Job ID = 10536388 sra ファイルのダウンロード中... Completed: 1351312K bytes transferred in 45 seconds (242560K 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 33825456 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3671145/SRR6696897.sra Written 33825456 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: 00:23:23 33825456 reads; of these: 33825456 (100.00%) were paired; of these: 3570810 (10.56%) aligned concordantly 0 times 26787857 (79.19%) aligned concordantly exactly 1 time 3466789 (10.25%) aligned concordantly >1 times ---- 3570810 pairs aligned concordantly 0 times; of these: 81551 (2.28%) aligned discordantly 1 time ---- 3489259 pairs aligned 0 times concordantly or discordantly; of these: 6978518 mates make up the pairs; of these: 6512328 (93.32%) aligned 0 times 386886 (5.54%) aligned exactly 1 time 79304 (1.14%) aligned >1 times 90.37% overall alignment rate Time searching: 00:23:23 Overall time: 00:23:23 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] 13874255 / 30266607 = 0.4584 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 09:51:35: # Command line: callpeak -t SRX3671145.bam -f BAM -g 12100000 -n SRX3671145.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3671145.05 # format = BAM # ChIP-seq file = ['SRX3671145.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 09:51:35: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:51:35: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:51:35: # Command line: callpeak -t SRX3671145.bam -f BAM -g 12100000 -n SRX3671145.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3671145.20 # format = BAM # ChIP-seq file = ['SRX3671145.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 09:51:35: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:51:35: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:51:35: # Command line: callpeak -t SRX3671145.bam -f BAM -g 12100000 -n SRX3671145.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3671145.10 # format = BAM # ChIP-seq file = ['SRX3671145.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 09:51:35: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:51:35: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:51:41: 1000000 INFO @ Thu, 05 Apr 2018 09:51:41: 1000000 INFO @ Thu, 05 Apr 2018 09:51:41: 1000000 INFO @ Thu, 05 Apr 2018 09:51:46: 2000000 INFO @ Thu, 05 Apr 2018 09:51:46: 2000000 INFO @ Thu, 05 Apr 2018 09:51:46: 2000000 INFO @ Thu, 05 Apr 2018 09:51:51: 3000000 INFO @ Thu, 05 Apr 2018 09:51:52: 3000000 INFO @ Thu, 05 Apr 2018 09:51:52: 3000000 INFO @ Thu, 05 Apr 2018 09:51:57: 4000000 INFO @ Thu, 05 Apr 2018 09:51:57: 4000000 INFO @ Thu, 05 Apr 2018 09:51:57: 4000000 INFO @ Thu, 05 Apr 2018 09:52:02: 5000000 INFO @ Thu, 05 Apr 2018 09:52:02: 5000000 INFO @ Thu, 05 Apr 2018 09:52:02: 5000000 INFO @ Thu, 05 Apr 2018 09:52:07: 6000000 INFO @ Thu, 05 Apr 2018 09:52:08: 6000000 INFO @ Thu, 05 Apr 2018 09:52:08: 6000000 INFO @ Thu, 05 Apr 2018 09:52:13: 7000000 INFO @ Thu, 05 Apr 2018 09:52:13: 7000000 INFO @ Thu, 05 Apr 2018 09:52:13: 7000000 INFO @ Thu, 05 Apr 2018 09:52:18: 8000000 INFO @ Thu, 05 Apr 2018 09:52:18: 8000000 INFO @ Thu, 05 Apr 2018 09:52:19: 8000000 INFO @ Thu, 05 Apr 2018 09:52:23: 9000000 INFO @ Thu, 05 Apr 2018 09:52:24: 9000000 INFO @ Thu, 05 Apr 2018 09:52:24: 9000000 INFO @ Thu, 05 Apr 2018 09:52:28: 10000000 INFO @ Thu, 05 Apr 2018 09:52:29: 10000000 INFO @ Thu, 05 Apr 2018 09:52:29: 10000000 INFO @ Thu, 05 Apr 2018 09:52:33: 11000000 INFO @ Thu, 05 Apr 2018 09:52:34: 11000000 INFO @ Thu, 05 Apr 2018 09:52:35: 11000000 INFO @ Thu, 05 Apr 2018 09:52:39: 12000000 INFO @ Thu, 05 Apr 2018 09:52:40: 12000000 INFO @ Thu, 05 Apr 2018 09:52:40: 12000000 INFO @ Thu, 05 Apr 2018 09:52:44: 13000000 INFO @ Thu, 05 Apr 2018 09:52:45: 13000000 INFO @ Thu, 05 Apr 2018 09:52:45: 13000000 INFO @ Thu, 05 Apr 2018 09:52:49: 14000000 INFO @ Thu, 05 Apr 2018 09:52:50: 14000000 INFO @ Thu, 05 Apr 2018 09:52:51: 14000000 INFO @ Thu, 05 Apr 2018 09:52:54: 15000000 INFO @ Thu, 05 Apr 2018 09:52:56: 15000000 INFO @ Thu, 05 Apr 2018 09:52:56: 15000000 INFO @ Thu, 05 Apr 2018 09:52:59: 16000000 INFO @ Thu, 05 Apr 2018 09:53:01: 16000000 INFO @ Thu, 05 Apr 2018 09:53:02: 16000000 INFO @ Thu, 05 Apr 2018 09:53:05: 17000000 INFO @ Thu, 05 Apr 2018 09:53:07: 17000000 INFO @ Thu, 05 Apr 2018 09:53:07: 17000000 INFO @ Thu, 05 Apr 2018 09:53:10: 18000000 INFO @ Thu, 05 Apr 2018 09:53:12: 18000000 INFO @ Thu, 05 Apr 2018 09:53:13: 18000000 INFO @ Thu, 05 Apr 2018 09:53:15: 19000000 INFO @ Thu, 05 Apr 2018 09:53:17: 19000000 INFO @ Thu, 05 Apr 2018 09:53:18: 19000000 INFO @ Thu, 05 Apr 2018 09:53:20: 20000000 INFO @ Thu, 05 Apr 2018 09:53:23: 20000000 INFO @ Thu, 05 Apr 2018 09:53:24: 20000000 INFO @ Thu, 05 Apr 2018 09:53:25: 21000000 INFO @ Thu, 05 Apr 2018 09:53:28: 21000000 INFO @ Thu, 05 Apr 2018 09:53:29: 21000000 INFO @ Thu, 05 Apr 2018 09:53:30: 22000000 INFO @ Thu, 05 Apr 2018 09:53:33: 22000000 INFO @ Thu, 05 Apr 2018 09:53:35: 22000000 INFO @ Thu, 05 Apr 2018 09:53:36: 23000000 INFO @ Thu, 05 Apr 2018 09:53:39: 23000000 INFO @ Thu, 05 Apr 2018 09:53:40: 23000000 INFO @ Thu, 05 Apr 2018 09:53:41: 24000000 INFO @ Thu, 05 Apr 2018 09:53:44: 24000000 INFO @ Thu, 05 Apr 2018 09:53:45: 24000000 INFO @ Thu, 05 Apr 2018 09:53:46: 25000000 INFO @ Thu, 05 Apr 2018 09:53:49: 25000000 INFO @ Thu, 05 Apr 2018 09:53:51: 25000000 INFO @ Thu, 05 Apr 2018 09:53:51: 26000000 INFO @ Thu, 05 Apr 2018 09:53:55: 26000000 INFO @ Thu, 05 Apr 2018 09:53:56: 26000000 INFO @ Thu, 05 Apr 2018 09:53:56: 27000000 INFO @ Thu, 05 Apr 2018 09:54:00: 27000000 INFO @ Thu, 05 Apr 2018 09:54:01: 27000000 INFO @ Thu, 05 Apr 2018 09:54:02: 28000000 INFO @ Thu, 05 Apr 2018 09:54:06: 28000000 INFO @ Thu, 05 Apr 2018 09:54:07: 28000000 INFO @ Thu, 05 Apr 2018 09:54:07: 29000000 INFO @ Thu, 05 Apr 2018 09:54:11: 29000000 INFO @ Thu, 05 Apr 2018 09:54:12: 29000000 INFO @ Thu, 05 Apr 2018 09:54:12: 30000000 INFO @ Thu, 05 Apr 2018 09:54:17: 30000000 INFO @ Thu, 05 Apr 2018 09:54:17: 30000000 INFO @ Thu, 05 Apr 2018 09:54:18: 31000000 INFO @ Thu, 05 Apr 2018 09:54:22: 31000000 INFO @ Thu, 05 Apr 2018 09:54:23: 31000000 INFO @ Thu, 05 Apr 2018 09:54:23: 32000000 INFO @ Thu, 05 Apr 2018 09:54:28: 32000000 INFO @ Thu, 05 Apr 2018 09:54:28: 32000000 INFO @ Thu, 05 Apr 2018 09:54:29: 33000000 INFO @ Thu, 05 Apr 2018 09:54:31: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:54:31: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:54:31: #1 total tags in treatment: 16384041 INFO @ Thu, 05 Apr 2018 09:54:31: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:54:31: #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 09:54:31: #1 tags after filtering in treatment: 10810868 INFO @ Thu, 05 Apr 2018 09:54:31: #1 Redundant rate of treatment: 0.34 INFO @ Thu, 05 Apr 2018 09:54:31: #1 finished! INFO @ Thu, 05 Apr 2018 09:54:31: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:54:31: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:54:32: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:54:32: 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 09:54:32: Process for pairing-model is terminated! cat: SRX3671145.05_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3671145.05_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 `SRX3671145.05_*.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 `SRX3671145.05_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 09:54:33: 33000000 INFO @ Thu, 05 Apr 2018 09:54:33: 33000000 INFO @ Thu, 05 Apr 2018 09:54:35: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:54:35: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:54:35: #1 total tags in treatment: 16384041 INFO @ Thu, 05 Apr 2018 09:54:35: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:54:35: #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 09:54:36: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:54:36: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:54:36: #1 total tags in treatment: 16384041 INFO @ Thu, 05 Apr 2018 09:54:36: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:54:36: #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 09:54:36: #1 tags after filtering in treatment: 10810868 INFO @ Thu, 05 Apr 2018 09:54:36: #1 Redundant rate of treatment: 0.34 INFO @ Thu, 05 Apr 2018 09:54:36: #1 finished! INFO @ Thu, 05 Apr 2018 09:54:36: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:54:36: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:54:36: #1 tags after filtering in treatment: 10810868 INFO @ Thu, 05 Apr 2018 09:54:36: #1 Redundant rate of treatment: 0.34 INFO @ Thu, 05 Apr 2018 09:54:36: #1 finished! INFO @ Thu, 05 Apr 2018 09:54:36: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:54:36: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:54:36: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:54:36: 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 09:54:36: Process for pairing-model is terminated! cat: SRX3671145.10_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 `SRX3671145.10_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 `SRX3671145.10_*.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 `SRX3671145.10_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 09:54:37: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:54:37: 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, 05 Apr 2018 09:54:37: Process for pairing-model is terminated! cat: SRX3671145.20_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3671145.20_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 `SRX3671145.20_*.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 `SRX3671145.20_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。