@HD VN:1.5 SO:coordinate @SQ SN:chr1 LN:249250621 M5:1b22b98cdeb4a9304cb5d48026a85128 UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:chr10 LN:135534747 M5:988c28e000e84c26d552359af1ea2e1d UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:chr11 LN:135006516 M5:98c59049a2df285c76ffb1c6db8f8b96 UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:chr12 LN:133851895 M5:51851ac0e1a115847ad36449b0015864 UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:chr13 LN:115169878 M5:283f8d7892baa81b510a015719ca7b0b UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:chr14 LN:107349540 M5:98f3cae32b2a2e9524bc19813927542e UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:chr15 LN:102531392 M5:e5645a794a8238215b2cd77acb95a078 UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:chr16 LN:90354753 M5:fc9b1a7b42b97a864f56b348b06095e6 UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:chr17 LN:81195210 M5:351f64d4f4f9ddd45b35336ad97aa6de UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:chr18 LN:78077248 M5:b15d4b2d29dde9d3e4f93d1d0f2cbc9c UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:chr19 LN:59128983 M5:1aacd71f30db8e561810913e0b72636d UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:chr2 LN:243199373 M5:a0d9851da00400dec1098a9255ac712e UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:chr20 LN:63025520 M5:0dec9660ec1efaaf33281c0d5ea2560f UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:chr21 LN:48129895 M5:2979a6085bfe28e3ad6f552f361ed74d UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:chr22 LN:51304566 M5:a718acaa6135fdca8357d5bfe94211dd UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:chr3 LN:198022430 M5:641e4338fa8d52a5b781bd2a2c08d3c3 UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:chr4 LN:191154276 M5:23dccd106897542ad87d2765d28a19a1 UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:chr5 LN:180915260 M5:0740173db9ffd264d728f32784845cd7 UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:chr6 LN:171115067 M5:1d3a93a248d92a729ee764823acbbc6b UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:chr7 LN:159138663 M5:618366e953d6aaad97dbe4777c29375e UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:chr8 LN:146364022 M5:96f514a9929e410c6651697bded59aec UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:chr9 LN:141213431 M5:3e273117f15e0a400f01055d9f393768 UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:chrMT LN:16569 M5:c68f52674c9fb33aef52dcf399755519 UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:chrX LN:155270560 M5:7e0e2e580297b7764e31dbc80c2540dd UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:chrY LN:59373566 M5:1fa3474750af0948bdf97d5a0ee52e51 UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:GL000192.1 LN:547496 M5:325ba9e808f669dfeee210fdd7b470ac UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:GL000225.1 LN:211173 M5:63945c3e6962f28ffd469719a747e73c UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:GL000194.1 LN:191469 M5:6ac8f815bf8e845bb3031b73f812c012 UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:GL000193.1 LN:189789 M5:dbb6e8ece0b5de29da56601613007c2a UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:GL000200.1 LN:187035 M5:75e4c8d17cd4addf3917d1703cacaf25 UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:GL000222.1 LN:186861 M5:6fe9abac455169f50470f5a6b01d0f59 UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:GL000212.1 LN:186858 M5:563531689f3dbd691331fd6c5730a88b UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:GL000195.1 LN:182896 M5:5d9ec007868d517e73543b005ba48535 UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:GL000223.1 LN:180455 M5:399dfa03bf32022ab52a846f7ca35b30 UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:GL000224.1 LN:179693 M5:d5b2fc04f6b41b212a4198a07f450e20 UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:GL000219.1 LN:179198 M5:f977edd13bac459cb2ed4a5457dba1b3 UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:GL000205.1 LN:174588 M5:d22441398d99caf673e9afb9a1908ec5 UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:GL000215.1 LN:172545 M5:5eb3b418480ae67a997957c909375a73 UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:GL000216.1 LN:172294 M5:642a232d91c486ac339263820aef7fe0 UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:GL000217.1 LN:172149 M5:6d243e18dea1945fb7f2517615b8f52e UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:GL000199.1 LN:169874 M5:569af3b73522fab4b40995ae4944e78e UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:GL000211.1 LN:166566 M5:7daaa45c66b288847b9b32b964e623d3 UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:GL000213.1 LN:164239 M5:9d424fdcc98866650b58f004080a992a UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:GL000220.1 LN:161802 M5:fc35de963c57bf7648429e6454f1c9db UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:GL000218.1 LN:161147 M5:1d708b54644c26c7e01c2dad5426d38c UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:GL000209.1 LN:159169 M5:f40598e2a5a6b26e84a3775e0d1e2c81 UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:GL000221.1 LN:155397 M5:3238fb74ea87ae857f9c7508d315babb UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:GL000214.1 LN:137718 M5:46c2032c37f2ed899eb41c0473319a69 UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:GL000228.1 LN:129120 M5:c5a17c97e2c1a0b6a9cc5a6b064b714f UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:GL000227.1 LN:128374 M5:a4aead23f8053f2655e468bcc6ecdceb UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:GL000191.1 LN:106433 M5:d75b436f50a8214ee9c2a51d30b2c2cc UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:GL000208.1 LN:92689 M5:aa81be49bf3fe63a79bdc6a6f279abf6 UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:GL000198.1 LN:90085 M5:868e7784040da90d900d2d1b667a1383 UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:GL000204.1 LN:81310 M5:efc49c871536fa8d79cb0a06fa739722 UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:GL000233.1 LN:45941 M5:7fed60298a8d62ff808b74b6ce820001 UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:GL000237.1 LN:45867 M5:e0c82e7751df73f4f6d0ed30cdc853c0 UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:GL000230.1 LN:43691 M5:b4eb71ee878d3706246b7c1dbef69299 UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:GL000242.1 LN:43523 M5:2f8694fc47576bc81b5fe9e7de0ba49e UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:GL000243.1 LN:43341 M5:cc34279a7e353136741c9fce79bc4396 UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:GL000241.1 LN:42152 M5:ef4258cdc5a45c206cea8fc3e1d858cf UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:GL000236.1 LN:41934 M5:fdcd739913efa1fdc64b6c0cd7016779 UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:GL000240.1 LN:41933 M5:445a86173da9f237d7bcf41c6cb8cc62 UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:GL000206.1 LN:41001 M5:43f69e423533e948bfae5ce1d45bd3f1 UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:GL000232.1 LN:40652 M5:3e06b6741061ad93a8587531307057d8 UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:GL000234.1 LN:40531 M5:93f998536b61a56fd0ff47322a911d4b UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:GL000202.1 LN:40103 M5:06cbf126247d89664a4faebad130fe9c UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:GL000238.1 LN:39939 M5:131b1efc3270cc838686b54e7c34b17b UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:GL000244.1 LN:39929 M5:0996b4475f353ca98bacb756ac479140 UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:GL000248.1 LN:39786 M5:5a8e43bec9be36c7b49c84d585107776 UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:GL000196.1 LN:38914 M5:d92206d1bb4c3b4019c43c0875c06dc0 UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:GL000249.1 LN:38502 M5:1d78abec37c15fe29a275eb08d5af236 UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:GL000246.1 LN:38154 M5:e4afcd31912af9d9c2546acf1cb23af2 UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:GL000203.1 LN:37498 M5:96358c325fe0e70bee73436e8bb14dbd UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:GL000197.1 LN:37175 M5:6f5efdd36643a9b8c8ccad6f2f1edc7b UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:GL000245.1 LN:36651 M5:89bc61960f37d94abf0df2d481ada0ec UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:GL000247.1 LN:36422 M5:7de00226bb7df1c57276ca6baabafd15 UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:GL000201.1 LN:36148 M5:dfb7e7ec60ffdcb85cb359ea28454ee9 UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:GL000235.1 LN:34474 M5:118a25ca210cfbcdfb6c2ebb249f9680 UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:GL000239.1 LN:33824 M5:99795f15702caec4fa1c4e15f8a29c07 UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:GL000210.1 LN:27682 M5:851106a74238044126131ce2a8e5847c UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:GL000231.1 LN:27386 M5:ba8882ce3a1efa2080e5d29b956568a4 UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:GL000229.1 LN:19913 M5:d0f40ec87de311d8e715b52e4c7062e1 UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:GL000226.1 LN:15008 M5:1c1b2cd1fccbc0a99b6a447fa24d1504 UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @SQ SN:GL000207.1 LN:4262 M5:f3814841f1939d3ca19072d9e89f3fd7 UR:file:/home/mce/RME/resources/genomes/human/Homo_sapiens.GRCh37.dna.primary_assembly.ucsc_naming.fa @RG ID:id LB:library PL:platform SM:sample PU:machine @PG ID:STAR PN:STAR VN:STAR_2.5.3a CL:STAR --runThreadN 50 --genomeDir /home/mce/RME/resources/indices/STAR/human/GRCh37-100bp --readFilesIn ../input-reads/1097_1.fq ../input-reads/1097_2.fq --outSAMtype BAM SortedByCoordinate --outFilterType BySJout @PG ID:STAR-19324542 PN:STAR VN:STAR_2.5.3a CL:STAR --runThreadN 50 --genomeDir /home/mce/RME/resources/indices/STAR/human/GRCh37-100bp --readFilesIn ../input-reads/1097_1.fq ../input-reads/1097_2.fq --outSAMtype BAM SortedByCoordinate --outFilterType BySJout @PG ID:MarkDuplicates VN:2.8.2-SNAPSHOT CL:picard.sam.markduplicates.MarkDuplicates INPUT=[test.rg_added_sorted.bam] OUTPUT=test.dedupped.bam METRICS_FILE=output.metrics VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag 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 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json PN:MarkDuplicates @CO user command line: STAR --genomeDir /home/mce/RME/resources/indices/STAR/human/GRCh37-100bp --readFilesIn ../input-reads/1097_1.fq ../input-reads/1097_2.fq --outFilterType BySJout --runThreadN 50 --outSAMtype BAM SortedByCoordinate @CO user command line: STAR --genomeDir /home/mce/RME/resources/indices/STAR/human/GRCh37-100bp --readFilesIn ../input-reads/1097_1.fq ../input-reads/1097_2.fq --outFilterType BySJout --runThreadN 50 --outSAMtype BAM SortedByCoordinate