates.java:254)
    at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:268)
    at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:98)
    at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:108)
    Exception in thread "Thread-1" Exception in thread "Thread-15" Exception in thread "Thread-13" htsjdk.samtools.util.RuntimeIOException: java.nio.file.NoSuchFileException: /var/folders/q0/_pthqshs7pddd_5p1xv_w1hw0000gn/T/yuanwenguo/sortingcollection.4476654554449842164.tmp
    at htsjdk.samtools.util.IOUtil$DeletePathThread.run(IOUtil.java:374)
    Caused by: java.nio.file.NoSuchFileException: /var/folders/q0/_pthqshs7pddd_5p1xv_w1hw0000gn/T/yuanwenguo/sortingcollection.4476654554449842164.tmp
    at sun.nio.fs.UnixException.translateToIOException(UnixException.java:86)
    at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:102)
    at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:107)
    at sun.nio.fs.UnixFileSystemProvider.implDelete(UnixFileSystemProvider.java:244)
    at sun.nio.fs.AbstractFileSystemProvider.delete(AbstractFileSystemProvider.java:103)
    at java.nio.file.Files.delete(Files.java:1126)
    at htsjdk.samtools.util.IOUtil$DeletePathThread.run(IOUtil.java:372)
    htsjdk.samtools.util.RuntimeIOException: java.nio.file.NoSuchFileException: /var/folders/q0/_pthqshs7pddd_5p1xv_w1hw0000gn/T/yuanwenguo/sortingcollection.5553322400880781157.tmp
    at htsjdk.samtools.util.IOUtil$DeletePathThread.run(IOUtil.java:374)
    Caused by: java.nio.file.NoSuchFileException: /var/folders/q0/_pthqshs7pddd_5p1xv_w1hw0000gn/T/yuanwenguo/sortingcollection.5553322400880781157.tmp
    at sun.nio.fs.UnixException.translateToIOException(UnixException.java:86)
    at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:102)
    at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:107)
    at sun.nio.fs.UnixFileSystemProvider.implDelete(UnixFileSystemProvider.java:244)
    at sun.nio.fs.AbstractFileSystemProvider.delete(AbstractFileSystemProvider.java:103)
    at java.nio.file.Files.delete(Files.java:1126)
    at htsjdk.samtools.util.IOUtil$DeletePathThread.run(IOUtil.java:372)
    Exception in thread "Thread-5" htsjdk.samtools.util.RuntimeIOException: java.nio.file.NoSuchFileException: /var/folders/q0/_pthqshs7pddd_5p1xv_w1hw0000gn/T/yuanwenguo/sortingcollection.8466195020220442214.tmp
    at htsjdk.samtools.util.IOUtil$DeletePathThread.run(IOUtil.java:374)
    Caused by: java.nio.file.NoSuchFileException: /var/folders/q0/_pthqshs7pddd_5p1xv_w1hw0000gn/T/yuanwenguo/sortingcollection.8466195020220442214.tmp
    at sun.nio.fs.UnixException.translateToIOException(UnixException.java:86)
    at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:102)
    at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:107)
    at sun.nio.fs.UnixFileSystemProvider.implDelete(UnixFileSystemProvider.java:244)
    at sun.nio.fs.AbstractFileSystemProvider.delete(AbstractFileSystemProvider.java:103)
    at java.nio.file.Files.delete(Files.java:1126)
    at htsjdk.samtools.util.IOUtil$DeletePathThread.run(IOUtil.java:372)
    Exception in thread "Thread-14" Exception in thread "Thread-12" htsjdk.samtools.util.RuntimeIOException: java.nio.file.NoSuchFileException: /var/folders/q0/_pthqshs7pddd_5p1xv_w1hw0000gn/T/yuanwenguo/sortingcollection.6389120246308144364.tmp
    at htsjdk.samtools.util.IOUtil$DeletePathThread.run(IOUtil.java:374)
    Caused by: java.nio.file.NoSuchFileException: /var/folders/q0/_pthqshs7pddd_5p1xv_w1hw0000gn/T/yuanwenguo/sortingcollection.6389120246308144364.tmp
    at sun.nio.fs.UnixException.translateToIOException(UnixException.java:86)
    at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:102)
