251.233Gb memory in total. Using: 226.11Gb. MEGAHIT v1.1.3 --- [Mon Apr 15 13:12:21 2019] Start assembly. Number of CPU threads 28 --- --- [Mon Apr 15 13:12:21 2019] Available memory: 269759385600, used: 242783447040 --- [Mon Apr 15 13:12:21 2019] Converting reads to binaries --- b' [read_lib_functions-inl.h : 209] Lib 0 (/gscratch/scrubbed/samwhite/outputs/20190415_metagenomics_pgen_megahit/pH71.all.R1.fq.gz,/gscratch/scrubbed/samwhite/outputs/20190415_metagenomics_pgen_megahit/pH71.all.R2.fq.gz): pe, 483522908 reads, 131 max length' b' [utils.h : 126] Real: 474.0778\tuser: 431.2777\tsys: 40.1223\tmaxrss: 154664' --- [Mon Apr 15 13:20:15 2019] k list: 21,29,39,59,79,99,119,141 --- --- [Mon Apr 15 13:20:15 2019] Extracting solid (k+1)-mers for k = 21 --- --- [Mon Apr 15 13:37:11 2019] Building graph for k = 21 --- --- [Mon Apr 15 13:57:15 2019] Assembling contigs from SdBG for k = 21 --- --- [Mon Apr 15 15:08:34 2019] Local assembling k = 21 --- --- [Mon Apr 15 15:23:00 2019] Extracting iterative edges from k = 21 to 29 --- --- [Mon Apr 15 15:40:27 2019] Building graph for k = 29 --- --- [Mon Apr 15 15:48:38 2019] Assembling contigs from SdBG for k = 29 --- --- [Mon Apr 15 16:21:21 2019] Local assembling k = 29 --- --- [Mon Apr 15 16:42:08 2019] Extracting iterative edges from k = 29 to 39 --- --- [Mon Apr 15 16:56:23 2019] Building graph for k = 39 --- --- [Mon Apr 15 17:04:13 2019] Assembling contigs from SdBG for k = 39 --- --- [Mon Apr 15 17:30:49 2019] Local assembling k = 39 --- --- [Mon Apr 15 17:58:39 2019] Extracting iterative edges from k = 39 to 59 --- --- [Mon Apr 15 18:11:27 2019] Building graph for k = 59 --- --- [Mon Apr 15 18:19:37 2019] Assembling contigs from SdBG for k = 59 --- --- [Mon Apr 15 18:40:06 2019] Local assembling k = 59 --- --- [Mon Apr 15 19:13:53 2019] Extracting iterative edges from k = 59 to 79 --- --- [Mon Apr 15 19:22:24 2019] Building graph for k = 79 --- --- [Mon Apr 15 19:28:15 2019] Assembling contigs from SdBG for k = 79 --- --- [Mon Apr 15 19:44:48 2019] Local assembling k = 79 --- --- [Mon Apr 15 20:09:45 2019] Extracting iterative edges from k = 79 to 99 --- --- [Mon Apr 15 20:15:10 2019] Building graph for k = 99 --- --- [Mon Apr 15 20:19:01 2019] Assembling contigs from SdBG for k = 99 --- --- [Mon Apr 15 20:30:25 2019] Local assembling k = 99 --- --- [Mon Apr 15 20:49:10 2019] Extracting iterative edges from k = 99 to 119 --- --- [Mon Apr 15 20:51:48 2019] Building graph for k = 119 --- --- [Mon Apr 15 20:54:34 2019] Assembling contigs from SdBG for k = 119 --- --- [Mon Apr 15 21:04:08 2019] Local assembling k = 119 --- --- [Mon Apr 15 21:19:24 2019] Extracting iterative edges from k = 119 to 141 --- --- [Mon Apr 15 21:20:07 2019] Building graph for k = 141 --- --- [Mon Apr 15 21:21:51 2019] Assembling contigs from SdBG for k = 141 --- --- [Mon Apr 15 21:30:36 2019] Merging to output final contigs --- --- [STAT] 1613870 contigs, total 1513177150 bp, min 200 bp, max 1436649 bp, avg 938 bp, N50 1261 bp --- [Mon Apr 15 21:30:42 2019] ALL DONE. Time elapsed: 29900.748773 seconds --- java -Djava.library.path=/gscratch/srlab/programs/bbmap_38.34/jni/ -ea -Xmx102809m -cp /gscratch/srlab/programs/bbmap_38.34/current/ align2.BBWrap build=1 overwrite=true fastareadlen=500 ref=megahit_out/pH71.contigs.fa in1=pH71.all.R1.fq.gz in2=pH71.all.R2.fq.gz out=pH71.aln.sam.gz Executing align2.BBWrap [build=1, overwrite=true, fastareadlen=500, ref=megahit_out/pH71.contigs.fa, in1=pH71.all.R1.fq.gz, in2=pH71.all.R2.fq.gz, out=pH71.aln.sam.gz] Exception in thread "main" java.lang.AssertionError: Invalid input file: 'pH71.all.R1.fq.gz' at align2.AbstractMapper.preparse0(AbstractMapper.java:821) at align2.AbstractMapper.(AbstractMapper.java:53) at align2.BBMap.(BBMap.java:43) at align2.BBMap.main(BBMap.java:31) at align2.BBWrap.execute(BBWrap.java:144) at align2.BBWrap.main(BBWrap.java:22) java -ea -Xmx102809m -cp /gscratch/srlab/programs/bbmap_38.34/current/ jgi.CoveragePileup in=pH71.aln.sam.gz out=pH71.coverage.txt Executing jgi.CoveragePileup [in=pH71.aln.sam.gz, out=pH71.coverage.txt] Found samtools 1.9 Exception in thread "main" java.lang.RuntimeException: Can't find file pH71.aln.sam.gz at fileIO.ReadWrite.getRawInputStream(ReadWrite.java:916) at fileIO.ReadWrite.getGZipInputStream(ReadWrite.java:1012) at fileIO.ReadWrite.getInputStream(ReadWrite.java:831) at fileIO.ByteFile1.open(ByteFile1.java:331) at fileIO.ByteFile1.(ByteFile1.java:101) at fileIO.ByteFile.makeByteFile(ByteFile.java:39) at fileIO.ByteFile.makeByteFile(ByteFile.java:28) at fileIO.ByteFile.makeByteFile(ByteFile.java:24) at jgi.CoveragePileup.process(CoveragePileup.java:395) at jgi.CoveragePileup.main(CoveragePileup.java:56) 251.233Gb memory in total. Using: 226.11Gb. MEGAHIT v1.1.3 --- [Mon Apr 15 21:30:51 2019] Start assembly. Number of CPU threads 28 --- --- [Mon Apr 15 21:30:51 2019] Available memory: 269759385600, used: 242783447040 --- [Mon Apr 15 21:30:51 2019] Converting reads to binaries --- b' [read_lib_functions-inl.h : 209] Lib 0 (/gscratch/scrubbed/samwhite/outputs/20190415_metagenomics_pgen_megahit/pH82.all.R1.fq.gz,/gscratch/scrubbed/samwhite/outputs/20190415_metagenomics_pgen_megahit/pH82.all.R2.fq.gz): pe, 464635604 reads, 131 max length' b' [utils.h : 126] Real: 462.8266\tuser: 420.8859\tsys: 38.8588\tmaxrss: 152876' --- [Mon Apr 15 21:38:34 2019] k list: 21,29,39,59,79,99,119,141 --- --- [Mon Apr 15 21:38:34 2019] Extracting solid (k+1)-mers for k = 21 --- --- [Mon Apr 15 21:55:33 2019] Building graph for k = 21 --- --- [Mon Apr 15 22:11:22 2019] Assembling contigs from SdBG for k = 21 --- --- [Mon Apr 15 23:17:06 2019] Local assembling k = 21 --- --- [Mon Apr 15 23:30:55 2019] Extracting iterative edges from k = 21 to 29 --- --- [Mon Apr 15 23:47:49 2019] Building graph for k = 29 --- --- [Mon Apr 15 23:55:11 2019] Assembling contigs from SdBG for k = 29 --- --- [Tue Apr 16 00:30:39 2019] Local assembling k = 29 --- --- [Tue Apr 16 00:49:14 2019] Extracting iterative edges from k = 29 to 39 --- --- [Tue Apr 16 01:02:19 2019] Building graph for k = 39 --- --- [Tue Apr 16 01:08:43 2019] Assembling contigs from SdBG for k = 39 --- --- [Tue Apr 16 01:29:56 2019] Local assembling k = 39 --- --- [Tue Apr 16 01:59:15 2019] Extracting iterative edges