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Mate not found for paired read on SplitNCigarReads

liuhuiliuhui ChinaMember

(1) I got errors when I ran the following command:

java -Xmx64g -Djava.io.tmpdir=/media/10TB/tmp/ \
-jar /home/liuhui/bin/GATK/GenomeAnalysisTK.jar \
-T SplitNCigarReads \
-R /media/10TB/conifer_genome/Ptaeda/STAR/Ptaeda.v1.01_1kScaffolds.fa \
-I NCPT_rg_added_sorted.bam \
-o NCPT_split.bam \
-rf ReassignOneMappingQuality \
-RMQF 255 \
-RMQT 60 \
-U ALLOW_N_CIGAR_READS

the errors I got:

INFO 00:24:49,304 HelpFormatter - --------------------------------------------------------------------------------
INFO 00:24:49,307 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.6-0-g89b7209, Compiled 2016/06/01 22:27:29
INFO 00:24:49,308 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute
INFO 00:24:49,308 HelpFormatter - For support and documentation go to https://www.broadinstitute.org/gatk
INFO 00:24:49,308 HelpFormatter - [Sun Jun 19 00:24:49 CST 2016] Executing on Linux 3.8.0-44-generic amd64
INFO 00:24:49,308 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14 JdkDeflater
INFO 00:24:49,313 HelpFormatter - Program Args: -T SplitNCigarReads -R /media/10TB/conifer_genome/Ptaeda/STAR/Ptaeda.v1.01_1kScaffolds.fa -I NCPT_rg_added_sorted.bam -o NCPT_split.bam -rf ReassignOneMappingQuality -RMQF 255 -RMQT 60 -U ALLOW_N_CIGAR_READS
INFO 00:24:49,317 HelpFormatter - Executing as [email protected] on Linux 3.8.0-44-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14.
INFO 00:24:49,318 HelpFormatter - Date/Time: 2016/06/19 00:24:49
INFO 00:24:49,318 HelpFormatter - --------------------------------------------------------------------------------
INFO 00:24:49,318 HelpFormatter - --------------------------------------------------------------------------------
INFO 00:24:49,396 GenomeAnalysisEngine - Strictness is SILENT
INFO 00:24:49,740 GenomeAnalysisEngine - Downsampling Settings: No downsampling
INFO 00:24:49,749 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 00:24:49,828 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
INFO 00:24:50,132 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
INFO 00:24:50,138 GenomeAnalysisEngine - Done preparing for traversal
INFO 00:24:50,138 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 00:24:50,139 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 00:24:50,139 ProgressMeter - Location | reads | elapsed | reads | completed | runtime | runtime
INFO 00:24:50,189 ReadShardBalancer$1 - Loading BAM index data
INFO 00:24:50,191 ReadShardBalancer$1 - Done loading BAM index data
DEBUG 2016-06-19 00:24:50 BlockCompressedOutputStream Using deflater: Deflater
INFO 00:25:20,144 ProgressMeter - Scaffold_685:84336993 1207219.0 30.0 s 24.0 s 12.4% 4.0 m 3.5 m
INFO 00:25:50,147 ProgressMeter - Scaffold_690:116358573 1624852.0 60.0 s 36.0 s 15.7% 6.4 m 5.4 m
INFO 00:26:20,151 ProgressMeter - Scaffold_812:162230 2320527.0 90.0 s 38.0 s 22.1% 6.8 m 5.3 m
INFO 00:26:50,154 ProgressMeter - Scaffold_827:72458 3068189.0 120.0 s 39.0 s 29.1% 6.9 m 4.9 m
INFO 00:27:21,579 ProgressMeter - Scaffold_842:42562972 3807371.0 2.5 m 39.0 s 35.8% 7.0 m 4.5 m
INFO 00:27:51,585 ProgressMeter - Scaffold_865:57346653 4713814.0 3.0 m 38.0 s 44.2% 6.8 m 3.8 m
INFO 00:28:21,810 ProgressMeter - Scaffold_891:6820448 5623162.0 3.5 m 37.0 s 51.6% 6.8 m 3.3 m
INFO 00:28:51,813 ProgressMeter - Scaffold_929:97449 6729275.0 4.0 m 35.0 s 61.1% 6.6 m 2.6 m
INFO 00:29:21,816 ProgressMeter - Scaffold_963:38212330 7802854.0 4.5 m 34.0 s 69.2% 6.5 m 120.0 s
INFO 00:29:51,829 ProgressMeter - Scaffold_974:6778144 8720387.0 5.0 m 34.0 s 72.3% 6.9 m 115.0 s
