Job ID = 10536385 sra ファイルのダウンロード中... Completed: 1238701K bytes transferred in 21 seconds (482667K 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 30958756 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3671142/SRR6696894.sra Written 30958756 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: 00:22:14 30958756 reads; of these: 30958756 (100.00%) were paired; of these: 4498817 (14.53%) aligned concordantly 0 times 22340811 (72.16%) aligned concordantly exactly 1 time 4119128 (13.31%) aligned concordantly >1 times ---- 4498817 pairs aligned concordantly 0 times; of these: 55926 (1.24%) aligned discordantly 1 time ---- 4442891 pairs aligned 0 times concordantly or discordantly; of these: 8885782 mates make up the pairs; of these: 8471574 (95.34%) aligned 0 times 324319 (3.65%) aligned exactly 1 time 89889 (1.01%) aligned >1 times 86.32% overall alignment rate Time searching: 00:22:14 Overall time: 00:22:14 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] 10772301 / 26474124 = 0.4069 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 09:47:27: # Command line: callpeak -t SRX3671142.bam -f BAM -g 12100000 -n SRX3671142.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3671142.20 # format = BAM # ChIP-seq file = ['SRX3671142.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 09:47:27: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:47:27: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:47:27: # Command line: callpeak -t SRX3671142.bam -f BAM -g 12100000 -n SRX3671142.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3671142.10 # format = BAM # ChIP-seq file = ['SRX3671142.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 09:47:27: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:47:27: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:47:27: # Command line: callpeak -t SRX3671142.bam -f BAM -g 12100000 -n SRX3671142.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3671142.05 # format = BAM # ChIP-seq file = ['SRX3671142.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 09:47:27: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:47:27: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:47:34: 1000000 INFO @ Thu, 05 Apr 2018 09:47:35: 1000000 INFO @ Thu, 05 Apr 2018 09:47:35: 1000000 INFO @ Thu, 05 Apr 2018 09:47:41: 2000000 INFO @ Thu, 05 Apr 2018 09:47:43: 2000000 INFO @ Thu, 05 Apr 2018 09:47:43: 2000000 INFO @ Thu, 05 Apr 2018 09:47:48: 3000000 INFO @ Thu, 05 Apr 2018 09:47:51: 3000000 INFO @ Thu, 05 Apr 2018 09:47:51: 3000000 INFO @ Thu, 05 Apr 2018 09:47:55: 4000000 INFO @ Thu, 05 Apr 2018 09:47:59: 4000000 INFO @ Thu, 05 Apr 2018 09:47:59: 4000000 INFO @ Thu, 05 Apr 2018 09:48:02: 5000000 INFO @ Thu, 05 Apr 2018 09:48:07: 5000000 INFO @ Thu, 05 Apr 2018 09:48:07: 5000000 INFO @ Thu, 05 Apr 2018 09:48:09: 6000000 INFO @ Thu, 05 Apr 2018 09:48:15: 6000000 INFO @ Thu, 05 Apr 2018 09:48:15: 6000000 INFO @ Thu, 05 Apr 2018 09:48:16: 7000000 INFO @ Thu, 05 Apr 2018 09:48:23: 7000000 INFO @ Thu, 05 Apr 2018 09:48:23: 7000000 INFO @ Thu, 05 Apr 2018 09:48:24: 8000000 INFO @ Thu, 05 Apr 2018 09:48:31: 8000000 INFO @ Thu, 05 Apr 2018 09:48:31: 8000000 INFO @ Thu, 05 Apr 2018 09:48:31: 9000000 INFO @ Thu, 05 Apr 2018 09:48:38: 10000000 INFO @ Thu, 05 Apr 2018 09:48:39: 9000000 INFO @ Thu, 05 Apr 2018 09:48:39: 9000000 INFO @ Thu, 05 Apr 2018 09:48:45: 11000000 INFO @ Thu, 05 Apr 2018 09:48:47: 10000000 INFO @ Thu, 05 Apr 2018 09:48:47: 10000000 INFO @ Thu, 05 Apr 2018 09:48:53: 12000000 INFO @ Thu, 05 Apr 2018 09:48:55: 11000000 INFO @ Thu, 05 Apr 2018 09:48:55: 11000000 INFO @ Thu, 05 Apr 2018 09:49:00: 13000000 INFO @ Thu, 05 Apr 2018 09:49:03: 12000000 INFO @ Thu, 05 Apr 2018 09:49:03: 12000000 INFO @ Thu, 05 Apr 2018 09:49:07: 14000000 INFO @ Thu, 05 Apr 2018 09:49:11: 13000000 INFO @ Thu, 05 Apr 2018 09:49:11: 13000000 INFO @ Thu, 05 Apr 2018 09:49:15: 15000000 INFO @ Thu, 05 Apr 2018 09:49:19: 14000000 INFO @ Thu, 05 Apr 2018 09:49:19: 14000000 INFO @ Thu, 05 Apr 2018 09:49:22: 16000000 INFO @ Thu, 05 Apr 2018 09:49:27: 15000000 INFO @ Thu, 05 Apr 2018 09:49:27: 15000000 INFO @ Thu, 05 Apr 2018 09:49:29: 17000000 INFO @ Thu, 05 Apr 2018 09:49:35: 16000000 INFO @ Thu, 05 Apr 2018 09:49:35: 16000000 INFO @ Thu, 05 Apr 2018 09:49:36: 18000000 INFO @ Thu, 05 Apr 2018 09:49:43: 19000000 INFO @ Thu, 05 Apr 2018 09:49:43: 17000000 INFO @ Thu, 05 Apr 2018 09:49:43: 17000000 INFO @ Thu, 05 Apr 2018 09:49:49: 20000000 INFO @ Thu, 05 Apr 2018 09:49:51: 18000000 INFO @ Thu, 05 Apr 2018 09:49:51: 18000000 INFO @ Thu, 05 Apr 2018 09:49:55: 21000000 INFO @ Thu, 05 Apr 2018 09:49:57: 19000000 INFO @ Thu, 05 Apr 2018 09:49:57: 19000000 INFO @ Thu, 05 Apr 2018 09:50:01: 22000000 INFO @ Thu, 05 Apr 2018 09:50:03: 