from k = 39 to 59 --- --- [Tue Apr 16 02:10:39 2019] Building graph for k = 59 --- --- [Tue Apr 16 02:17:10 2019] Assembling contigs from SdBG for k = 59 --- --- [Tue Apr 16 02:32:25 2019] Local assembling k = 59 --- --- [Tue Apr 16 03:03:01 2019] Extracting iterative edges from k = 59 to 79 --- --- [Tue Apr 16 03:10:54 2019] Building graph for k = 79 --- --- [Tue Apr 16 03:15:30 2019] Assembling contigs from SdBG for k = 79 --- --- [Tue Apr 16 03:27:27 2019] Local assembling k = 79 --- --- [Tue Apr 16 03:51:17 2019] Extracting iterative edges from k = 79 to 99 --- --- [Tue Apr 16 03:56:37 2019] Building graph for k = 99 --- --- [Tue Apr 16 03:59:56 2019] Assembling contigs from SdBG for k = 99 --- --- [Tue Apr 16 04:10:47 2019] Local assembling k = 99 --- --- [Tue Apr 16 04:28:34 2019] Extracting iterative edges from k = 99 to 119 --- --- [Tue Apr 16 04:31:16 2019] Building graph for k = 119 --- --- [Tue Apr 16 04:33:46 2019] Assembling contigs from SdBG for k = 119 --- --- [Tue Apr 16 04:42:01 2019] Local assembling k = 119 --- --- [Tue Apr 16 04:55:43 2019] Extracting iterative edges from k = 119 to 141 --- --- [Tue Apr 16 04:56:29 2019] Building graph for k = 141 --- --- [Tue Apr 16 04:57:55 2019] Assembling contigs from SdBG for k = 141 --- --- [Tue Apr 16 05:05:31 2019] Merging to output final contigs --- --- [STAT] 1323001 contigs, total 1214985250 bp, min 200 bp, max 508506 bp, avg 918 bp, N50 1274 bp --- [Tue Apr 16 05:05:36 2019] ALL DONE. Time elapsed: 27284.737361 seconds --- java -Djava.library.path=/gscratch/srlab/programs/bbmap_38.34/jni/ -ea -Xmx102809m -cp /gscratch/srlab/programs/bbmap_38.34/current/ align2.BBWrap build=1 overwrite=true fastareadlen=500 ref=megahit_out/pH82.contigs.fa in1=pH82.all.R1.fq.gz in2=pH82.all.R2.fq.gz out=pH82.aln.sam.gz Executing align2.BBWrap [build=1, overwrite=true, fastareadlen=500, ref=megahit_out/pH82.contigs.fa, in1=pH82.all.R1.fq.gz, in2=pH82.all.R2.fq.gz, out=pH82.aln.sam.gz] Exception in thread "main" java.lang.AssertionError: Invalid input file: 'pH82.all.R1.fq.gz' at align2.AbstractMapper.preparse0(AbstractMapper.java:821) at align2.AbstractMapper.(AbstractMapper.java:53) at align2.BBMap.(BBMap.java:43) at align2.BBMap.main(BBMap.java:31) at align2.BBWrap.execute(BBWrap.java:144) at align2.BBWrap.main(BBWrap.java:22) java -ea -Xmx102809m -cp /gscratch/srlab/programs/bbmap_38.34/current/ jgi.CoveragePileup in=pH82.aln.sam.gz out=pH82.coverage.txt Executing jgi.CoveragePileup [in=pH82.aln.sam.gz, out=pH82.coverage.txt] Found samtools 1.9 Exception in thread "main" java.lang.RuntimeException: Can't find file pH82.aln.sam.gz at fileIO.ReadWrite.getRawInputStream(ReadWrite.java:916) at fileIO.ReadWrite.getGZipInputStream(ReadWrite.java:1012) at fileIO.ReadWrite.getInputStream(ReadWrite.java:831) at fileIO.ByteFile1.open(ByteFile1.java:331) at fileIO.ByteFile1.(ByteFile1.java:101) at fileIO.ByteFile.makeByteFile(ByteFile.java:39) at fileIO.ByteFile.makeByteFile(ByteFile.java:28) at fileIO.ByteFile.makeByteFile(ByteFile.java:24) at jgi.CoveragePileup.process(CoveragePileup.java:395) at jgi.CoveragePileup.main(CoveragePileup.java:56)