INFO 00:30:21,831 ProgressMeter - Scaffold_984:58425420 9606398.0 5.5 m 34.0 s 76.2% 7.2 m 103.0 s
INFO 00:30:54,521 ProgressMeter - Scaffold_992:100546101 1.0270348E7 6.1 m 35.0 s 80.5% 7.5 m 88.0 s
INFO 00:31:24,524 ProgressMeter - Scaffold_996:51973478 1.07465E7 6.6 m 36.0 s 83.1% 7.9 m 80.0 s
INFO 00:31:54,527 ProgressMeter - Scaffold_996:111690220 1.0946572E7 7.1 m 38.0 s 83.4% 8.5 m 84.0 s
INFO 00:32:24,529 ProgressMeter - Scaffold_996:148356657 1.1146574E7 7.6 m 40.0 s 83.6% 9.0 m 88.0 s
INFO 00:32:54,532 ProgressMeter - Scaffold_996:166825326 1.1446589E7 8.1 m 42.0 s 83.7% 9.6 m 93.0 s
INFO 00:33:24,534 ProgressMeter - Scaffold_996:216307491 1.1746595E7 8.6 m 43.0 s 84.0% 10.2 m 97.0 s
INFO 00:33:54,537 ProgressMeter - Scaffold_996:286352857 1.1946614E7 9.1 m 45.0 s 84.4% 10.7 m 100.0 s
INFO 00:34:24,540 ProgressMeter - Scaffold_996:318757024 1.2246728E7 9.6 m 46.0 s 84.6% 11.3 m 104.0 s
INFO 00:34:54,547 ProgressMeter - Scaffold_996:384777823 1.2446731E7 10.1 m 48.0 s 84.9% 11.9 m 107.0 s
INFO 00:35:24,550 ProgressMeter - Scaffold_996:438505276 1.2646752E7 10.6 m 50.0 s 85.2% 12.4 m 110.0 s
INFO 00:35:54,552 ProgressMeter - Scaffold_996:475455363 1.2946856E7 11.1 m 51.0 s 85.4% 13.0 m 113.0 s
INFO 00:36:24,554 ProgressMeter - Scaffold_996:502144597 1.314711E7 11.6 m 52.0 s 85.5% 13.5 m 117.0 s
INFO 00:36:54,556 ProgressMeter - Scaffold_996:554620603 1.3447253E7 12.1 m 53.0 s 85.8% 14.1 m 119.0 s
INFO 00:37:24,558 ProgressMeter - Scaffold_997:36577286 1.3689748E7 12.6 m 55.0 s 86.3% 14.6 m 119.0 s
INFO 00:37:54,559 ProgressMeter - Scaffold_997:91431918 1.3889752E7 13.1 m 56.0 s 86.6% 15.1 m 2.0 m
INFO 00:38:24,566 ProgressMeter - Scaffold_997:130122888 1.4089756E7 13.6 m 57.0 s 86.8% 15.6 m 2.1 m
INFO 00:38:54,569 ProgressMeter - Scaffold_997:169599519 1.4389995E7 14.1 m 58.0 s 87.0% 16.2 m 2.1 m
INFO 00:39:24,577 ProgressMeter - Scaffold_997:193590883 1.4490048E7 14.6 m 60.0 s 87.2% 16.7 m 2.1 m
INFO 00:39:54,578 ProgressMeter - Scaffold_997:241805827 1.4790057E7 15.1 m 61.0 s 87.4% 17.2 m 2.2 m
INFO 00:40:24,584 ProgressMeter - Scaffold_997:279873993 1.499006E7 15.6 m 62.0 s 87.6% 17.8 m 2.2 m
INFO 00:40:54,591 ProgressMeter - Scaffold_997:345193335 1.5190063E7 16.1 m 63.0 s 88.0% 18.3 m 2.2 m
INFO 00:41:24,593 ProgressMeter - Scaffold_997:388841309 1.5490685E7 16.6 m 64.0 s 88.2% 18.8 m 2.2 m
INFO 00:41:54,594 ProgressMeter - Scaffold_997:436718329 1.5690687E7 17.1 m 65.0 s 88.5% 19.3 m 2.2 m
INFO 00:42:24,596 ProgressMeter - Scaffold_997:473650192 1.5890693E7 17.6 m 66.0 s 88.7% 19.8 m 2.2 m
INFO 00:42:54,602 ProgressMeter - Scaffold_997:518870643 1.6090695E7 18.1 m 67.0 s 88.9% 20.3 m 2.3 m
INFO 00:43:24,604 ProgressMeter - Scaffold_997:569312928 1.6491077E7 18.6 m 67.0 s 89.2% 20.8 m 2.3 m
INFO 00:43:54,606 ProgressMeter - Scaffold_997:619378047 1.669108E7 19.1 m 68.0 s 89.4% 21.3 m 2.3 m
INFO 00:44:24,608 ProgressMeter - Scaffold_997:669922947 1.6991202E7 19.6 m 69.0 s 89.7% 21.8 m 2.2 m
INFO 00:44:54,611 ProgressMeter - Scaffold_998:59624739 1.7252756E7 20.1 m 69.0 s 90.1% 22.3 m 2.2 m
INFO 00:45:24,614 ProgressMeter - Scaffold_998:127841924 1.7552769E7 20.6 m 70.0 s 90.5% 22.7 m 2.2 m
INFO 00:45:54,616 ProgressMeter - Scaffold_998:184142471 1.7852989E7 21.1 m 70.0 s 90.8% 23.2 m 2.1 m
INFO 00:46:24,619 ProgressMeter - Scaffold_998:239401308 1.8053003E7 21.6 m 71.0 s 91.1% 23.7 m 2.1 m
INFO 00:46:54,621 ProgressMeter - Scaffold_998:303193637 1.825301E7 22.1 m 72.0 s 91.4% 24.1 m 2.1 m
INFO 00:47:24,623 ProgressMeter - Scaffold_998:375872351 1.8553047E7 22.6 m 73.0 s 91.8% 24.6 m 120.0 s
