Job ID = 10536384 sra ファイルのダウンロード中... Completed: 1325079K bytes transferred in 42 seconds (254805K 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 33047484 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3671141/SRR6696893.sra Written 33047484 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: 00:22:52 33047484 reads; of these: 33047484 (100.00%) were paired; of these: 4842173 (14.65%) aligned concordantly 0 times 24856256 (75.21%) aligned concordantly exactly 1 time 3349055 (10.13%) aligned concordantly >1 times ---- 4842173 pairs aligned concordantly 0 times; of these: 57123 (1.18%) aligned discordantly 1 time ---- 4785050 pairs aligned 0 times concordantly or discordantly; of these: 9570100 mates make up the pairs; of these: 9202800 (96.16%) aligned 0 times 304074 (3.18%) aligned exactly 1 time 63226 (0.66%) aligned >1 times 86.08% overall alignment rate Time searching: 00:22:52 Overall time: 00:22:52 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 24 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] 11046096 / 28216727 = 0.3915 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 09:49:30: # Command line: callpeak -t SRX3671141.bam -f BAM -g 12100000 -n SRX3671141.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3671141.05 # format = BAM # ChIP-seq file = ['SRX3671141.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 09:49:30: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:49:30: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:49:30: # Command line: callpeak -t SRX3671141.bam -f BAM -g 12100000 -n SRX3671141.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3671141.10 # format = BAM # ChIP-seq file = ['SRX3671141.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 09:49:30: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:49:30: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:49:30: # Command line: callpeak -t SRX3671141.bam -f BAM -g 12100000 -n SRX3671141.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3671141.20 # format = BAM # ChIP-seq file = ['SRX3671141.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 09:49:30: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:49:30: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:49:37: 1000000 INFO @ Thu, 05 Apr 2018 09:49:37: 1000000 INFO @ Thu, 05 Apr 2018 09:49:37: 1000000 INFO @ Thu, 05 Apr 2018 09:49:43: 2000000 INFO @ Thu, 05 Apr 2018 09:49:44: 2000000 INFO @ Thu, 05 Apr 2018 09:49:44: 2000000 INFO @ Thu, 05 Apr 2018 09:49:50: 3000000 INFO @ Thu, 05 Apr 2018 09:49:51: 3000000 INFO @ Thu, 05 Apr 2018 09:49:51: 3000000 INFO @ Thu, 05 Apr 2018 09:49:57: 4000000 INFO @ Thu, 05 Apr 2018 09:49:58: 4000000 INFO @ Thu, 05 Apr 2018 09:49:58: 4000000 INFO @ Thu, 05 Apr 2018 09:50:03: 5000000 INFO @ Thu, 05 Apr 2018 09:50:05: 5000000 INFO @ Thu, 05 Apr 2018 09:50:05: 5000000 INFO @ Thu, 05 Apr 2018 09:50:10: 6000000 INFO @ Thu, 05 Apr 2018 09:50:12: 6000000 INFO @ Thu, 05 Apr 2018 09:50:12: 6000000 INFO @ Thu, 05 Apr 2018 09:50:16: 7000000 INFO @ Thu, 05 Apr 2018 09:50:19: 7000000 INFO @ Thu, 05 Apr 2018 09:50:19: 7000000 INFO @ Thu, 05 Apr 2018 09:50:23: 8000000 INFO @ Thu, 05 Apr 2018 09:50:26: 8000000 INFO @ Thu, 05 Apr 2018 09:50:26: 8000000 INFO @ Thu, 05 Apr 2018 09:50:29: 9000000 INFO @ Thu, 05 Apr 2018 09:50:33: 9000000 INFO @ Thu, 05 Apr 2018 09:50:33: 