Job ID = 10536420 sra ファイルのダウンロード中... Completed: 1542034K bytes transferred in 53 seconds (234087K 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 34066342 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3671159/SRR6696911.sra Written 34066342 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: 00:25:12 34066342 reads; of these: 34066342 (100.00%) were paired; of these: 1584604 (4.65%) aligned concordantly 0 times 28560253 (83.84%) aligned concordantly exactly 1 time 3921485 (11.51%) aligned concordantly >1 times ---- 1584604 pairs aligned concordantly 0 times; of these: 46346 (2.92%) aligned discordantly 1 time ---- 1538258 pairs aligned 0 times concordantly or discordantly; of these: 3076516 mates make up the pairs; of these: 2650903 (86.17%) aligned 0 times 352517 (11.46%) aligned exactly 1 time 73096 (2.38%) aligned >1 times 96.11% overall alignment rate Time searching: 00:25:12 Overall time: 00:25:13 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 28 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] 26652505 / 32510078 = 0.8198 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, 05 Apr 2018 10:05:23: # Command line: callpeak -t SRX3671159.bam -f BAM -g 12100000 -n SRX3671159.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3671159.10 # format = BAM # ChIP-seq file = ['SRX3671159.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, 05 Apr 2018 10:05:23: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:05:23: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:05:23: # Command line: callpeak -t SRX3671159.bam -f BAM -g 12100000 -n SRX3671159.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3671159.05 # format = BAM # ChIP-seq file = ['SRX3671159.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, 05 Apr 2018 10:05:23: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:05:23: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:05:23: # Command line: callpeak -t SRX3671159.bam -f BAM -g 12100000 -n SRX3671159.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3671159.20 # format = BAM # ChIP-seq file = ['SRX3671159.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, 05 Apr 2018 10:05:23: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:05:23: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:05:29: 1000000 INFO @ Thu, 05 Apr 2018 10:05:29: 1000000 INFO @ Thu, 05 Apr 2018 10:05:29: 1000000 INFO @ Thu, 05 Apr 2018 10:05:34: 2000000 INFO @ Thu, 05 Apr 2018 10:05:35: 2000000 INFO @ Thu, 05 Apr 2018 10:05:35: 2000000 INFO @ Thu, 05 Apr 2018 10:05:39: 3000000 INFO @ Thu, 05 Apr 2018 10:05:40: 3000000 INFO @ Thu, 05 Apr 2018 10:05:40: 3000000 INFO @ Thu, 05 Apr 2018 10:05:45: 4000000 INFO @ Thu, 05 Apr 2018 10:05:46: 4000000 INFO @ Thu, 05 Apr 2018 10:05:46: 4000000 INFO @ Thu, 05 Apr 2018 10:05:50: 5000000 INFO @ Thu, 05 Apr 2018 10:05:51: 5000000 INFO @ Thu, 05 Apr 2018 10:05:52: 5000000 INFO @ Thu, 05 Apr 2018 10:05:55: 6000000 INFO @ Thu, 05 Apr 2018 10:05:57: 6000000 INFO @ Thu, 05 Apr 2018 10:05:57: 6000000 INFO @ Thu, 05 Apr 2018 10:06:01: 7000000 INFO @ Thu, 05 Apr 2018 10:06:03: 7000000 INFO @ Thu, 05 Apr 2018 10:06:03: 7000000 INFO @ Thu, 05 Apr 2018 10:06:06: 8000000 INFO @ Thu, 05 Apr 2018 10:06:08: 8000000 INFO @ Thu, 05 Apr 2018 10:06:09: 8000000 INFO @ Thu, 05 Apr 2018 10:06:11: 9000000 INFO @ Thu, 05 Apr 2018 10:06:14: 9000000 INFO @ Thu, 05 Apr 2018 10:06:15: 9000000 INFO @ Thu, 05 Apr 2018 10:06:17: 10000000 INFO @ Thu, 05 Apr 2018 10:06:19: 10000000 INFO @ Thu, 05 Apr 2018 10:06:20: 10000000 INFO @ Thu, 05 Apr 2018 10:06:23: 11000000 INFO @ Thu, 05 Apr 2018 10:06:25: 11000000 INFO @ Thu, 05 Apr 2018 10:06:26: 11000000 INFO @ Thu, 05 Apr 2018 10:06:29: 12000000 INFO @ Thu, 05 Apr 2018 10:06:30: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:06:30: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:06:30: #1 total tags in treatment: 5836293 INFO @ Thu, 05 Apr 2018 10:06:30: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:06:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 10:06:30: #1 tags after filtering in treatment: 4670392 INFO @ Thu, 05 Apr 2018 10:06:30: #1 Redundant rate of treatment: 0.20 INFO @ Thu, 05 Apr 2018 10:06:30: #1 finished! INFO @ Thu, 05 Apr 2018 10:06:30: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:06:30: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:06:30: #2 number of paired peaks: 26 WARNING @ Thu, 05 Apr 2018 10:06:30: Too few paired peaks (26) 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, 05 Apr 2018 10:06:30: Process for pairing-model is terminated! cat: SRX3671159.05_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): 13 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3671159.05_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 `SRX3671159.05_*.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 `SRX3671159.05_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, 05 Apr 2018 10:06:31: 12000000 INFO @ Thu, 05 Apr 2018 10:06:32: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:06:32: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:06:32: #1 total tags in treatment: 5836293 INFO @ Thu, 05 Apr 2018 10:06:32: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:06:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 10:06:32: #1 tags after filtering in treatment: 4670392 INFO @ Thu, 05 Apr 2018 10:06:32: #1 Redundant rate of treatment: 0.20 INFO @ Thu, 05 Apr 2018 10:06:32: #1 finished! INFO @ Thu, 05 Apr 2018 10:06:32: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:06:32: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:06:32: 12000000 INFO @ Thu, 05 Apr 2018 10:06:32: #2 number of paired peaks: 26 WARNING @ Thu, 05 Apr 2018 10:06:32: Too few paired peaks (26) 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, 05 Apr 2018 10:06:32: Process for pairing-model is terminated! cat: SRX3671159.20_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 `SRX3671159.20_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 `SRX3671159.20_*.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 `SRX3671159.20_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 INFO @ Thu, 05 Apr 2018 10:06:33: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:06:33: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:06:33: #1 total tags in treatment: 5836293 INFO @ Thu, 05 Apr 2018 10:06:33: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:06:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 10:06:33: #1 tags after filtering in treatment: 4670392 INFO @ Thu, 05 Apr 2018 10:06:33: #1 Redundant rate of treatment: 0.20 INFO @ Thu, 05 Apr 2018 10:06:33: #1 finished! INFO @ Thu, 05 Apr 2018 10:06:33: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:06:33: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:06:34: #2 number of paired peaks: 26 WARNING @ Thu, 05 Apr 2018 10:06:34: Too few paired peaks (26) 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, 05 Apr 2018 10:06:34: Process for pairing-model is terminated! cat: SRX3671159.10_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): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3671159.10_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 `SRX3671159.10_*.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 `SRX3671159.10_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。