INFO 00:47:54,624 ProgressMeter - Scaffold_998:428643278 1.8753193E7 23.1 m 73.0 s 92.1% 25.1 m 119.0 s
INFO 00:48:24,626 ProgressMeter - Scaffold_998:479186787 1.9053201E7 23.6 m 74.0 s 92.4% 25.5 m 117.0 s
INFO 00:48:54,628 ProgressMeter - Scaffold_998:513256840 1.9253254E7 24.1 m 75.0 s 92.5% 26.0 m 116.0 s
INFO 00:49:24,630 ProgressMeter - Scaffold_998:520290810 1.9553685E7 24.6 m 75.0 s 92.6% 26.5 m 118.0 s
INFO 00:49:54,635 ProgressMeter - Scaffold_998:571221837 1.9753687E7 25.1 m 76.0 s 92.8% 27.0 m 115.0 s
INFO 00:50:24,637 ProgressMeter - Scaffold_999:8334532 2.0012916E7 25.6 m 76.0 s 93.2% 27.4 m 111.0 s
INFO 00:50:54,639 ProgressMeter - Scaffold_999:84941146 2.0212919E7 26.1 m 77.0 s 93.6% 27.8 m 106.0 s
INFO 00:51:24,641 ProgressMeter - Scaffold_999:150737649 2.0513004E7 26.6 m 77.0 s 94.0% 28.3 m 101.0 s
INFO 00:51:54,643 ProgressMeter - Scaffold_999:215351527 2.0813029E7 27.1 m 78.0 s 94.3% 28.7 m 97.0 s
INFO 00:52:24,645 ProgressMeter - Scaffold_999:284187860 2.1013031E7 27.6 m 78.0 s 94.7% 29.1 m 92.0 s
INFO 00:52:54,647 ProgressMeter - Scaffold_999:337383984 2.1213042E7 28.1 m 79.0 s 95.0% 29.5 m 88.0 s
INFO 00:53:24,648 ProgressMeter - Scaffold_999:402951420 2.1513141E7 28.6 m 79.0 s 95.3% 30.0 m 83.0 s
INFO 00:53:54,650 ProgressMeter - Scaffold_999:455705501 2.1813184E7 29.1 m 79.0 s 95.6% 30.4 m 79.0 s
INFO 00:54:24,651 ProgressMeter - Scaffold_999:517926272 2.2013196E7 29.6 m 80.0 s 96.0% 30.8 m 74.0 s
INFO 00:54:54,653 ProgressMeter - Scaffold_1000:36341205 2.2351149E7 30.1 m 80.0 s 96.4% 31.2 m 66.0 s
INFO 00:55:24,656 ProgressMeter - Scaffold_1000:95414757 2.2651157E7 30.6 m 80.0 s 96.7% 31.6 m 61.0 s
INFO 00:55:54,658 ProgressMeter - Scaffold_1000:162885922 2.2851159E7 31.1 m 81.0 s 97.1% 32.0 m 55.0 s
INFO 00:56:24,660 ProgressMeter - Scaffold_1000:238123004 2.3151166E7 31.6 m 81.0 s 97.5% 32.4 m 48.0 s
INFO 00:56:54,661 ProgressMeter - Scaffold_1000:268779585 2.345215E7 32.1 m 82.0 s 97.7% 32.8 m 45.0 s
INFO 00:57:24,663 ProgressMeter - Scaffold_1000:334629805 2.3652155E7 32.6 m 82.0 s 98.0% 33.2 m 39.0 s
INFO 00:57:54,665 ProgressMeter - Scaffold_1000:407690219 2.3952188E7 33.1 m 82.0 s 98.4% 33.6 m 31.0 s
INFO 00:58:24,666 ProgressMeter - Scaffold_1000:458249870 2.4252193E7 33.6 m 83.0 s 98.7% 34.0 m 26.0 s
INFO 00:58:54,668 ProgressMeter - Scaffold_1000:505888707 2.4452199E7 34.1 m 83.0 s 98.9% 34.4 m 21.0 s
INFO 00:59:24,670 ProgressMeter - Scaffold_1000:564733872 2.4752243E7 34.6 m 83.0 s 99.3% 34.8 m 15.0 s
INFO 00:59:54,671 ProgressMeter - Scaffold_1000:631387244 2.50523E7 35.1 m 84.0 s 99.6% 35.2 m 7.0 s
INFO 01:00:24,673 ProgressMeter - Scaffold_1000:665205523 2.5352329E7 35.6 m 84.0 s 99.8% 35.6 m 4.0 s
INFO 01:00:54,674 ProgressMeter - Scaffold_1000:700456776 2.545233E7 36.1 m 85.0 s 100.0% 36.1 m 0.0 s
INFO 01:01:24,676 ProgressMeter - Scaffold_1000:700456776 2.545233E7 36.6 m 86.0 s 100.0% 36.6 m 0.0 s
INFO 01:01:54,678 ProgressMeter - Scaffold_1000:700456776 2.545233E7 37.1 m 87.0 s 100.0% 37.1 m 0.0 s
INFO 01:02:24,679 ProgressMeter - Scaffold_1000:700456776 2.545233E7 37.6 m 88.0 s 100.0% 37.6 m 0.0 s
INFO 01:02:54,681 ProgressMeter - Scaffold_1000:700456776 2.545233E7 38.1 m 89.0 s 100.0% 38.1 m 0.0 s
INFO 01:03:24,683 ProgressMeter - Scaffold_1000:700456776 2.545233E7 38.6 m 90.0 s 100.0% 38.6 m 0.0 s
INFO 01:03:54,685 ProgressMeter - Scaffold_1000:700456776 2.545233E7 39.1 m 92.0 s 100.0% 39.1 m 0.0 s
INFO 01:04:24,686 ProgressMeter - Scaffold_1000:700456776 2.545233E7 39.6 m 93.0 s 100.0% 39.6 m 0.0 s
INFO 01:04:54,688 ProgressMeter - Scaffold_1000:700456776 2.545233E7 40.1 m 94.0 s 100.0% 40.1 m 0.0 s