20000000 INFO @ Thu, 05 Apr 2018 09:50:04: 20000000 INFO @ Thu, 05 Apr 2018 09:50:07: 23000000 INFO @ Thu, 05 Apr 2018 09:50:09: 21000000 INFO @ Thu, 05 Apr 2018 09:50:10: 21000000 INFO @ Thu, 05 Apr 2018 09:50:13: 24000000 INFO @ Thu, 05 Apr 2018 09:50:15: 22000000 INFO @ Thu, 05 Apr 2018 09:50:16: 22000000 INFO @ Thu, 05 Apr 2018 09:50:19: 25000000 INFO @ Thu, 05 Apr 2018 09:50:21: 23000000 INFO @ Thu, 05 Apr 2018 09:50:22: 23000000 INFO @ Thu, 05 Apr 2018 09:50:25: 26000000 INFO @ Thu, 05 Apr 2018 09:50:28: 24000000 INFO @ Thu, 05 Apr 2018 09:50:29: 24000000 INFO @ Thu, 05 Apr 2018 09:50:31: 27000000 INFO @ Thu, 05 Apr 2018 09:50:34: 25000000 INFO @ Thu, 05 Apr 2018 09:50:35: 25000000 INFO @ Thu, 05 Apr 2018 09:50:37: 28000000 INFO @ Thu, 05 Apr 2018 09:50:40: 26000000 INFO @ Thu, 05 Apr 2018 09:50:41: 26000000 INFO @ Thu, 05 Apr 2018 09:50:42: 29000000 INFO @ Thu, 05 Apr 2018 09:50:46: 27000000 INFO @ Thu, 05 Apr 2018 09:50:48: 27000000 INFO @ Thu, 05 Apr 2018 09:50:50: 30000000 INFO @ Thu, 05 Apr 2018 09:50:53: 28000000 INFO @ Thu, 05 Apr 2018 09:50:55: 28000000 INFO @ Thu, 05 Apr 2018 09:50:57: 31000000 INFO @ Thu, 05 Apr 2018 09:50:59: 29000000 INFO @ Thu, 05 Apr 2018 09:51:02: 29000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 05 Apr 2018 09:51:04: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:51:04: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:51:04: #1 total tags in treatment: 15690444 INFO @ Thu, 05 Apr 2018 09:51:04: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:51:04: #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 09:51:04: #1 tags after filtering in treatment: 10317262 INFO @ Thu, 05 Apr 2018 09:51:04: #1 Redundant rate of treatment: 0.34 INFO @ Thu, 05 Apr 2018 09:51:04: #1 finished! INFO @ Thu, 05 Apr 2018 09:51:04: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:51:04: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:51:05: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:51:05: 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 09:51:05: Process for pairing-model is terminated! cat: SRX3671142.05_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 `SRX3671142.05_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 `SRX3671142.05_*.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 `SRX3671142.05_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 09:51:06: 30000000 INFO @ Thu, 05 Apr 2018 09:51:08: 30000000 INFO @ Thu, 05 Apr 2018 09:51:12: 31000000 INFO @ Thu, 05 Apr 2018 09:51:15: 31000000 INFO @ Thu, 05 Apr 2018 09:51:17: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:51:17: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:51:17: #1 total tags in treatment: 15690444 INFO @ Thu, 05 Apr 2018 09:51:17: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:51:17: #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 09:51:18: #1 tags after filtering in treatment: 10317262 INFO @ Thu, 05 Apr 2018 09:51:18: #1 Redundant rate of treatment: 0.34 INFO @ Thu, 05 Apr 2018 09:51:18: #1 finished! INFO @ Thu, 05 Apr 2018 09:51:18: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:51:18: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:51:18: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:51:18: 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 09:51:18: Process for pairing-model is terminated! cat: SRX3671142.10_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 `SRX3671142.10_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 `SRX3671142.10_*.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 `SRX3671142.10_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, 05 Apr 2018 09:51:20: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:51:20: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:51:20: #1 total tags in treatment: 15690444 INFO @ Thu, 05 Apr 2018 09:51:20: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:51:20: #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 09:51:21: #1 tags after filtering in treatment: 10317262 INFO @ Thu, 05 Apr 2018 09:51:21: #1 Redundant rate of treatment: 0.34 INFO @ Thu, 05 Apr 2018 09:51:21: #1 finished! INFO @ Thu, 05 Apr 2018 09:51:21: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:51:21: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:51:21: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:51:21: 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 09:51:21: Process for pairing-model is terminated! cat: SRX3671142.20_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 `SRX3671142.20_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 `SRX3671142.20_*.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 `SRX3671142.20_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 BigWig に変換しました。