    at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:107)
    at sun.nio.fs.UnixFileSystemProvider.implDelete(UnixFileSystemProvider.java:244)
    at sun.nio.fs.AbstractFileSystemProvider.delete(AbstractFileSystemProvider.java:103)
    at java.nio.file.Files.delete(Files.java:1126)
    at htsjdk.samtools.util.IOUtil$DeletePathThread.run(IOUtil.java:372)
    Exception in thread "Thread-10" Exception in thread "Thread-2" htsjdk.samtools.util.RuntimeIOException: java.nio.file.NoSuchFileException: /var/folders/q0/_pthqshs7pddd_5p1xv_w1hw0000gn/T/yuanwenguo/sortingcollection.1802568126788770186.tmp
    at htsjdk.samtools.util.IOUtil$DeletePathThread.run(IOUtil.java:374)
    Caused by: java.nio.file.NoSuchFileException: /var/folders/q0/_pthqshs7pddd_5p1xv_w1hw0000gn/T/yuanwenguo/sortingcollection.1802568126788770186.tmp
    at sun.nio.fs.UnixException.translateToIOException(UnixException.java:86)
    at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:102)
    at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:107)
    at sun.nio.fs.UnixFileSystemProvider.implDelete(UnixFileSystemProvider.java:244)
    at sun.nio.fs.AbstractFileSystemProvider.delete(AbstractFileSystemProvider.java:103)
    at java.nio.file.Files.delete(Files.java:1126)
    at htsjdk.samtools.util.IOUtil$DeletePathThread.run(IOUtil.java:372)
    htsjdk.samtools.util.RuntimeIOException: java.nio.file.NoSuchFileException: /var/folders/q0/_pthqshs7pddd_5p1xv_w1hw0000gn/T/yuanwenguo/sortingcollection.3957399477718005702.tmp
    at htsjdk.samtools.util.IOUtil$DeletePathThread.run(IOUtil.java:374)
    Caused by: java.nio.file.NoSuchFileException: /var/folders/q0/_pthqshs7pddd_5p1xv_w1hw0000gn/T/yuanwenguo/sortingcollection.3957399477718005702.tmp
    at sun.nio.fs.UnixException.translateToIOException(UnixException.java:86)
    at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:102)
    at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:107)
    at sun.nio.fs.UnixFileSystemProvider.implDelete(UnixFileSystemProvider.java:244)
    at sun.nio.fs.AbstractFileSystemProvider.delete(AbstractFileSystemProvider.java:103)
    at java.nio.file.Files.delete(Files.java:1126)
    at htsjdk.samtools.util.IOUtil$DeletePathThread.run(IOUtil.java:372)
    htsjdk.samtools.util.RuntimeIOException: java.nio.file.NoSuchFileException: /var/folders/q0/_pthqshs7pddd_5p1xv_w1hw0000gn/T/yuanwenguo/sortingcollection.6972374211580862587.tmp
    at htsjdk.samtools.util.IOUtil$DeletePathThread.run(IOUtil.java:374)
    Caused by: java.nio.file.NoSuchFileException: /var/folders/q0/_pthqshs7pddd_5p1xv_w1hw0000gn/T/yuanwenguo/sortingcollection.6972374211580862587.tmp
    at sun.nio.fs.UnixException.translateToIOException(UnixException.java:86)
    at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:102)
    at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:107)
    at sun.nio.fs.UnixFileSystemProvider.implDelete(UnixFileSystemProvider.java:244)
    at sun.nio.fs.AbstractFileSystemProvider.delete(AbstractFileSystemProvider.java:103)
    at java.nio.file.Files.delete(Files.java:1126)
    at htsjdk.samtools.util.IOUtil$DeletePathThread.run(IOUtil.java:372)
    htsjdk.samtools.util.RuntimeIOException: java.nio.file.NoSuchFileException: /var/folders/q0/_pthqshs7pddd_5p1xv_w1hw0000gn/T/yuanwenguo/sortingcollection.5865380701168207862.tmp
    at htsjdk.samtools.util.IOUtil$DeletePathThread.run(IOUtil.java:374)
    Caused by: java.nio.file.NoSuchFileException: /var/folders/q0/_pthqshs7pddd_5p1xv_w1hw0000gn/T/yuanwenguo/sortingcollection.5865380701168207862.tmp
    at sun.nio.fs.UnixException.translateToIOException(UnixException.java:86)
    at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:102)