ERROR ------------------------------------------------------------------------------------------
ERROR A BAM/CRAM ERROR has occurred (version 3.6-0-g89b7209):
ERROR
ERROR This means that there is something wrong with the BAM/CRAM file(s) you provided.
ERROR The error message below tells you what is the problem.
ERROR
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions https://www.broadinstitute.org/gatk
ERROR
ERROR Please do NOT post this error to the GATK forum until you have followed these instructions:
ERROR - Make sure that your BAM file is well-formed by running Picard's validator on it
ERROR (see http://picard.sourceforge.net/command-line-overview.shtml#ValidateSamFile for details)
ERROR - Ensure that your BAM index is not corrupted: delete the current one and regenerate it with 'samtools index'
ERROR - Ensure that your CRAM index is not corrupted: delete the current one and regenerate it with
ERROR 'java -jar cramtools-3.0.jar index --bam-style-index --input-file --reference-fasta-file '
ERROR (see https://github.com/enasequence/cramtools/tree/v3.0 for details)
ERROR
ERROR MESSAGE: Exception when processing alignment for BAM index K00159:42:H5K2GBBXX:2:1227:13311:5042 1/2 14b aligned read.
ERROR ------------------------------------------------------------------------------------------

(2) When I ran ValidateSamFile I got the following informations:

