Job ID = 10608970 sra ファイルのダウンロード中... Completed: 1812518K bytes transferred in 179 seconds (82924K bits/sec), in 1 file. sra ファイルのダウンロードが完了しました。 Read layout: PAIRED fastq に変換中... Written 14360997 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2741969/SRR5453803.sra Written 14360997 spots total rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:18:37 14360997 reads; of these: 14360997 (100.00%) were paired; of these: 1836408 (12.79%) aligned concordantly 0 times 11464778 (79.83%) aligned concordantly exactly 1 time 1059811 (7.38%) aligned concordantly >1 times ---- 1836408 pairs aligned concordantly 0 times; of these: 687467 (37.44%) aligned discordantly 1 time ---- 1148941 pairs aligned 0 times concordantly or discordantly; of these: 2297882 mates make up the pairs; of these: 1621660 (70.57%) aligned 0 times 491339 (21.38%) aligned exactly 1 time 184883 (8.05%) aligned >1 times 94.35% overall alignment rate Time searching: 00:18:37 Overall time: 00:18:37 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_sort_core] merging from 12 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 529896 / 13147527 = 0.0403 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Thu, 03 May 2018 23:25:28: # Command line: callpeak -t SRX2741969.bam -f BAM -g 12100000 -n SRX2741969.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2741969.20 # format = BAM # ChIP-seq file = ['SRX2741969.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Thu, 03 May 2018 23:25:28: #1 read tag files... INFO @ Thu, 03 May 2018 23:25:28: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:25:28: # Command line: callpeak -t SRX2741969.bam -f BAM -g 12100000 -n SRX2741969.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2741969.05 # format = BAM # ChIP-seq file = ['SRX2741969.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Thu, 03 May 2018 23:25:28: #1 read tag files... INFO @ Thu, 03 May 2018 23:25:28: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:25:28: # Command line: callpeak -t SRX2741969.bam -f BAM -g 12100000 -n SRX2741969.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2741969.10 # format = BAM # ChIP-seq file = ['SRX2741969.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Thu, 03 May 2018 23:25:28: #1 read tag files... INFO @ Thu, 03 May 2018 23:25:28: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:25:35: 1000000 INFO @ Thu, 03 May 2018 23:25:35: 1000000 INFO @ Thu, 03 May 2018 23:25:35: 1000000 INFO @ Thu, 03 May 2018 23:25:42: 2000000 INFO @ Thu, 03 May 2018 23:25:42: 2000000 INFO @ Thu, 03 May 2018 23:25:42: 2000000 INFO @ Thu, 03 May 2018 23:25:49: 3000000 INFO @ Thu, 03 May 2018 23:25:49: 3000000 INFO @ Thu, 03 May 2018 23:25:49: 3000000 INFO @ Thu, 03 May 2018 23:25:56: 4000000 INFO @ Thu, 03 May 2018 23:25:57: 4000000 INFO @ Thu, 03 May 2018 23:25:57: 4000000 INFO @ Thu, 03 May 2018 23:26:02: 5000000 INFO @ Thu, 03 May 2018 23:26:04: 5000000 INFO @ Thu, 03 May 2018 23:26:04: 5000000 INFO @ Thu, 03 May 2018 23:26:09: 6000000 INFO @ Thu, 03 May 2018 23:26:11: 6000000 INFO @ Thu, 03 May 2018 23:26:11: 6000000 INFO @ Thu, 03 May 2018 23:26:16: 7000000 INFO @ Thu, 03 May 2018 23:26:18: 7000000 INFO @ Thu, 03 May 2018 23:26:19: 7000000 INFO @ Thu, 03 May 2018 23:26:22: 8000000 INFO @ Thu, 03 May 2018 23:26:25: 8000000 INFO @ Thu, 03 May 2018 23:26:26: 8000000 INFO @ Thu, 03 May 2018 23:26:29: 9000000 INFO @ Thu, 03 May 2018 23:26:33: 9000000 INFO @ Thu, 03 May 2018 23:26:34: 9000000 INFO @ Thu, 03 May 2018 23:26:36: 10000000 INFO @ Thu, 03 May 2018 23:26:40: 10000000 INFO @ Thu, 03 May 2018 23:26:41: 10000000 INFO @ Thu, 03 May 2018 23:26:43: 11000000 INFO @ Thu, 03 May 2018 23:26:47: 11000000 INFO @ Thu, 03 May 2018 23:26:48: 11000000 INFO @ Thu, 03 May 2018 23:26:50: 12000000 INFO @ Thu, 03 May 2018 23:26:54: 12000000 INFO @ Thu, 03 May 2018 23:26:55: 12000000 INFO @ Thu, 03 May 2018 23:26:57: 13000000 INFO @ Thu, 03 May 2018 23:27:01: 13000000 INFO @ Thu, 03 May 2018 23:27:03: 13000000 INFO @ Thu, 03 May 2018 23:27:04: 14000000 INFO @ Thu, 03 May 2018 23:27:08: 14000000 INFO @ Thu, 03 May 2018 23:27:10: 14000000 INFO @ Thu, 03 May 2018 23:27:11: 15000000 INFO @ Thu, 03 May 2018 23:27:16: 15000000 INFO @ Thu, 03 May 2018 23:27:17: 15000000 INFO @ Thu, 03 May 2018 23:27:18: 16000000 INFO @ Thu, 03 May 2018 23:27:23: 16000000 INFO @ Thu, 03 May 2018 23:27:24: 16000000 INFO @ Thu, 03 May 2018 23:27:25: 17000000 INFO @ Thu, 03 May 2018 23:27:30: 17000000 INFO @ Thu, 03 May 2018 23:27:31: 17000000 INFO @ Thu, 03 May 2018 23:27:32: 18000000 INFO @ Thu, 03 May 2018 23:27:37: 18000000 INFO @ Thu, 03 May 2018 23:27:38: 19000000 INFO @ Thu, 03 May 2018 23:27:39: 18000000 INFO @ Thu, 03 May 2018 23:27:44: 19000000 INFO @ Thu, 03 May 2018 23:27:45: 20000000 INFO @ Thu, 03 May 2018 23:27:46: 19000000 INFO @ Thu, 03 May 2018 23:27:51: 20000000 INFO @ Thu, 03 May 2018 23:27:52: 21000000 INFO @ Thu, 03 May 2018 23:27:53: 20000000 INFO @ Thu, 03 May 2018 23:27:58: 21000000 INFO @ Thu, 03 May 2018 23:27:58: 22000000 INFO @ Thu, 03 May 2018 23:28:00: 21000000 INFO @ Thu, 03 May 2018 23:28:05: 23000000 INFO @ Thu, 03 May 2018 23:28:05: 22000000 INFO @ Thu, 03 May 2018 23:28:07: 22000000 INFO @ Thu, 03 May 2018 23:28:12: 24000000 INFO @ Thu, 03 May 2018 23:28:12: 23000000 INFO @ Thu, 03 May 2018 23:28:14: 23000000 INFO @ Thu, 03 May 2018 23:28:19: 25000000 INFO @ Thu, 03 May 2018 23:28:19: 24000000 INFO @ Thu, 03 May 2018 23:28:22: 24000000 INFO @ Thu, 03 May 2018 23:28:25: 26000000 INFO @ Thu, 03 May 2018 23:28:26: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 23:28:26: #1 tag size = 100 INFO @ Thu, 03 May 2018 23:28:26: #1 total tags in treatment: 12016174 INFO @ Thu, 03 May 2018 23:28:26: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:28:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 23:28:26: #1 tags after filtering in treatment: 8390901 INFO @ Thu, 03 May 2018 23:28:26: #1 Redundant rate of treatment: 0.30 INFO @ Thu, 03 May 2018 23:28:26: #1 finished! INFO @ Thu, 03 May 2018 23:28:26: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:28:26: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:28:26: 25000000 INFO @ Thu, 03 May 2018 23:28:27: #2 number of paired peaks: 0 WARNING @ Thu, 03 May 2018 23:28:27: Too few paired peaks (0) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Thu, 03 May 2018 23:28:27: Process for pairing-model is terminated! cat: SRX2741969.10_peaks.narrowPeak: そのようなファイルやディレクトリはありません pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2741969.10_model.r': そのようなファイルやディレクトリはありません rm: cannot remove `SRX2741969.10_*.xls': そのようなファイルやディレクトリはありません rm: cannot remove `SRX2741969.10_peaks.narrowPeak': そのようなファイルやディレクトリはありません CompletedMACS2peakCalling INFO @ Thu, 03 May 2018 23:28:29: 25000000 INFO @ Thu, 03 May 2018 23:28:33: 26000000 INFO @ Thu, 03 May 2018 23:28:34: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 23:28:34: #1 tag size = 100 INFO @ Thu, 03 May 2018 23:28:34: #1 total tags in treatment: 12016174 INFO @ Thu, 03 May 2018 23:28:34: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:28:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 23:28:34: #1 tags after filtering in treatment: 8390901 INFO @ Thu, 03 May 2018 23:28:34: #1 Redundant rate of treatment: 0.30 INFO @ Thu, 03 May 2018 23:28:34: #1 finished! INFO @ Thu, 03 May 2018 23:28:34: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:28:34: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:28:34: #2 number of paired peaks: 0 WARNING @ Thu, 03 May 2018 23:28:34: Too few paired peaks (0) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Thu, 03 May 2018 23:28:34: Process for pairing-model is terminated! cat: SRX2741969.05_peaks.narrowPeak: そのようなファイルやディレクトリはありません pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2741969.05_model.r': そのようなファイルやディレクトリはありません rm: cannot remove `SRX2741969.05_*.xls': そのようなファイルやディレクトリはありません rm: cannot remove `SRX2741969.05_peaks.narrowPeak': そのようなファイルやディレクトリはありません CompletedMACS2peakCalling INFO @ Thu, 03 May 2018 23:28:35: 26000000 INFO @ Thu, 03 May 2018 23:28:36: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 23:28:36: #1 tag size = 100 INFO @ Thu, 03 May 2018 23:28:36: #1 total tags in treatment: 12016174 INFO @ Thu, 03 May 2018 23:28:36: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:28:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 23:28:36: #1 tags after filtering in treatment: 8390901 INFO @ Thu, 03 May 2018 23:28:36: #1 Redundant rate of treatment: 0.30 INFO @ Thu, 03 May 2018 23:28:36: #1 finished! INFO @ Thu, 03 May 2018 23:28:36: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:28:36: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:28:37: #2 number of paired peaks: 0 WARNING @ Thu, 03 May 2018 23:28:37: Too few paired peaks (0) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Thu, 03 May 2018 23:28:37: Process for pairing-model is terminated! cat: SRX2741969.20_peaks.narrowPeak: そのようなファイルやディレクトリはありません pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2741969.20_model.r': そのようなファイルやディレクトリはありません rm: cannot remove `SRX2741969.20_*.xls': そのようなファイルやディレクトリはありません rm: cannot remove `SRX2741969.20_peaks.narrowPeak': そのようなファイルやディレクトリはありません CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。