    at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:107)
    at sun.nio.fs.UnixFileSystemProvider.implDelete(UnixFileSystemProvider.java:244)
    at sun.nio.fs.AbstractFileSystemProvider.delete(AbstractFileSystemProvider.java:103)
    at java.nio.file.Files.delete(Files.java:1126)
    at htsjdk.samtools.util.IOUtil$DeletePathThread.run(IOUtil.java:372)
    Exception in thread "Thread-11" Exception in thread "Thread-3" Exception in thread "Thread-6" Exception in thread "Thread-8" Exception in thread "Thread-4" Exception in thread "Thread-7" Exception in thread "Thread-9" htsjdk.samtools.util.RuntimeIOException: java.nio.file.NoSuchFileException: /var/folders/q0/_pthqshs7pddd_5p1xv_w1hw0000gn/T/yuanwenguo/sortingcollection.2285578967023641701.tmp
    at htsjdk.samtools.util.IOUtil$DeletePathThread.run(IOUtil.java:374)
    Caused by: java.nio.file.NoSuchFileException: /var/folders/q0/_pthqshs7pddd_5p1xv_w1hw0000gn/T/yuanwenguo/sortingcollection.2285578967023641701.tmp
    at sun.nio.fs.UnixException.translateToIOException(UnixException.java:86)
    at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:102)
    at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:107)
    at sun.nio.fs.UnixFileSystemProvider.implDelete(UnixFileSystemProvider.java:244)
    at sun.nio.fs.AbstractFileSystemProvider.delete(AbstractFileSystemProvider.java:103)
    at java.nio.file.Files.delete(Files.java:1126)
    at htsjdk.samtools.util.IOUtil$DeletePathThread.run(IOUtil.java:372)
    htsjdk.samtools.util.RuntimeIOException: java.nio.file.NoSuchFileException: /var/folders/q0/_pthqshs7pddd_5p1xv_w1hw0000gn/T/yuanwenguo/sortingcollection.8585483847477630742.tmp
    at htsjdk.samtools.util.IOUtil$DeletePathThread.run(IOUtil.java:374)
    Caused by: java.nio.file.NoSuchFileException: /var/folders/q0/_pthqshs7pddd_5p1xv_w1hw0000gn/T/yuanwenguo/sortingcollection.8585483847477630742.tmp
    at sun.nio.fs.UnixException.translateToIOException(UnixException.java:86)
    at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:102)
    at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:107)
    at sun.nio.fs.UnixFileSystemProvider.implDelete(UnixFileSystemProvider.java:244)
    at sun.nio.fs.AbstractFileSystemProvider.delete(AbstractFileSystemProvider.java:103)
    at java.nio.file.Files.delete(Files.java:1126)
    at htsjdk.samtools.util.IOUtil$DeletePathThread.run(IOUtil.java:372)
    htsjdk.samtools.util.RuntimeIOException: java.nio.file.NoSuchFileException: /var/folders/q0/_pthqshs7pddd_5p1xv_w1hw0000gn/T/yuanwenguo/sortingcollection.5534992230294178765.tmp
    at htsjdk.samtools.util.IOUtil$DeletePathThread.run(IOUtil.java:374)
    Caused by: java.nio.file.NoSuchFileException: /var/folders/q0/_pthqshs7pddd_5p1xv_w1hw0000gn/T/yuanwenguo/sortingcollection.5534992230294178765.tmp
    at sun.nio.fs.UnixException.translateToIOException(UnixException.java:86)
    at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:102)
    at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:107)
    at sun.nio.fs.UnixFileSystemProvider.implDelete(UnixFileSystemProvider.java:244)
    at sun.nio.fs.AbstractFileSystemProvider.delete(AbstractFileSystemProvider.java:103)
    at java.nio.file.Files.delete(Files.java:1126)
    at htsjdk.samtools.util.IOUtil$DeletePathThread.run(IOUtil.java:372)
    htsjdk.samtools.util.RuntimeIOException: java.nio.file.NoSuchFileException: /var/folders/q0/_pthqshs7pddd_5p1xv_w1hw0000gn/T/yuanwenguo/sortingcollection.5420601163654261825.tmp
    at htsjdk.samtools.util.IOUtil$DeletePathThread.run(IOUtil.java:374)
    Caused by: java.nio.file.NoSuchFileException: /var/folders/q0/_pthqshs7pddd_5p1xv_w1hw0000gn/T/yuanwenguo/sortingcollection.5420601163654261825.tmp