[Sun Jun 19 01:43:15 CST 2016] picard.sam.ValidateSamFile INPUT=NCPT_rg_added_sorted.bam MODE=VERBOSE IGNORE_WARNINGS=true MAX_OUTPUT=100 VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 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
[Sun Jun 19 01:43:15 CST 2016] Executing as [email protected] on Linux 3.8.0-44-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: 2.4.1(7c4d36e011df1aec4689b51efcada44e92d1817f_1464389670) JdkDeflater
INFO 2016-06-19 01:44:48 SamFileValidator Validated Read 10,000,000 records. Elapsed time: 00:01:33s. Time for last 10,000,000: 93s. Last read position: Scaffold_990:53,468,718
INFO 2016-06-19 01:46:22 SamFileValidator Validated Read 20,000,000 records. Elapsed time: 00:03:07s. Time for last 10,000,000: 93s. Last read position: Scaffold_998:626,572,484
ERROR: Read name K00159:42:H5K2GBBXX:2:2222:8826:42460, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:1206:22353:14801, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:2115:2930:22502, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:1117:2575:2299, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:1218:1783:34442, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:1215:32126:9719, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:1201:14215:49124, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:1219:4432:13007, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:2220:12347:9209, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:1216:26656:43181, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:2125:6705:47436, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:2203:31061:9420, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:2223:26727:2650, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:2207:22861:22010, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:1207:15371:25668, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:1215:32370:48614, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:2103:5913:46768, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:2226:17807:24437, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:1122:32065:31699, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:1101:7608:18933, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:1213:21755:11337, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:1203:3752:10528, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:2201:16589:25632, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:1220:27032:8981, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:2202:11312:15821, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:2211:17127:34618, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:1102:8258:31558, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:2109:4107:7556, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:2127:3285:46469, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:1223:4188:31470, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:1214:20141:46944, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:2228:30543:25685, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:2127:13636:42882, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:1205:27103:27883, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:1110:24261:42442, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:1213:21785:11354, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:1111:6461:38328, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:2221:3904:24999, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:2113:28838:18898, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:1218:12347:19126, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:1116:25672:28745, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:1225:32705:27742, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:1119:18213:39453, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:1216:10247:3952, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:1112:16518:43620, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:1124:3539:12198, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:1102:10551:25122, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:2113:7730:28147, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:2215:27225:41423, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:2113:17289:18405, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:1218:15970:17069, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:1116:30107:6431, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:2224:10998:16049, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:1128:31020:8400, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:2222:22709:48860, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:1204:31304:25703, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:1114:3995:25615, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:1110:11677:17016, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:2222:28331:38803, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:2215:17959:23048, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:1225:10642:19232, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:2224:26880:47542, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:1210:29041:22520, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:2107:28686:10757, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:1211:31517:5042, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:1215:27630:2985, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:1203:15524:5640, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:1215:27641:3037, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:1227:8643:4092, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:2118:2169:31980, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:1210:5477:46328, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:1126:2554:22696, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:2109:25641:33826, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:1101:28402:32314, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:1125:5954:30521, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:2126:20040:41071, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:1123:9475:41862, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:2227:24180:14590, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:1113:28442:37202, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:1105:6167:4374, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:2120:15179:14607, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:2122:6969:39523, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:1126:8826:17878, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:1101:13951:18845, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:2126:20770:46135, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:1205:14945:35092, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:2219:31659:26986, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:2222:7121:10598, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:2204:5264:19443, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:2119:24282:9033, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:2210:27346:19443, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:2123:24992:34706, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:2217:23135:10493, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:2128:14539:24015, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:2202:5061:12796, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:2102:28118:18212, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:2109:21775:2791, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:2116:26200:11829, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:1101:24211:5886, Mate not found for paired read
ERROR: Read name K00159:42:H5K2GBBXX:2:1209:5416:24454, Mate not found for paired read
Maximum output of [100] errors reached.
[Sun Jun 19 01:47:12 CST 2016] picard.sam.ValidateSamFile done. Elapsed time: 3.95 minutes.
Runtime.totalMemory()=1987575808
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp

How can I fix this problem?

Issue · Github
by Sheila

Issue Number
1012
State
closed
Last Updated
Assignee
Array
Milestone
Array
Closed By
vdauwera

Best Answer

Answers

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