9000000 INFO @ Thu, 05 Apr 2018 09:50:36: 10000000 INFO @ Thu, 05 Apr 2018 09:50:40: 10000000 INFO @ Thu, 05 Apr 2018 09:50:40: 10000000 INFO @ Thu, 05 Apr 2018 09:50:42: 11000000 INFO @ Thu, 05 Apr 2018 09:50:47: 11000000 INFO @ Thu, 05 Apr 2018 09:50:47: 11000000 INFO @ Thu, 05 Apr 2018 09:50:49: 12000000 INFO @ Thu, 05 Apr 2018 09:50:54: 12000000 INFO @ Thu, 05 Apr 2018 09:50:54: 12000000 INFO @ Thu, 05 Apr 2018 09:50:55: 13000000 INFO @ Thu, 05 Apr 2018 09:51:01: 13000000 INFO @ Thu, 05 Apr 2018 09:51:01: 13000000 INFO @ Thu, 05 Apr 2018 09:51:01: 14000000 INFO @ Thu, 05 Apr 2018 09:51:08: 14000000 INFO @ Thu, 05 Apr 2018 09:51:08: 14000000 INFO @ Thu, 05 Apr 2018 09:51:08: 15000000 INFO @ Thu, 05 Apr 2018 09:51:14: 16000000 INFO @ Thu, 05 Apr 2018 09:51:15: 15000000 INFO @ Thu, 05 Apr 2018 09:51:15: 15000000 INFO @ Thu, 05 Apr 2018 09:51:21: 17000000 INFO @ Thu, 05 Apr 2018 09:51:22: 16000000 INFO @ Thu, 05 Apr 2018 09:51:22: 16000000 INFO @ Thu, 05 Apr 2018 09:51:27: 18000000 INFO @ Thu, 05 Apr 2018 09:51:29: 17000000 INFO @ Thu, 05 Apr 2018 09:51:29: 17000000 INFO @ Thu, 05 Apr 2018 09:51:34: 19000000 INFO @ Thu, 05 Apr 2018 09:51:36: 18000000 INFO @ Thu, 05 Apr 2018 09:51:36: 18000000 INFO @ Thu, 05 Apr 2018 09:51:40: 20000000 INFO @ Thu, 05 Apr 2018 09:51:43: 19000000 INFO @ Thu, 05 Apr 2018 09:51:43: 19000000 INFO @ Thu, 05 Apr 2018 09:51:46: 21000000 INFO @ Thu, 05 Apr 2018 09:51:50: 20000000 INFO @ Thu, 05 Apr 2018 09:51:50: 20000000 INFO @ Thu, 05 Apr 2018 09:51:53: 22000000 INFO @ Thu, 05 Apr 2018 09:51:57: 21000000 INFO @ Thu, 05 Apr 2018 09:51:57: 21000000 INFO @ Thu, 05 Apr 2018 09:51:59: 23000000 INFO @ Thu, 05 Apr 2018 09:52:04: 22000000 INFO @ Thu, 05 Apr 2018 09:52:04: 22000000 INFO @ Thu, 05 Apr 2018 09:52:06: 24000000 INFO @ Thu, 05 Apr 2018 09:52:11: 23000000 INFO @ Thu, 05 Apr 2018 09:52:11: 23000000 INFO @ Thu, 05 Apr 2018 09:52:12: 25000000 INFO @ Thu, 05 Apr 2018 09:52:17: 24000000 INFO @ Thu, 05 Apr 2018 09:52:17: 24000000 INFO @ Thu, 05 Apr 2018 09:52:19: 26000000 INFO @ Thu, 05 Apr 2018 09:52:24: 25000000 INFO @ Thu, 05 Apr 2018 09:52:24: 25000000 INFO @ Thu, 05 Apr 2018 09:52:25: 27000000 INFO @ Thu, 05 Apr 2018 09:52:32: 26000000 INFO @ Thu, 05 Apr 2018 09:52:32: 26000000 INFO @ Thu, 05 Apr 2018 09:52:32: 28000000 INFO @ Thu, 05 Apr 2018 09:52:38: 29000000 INFO @ Thu, 05 Apr 2018 09:52:39: 27000000 INFO @ Thu, 05 Apr 2018 09:52:39: 27000000 INFO @ Thu, 05 Apr 2018 09:52:44: 30000000 INFO @ Thu, 05 Apr 2018 09:52:46: 28000000 INFO @ Thu, 05 Apr 2018 09:52:46: 28000000 INFO @ Thu, 05 Apr 2018 09:52:51: 31000000 INFO @ Thu, 05 Apr 2018 09:52:53: 29000000 INFO @ Thu, 05 Apr 2018 09:52:53: 29000000 INFO @ Thu, 05 Apr 2018 09:52:57: 32000000 INFO @ Thu, 05 Apr 2018 09:52:59: 30000000 INFO @ Thu, 05 Apr 2018 09:52:59: 30000000 INFO @ Thu, 05 Apr 2018 09:53:04: 33000000 INFO @ Thu, 05 Apr 2018 09:53:06: 31000000 INFO @ Thu, 05 Apr 2018 09:53:06: 31000000 INFO @ Thu, 05 Apr 2018 09:53:11: 34000000 INFO @ Thu, 05 Apr 2018 09:53:15: 32000000 INFO @ Thu, 05 Apr 2018 09:53:15: 32000000 INFO @ Thu, 05 Apr 2018 09:53:18: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:53:18: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:53:18: #1 total tags in treatment: 17161895 INFO @ Thu, 05 Apr 2018 09:53:18: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:53:18: #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 09:53:18: #1 tags after filtering in treatment: 11221545 INFO @ Thu, 05 Apr 2018 09:53:18: #1 Redundant rate of treatment: 0.35 INFO @ Thu, 05 Apr 2018 09:53:18: #1 finished! INFO @ Thu, 05 Apr 2018 09:53:18: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:53:18: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:53:19: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:53:19: 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, 05 Apr 2018 09:53:19: Process for pairing-model is terminated! cat: SRX3671141.20_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 `SRX3671141.20_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 `SRX3671141.20_*.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 `SRX3671141.20_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... INFO @ Thu, 05 Apr 2018 09:53:24: 33000000 INFO @ Thu, 05 Apr 2018 09:53:24: 33000000 INFO @ Thu, 05 Apr 2018 09:53:32: 34000000 INFO @ Thu, 05 Apr 2018 09:53:32: 34000000 INFO @ Thu, 05 Apr 2018 09:53:39: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:53:39: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:53:39: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:53:39: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:53:39: #1 total tags in treatment: 17161895 INFO @ Thu, 05 Apr 2018 09:53:39: #1 total tags in treatment: 17161895 INFO @ Thu, 05 Apr 2018 09:53:39: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:53:39: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:53:39: #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 09:53:39: #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 09:53:39: #1 tags after filtering in treatment: 11221545 INFO @ Thu, 05 Apr 2018 09:53:39: #1 tags after filtering in treatment: 11221545 INFO @ Thu, 05 Apr 2018 09:53:39: #1 Redundant rate of treatment: 0.35 INFO @ Thu, 05 Apr 2018 09:53:39: #1 Redundant rate of treatment: 0.35 INFO @ Thu, 05 Apr 2018 09:53:39: #1 finished! INFO @ Thu, 05 Apr 2018 09:53:39: #1 finished! INFO @ Thu, 05 Apr 2018 09:53:39: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:53:39: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:53:39: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:53:39: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:53:40: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:53:40: 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, 05 Apr 2018 09:53:40: Process for pairing-model is terminated! INFO @ Thu, 05 Apr 2018 09:53:40: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:53:40: 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, 05 Apr 2018 09:53:40: Process for pairing-model is terminated! cat: SRX3671141.05_peaks.narrowPeakcat: SRX3671141.10_peaks.narrowPeak: そのようなファイルやディレクトリはありません : 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 `SRX3671141.10_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 `SRX3671141.10_*.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 `SRX3671141.10_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 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3671141.05_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 `SRX3671141.05_*.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 `SRX3671141.05_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 BigWig に変換しました。