    at sun.nio.fs.UnixException.translateToIOException(UnixException.java:86)
    at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:102)
    at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:107)
    at sun.nio.fs.UnixFileSystemProvider.implDelete(UnixFileSystemProvider.java:244)
    at sun.nio.fs.AbstractFileSystemProvider.delete(AbstractFileSystemProvider.java:103)
    at java.nio.file.Files.delete(Files.java:1126)
    at htsjdk.samtools.util.IOUtil$DeletePathThread.run(IOUtil.java:372)
    htsjdk.samtools.util.RuntimeIOException: java.nio.file.NoSuchFileException: /var/folders/q0/_pthqshs7pddd_5p1xv_w1hw0000gn/T/yuanwenguo/sortingcollection.8664303820316821355.tmp
    at htsjdk.samtools.util.IOUtil$DeletePathThread.run(IOUtil.java:374)
    Caused by: java.nio.file.NoSuchFileException: /var/folders/q0/_pthqshs7pddd_5p1xv_w1hw0000gn/T/yuanwenguo/sortingcollection.8664303820316821355.tmp
    at sun.nio.fs.UnixException.translateToIOException(UnixException.java:86)
    at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:102)
    at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:107)
    at sun.nio.fs.UnixFileSystemProvider.implDelete(UnixFileSystemProvider.java:244)
    at sun.nio.fs.AbstractFileSystemProvider.delete(AbstractFileSystemProvider.java:103)
    at java.nio.file.Files.delete(Files.java:1126)
    at htsjdk.samtools.util.IOUtil$DeletePathThread.run(IOUtil.java:372)
    htsjdk.samtools.util.RuntimeIOException: java.nio.file.NoSuchFileException: /var/folders/q0/_pthqshs7pddd_5p1xv_w1hw0000gn/T/yuanwenguo/sortingcollection.4913999957370563612.tmp
    at htsjdk.samtools.util.IOUtil$DeletePathThread.run(IOUtil.java:374)
    Caused by: java.nio.file.NoSuchFileException: /var/folders/q0/_pthqshs7pddd_5p1xv_w1hw0000gn/T/yuanwenguo/sortingcollection.4913999957370563612.tmp
    at sun.nio.fs.UnixException.translateToIOException(UnixException.java:86)
    at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:102)
    at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:107)
    at sun.nio.fs.UnixFileSystemProvider.implDelete(UnixFileSystemProvider.java:244)
    at sun.nio.fs.AbstractFileSystemProvider.delete(AbstractFileSystemProvider.java:103)
    at java.nio.file.Files.delete(Files.java:1126)
    at htsjdk.samtools.util.IOUtil$DeletePathThread.run(IOUtil.java:372)
    htsjdk.samtools.util.RuntimeIOException: java.nio.file.NoSuchFileException: /var/folders/q0/_pthqshs7pddd_5p1xv_w1hw0000gn/T/yuanwenguo/sortingcollection.1906462251204193547.tmp
    at htsjdk.samtools.util.IOUtil$DeletePathThread.run(IOUtil.java:374)
    Caused by: java.nio.file.NoSuchFileException: /var/folders/q0/_pthqshs7pddd_5p1xv_w1hw0000gn/T/yuanwenguo/sortingcollection.1906462251204193547.tmp
    at sun.nio.fs.UnixException.translateToIOException(UnixException.java:86)
    at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:102)
    at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:107)
    at sun.nio.fs.UnixFileSystemProvider.implDelete(UnixFileSystemProvider.java:244)
    at sun.nio.fs.AbstractFileSystemProvider.delete(AbstractFileSystemProvider.java:103)
    at java.nio.file.Files.delete(Files.java:1126)
    at htsjdk.samtools.util.IOUtil$DeletePathThread.run(IOUtil.java:372)

    Any help will be appreciated!

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @yuanwen
    Hi,

    The error message at the beginning states "This program requires input that are either coordinate or query sorted. Found unsorted"

    You can use SortSam to fix this. Let us know if that resolves the issue.

    -Sheila

  • @Sheila, thank you for the help! I noticed it.

    Best,
    Yuanwen

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