Job ID = 10536389 sra ファイルのダウンロード中... Completed: 1365097K bytes transferred in 46 seconds (240871K 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 33859031 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3671146/SRR6696898.sra Written 33859031 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: 00:23:00 33859031 reads; of these: 33859031 (100.00%) were paired; of these: 5871746 (17.34%) aligned concordantly 0 times 24687781 (72.91%) aligned concordantly exactly 1 time 3299504 (9.74%) aligned concordantly >1 times ---- 5871746 pairs aligned concordantly 0 times; of these: 63077 (1.07%) aligned discordantly 1 time ---- 5808669 pairs aligned 0 times concordantly or discordantly; of these: 11617338 mates make up the pairs; of these: 11210701 (96.50%) aligned 0 times 337632 (2.91%) aligned exactly 1 time 69005 (0.59%) aligned >1 times 83.45% overall alignment rate Time searching: 00:23:00 Overall time: 00:23:00 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] 9939187 / 28003014 = 0.3549 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 09:51:55: # Command line: callpeak -t SRX3671146.bam -f BAM -g 12100000 -n SRX3671146.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3671146.10 # format = BAM # ChIP-seq file = ['SRX3671146.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 09:51:55: # Command line: callpeak -t SRX3671146.bam -f BAM -g 12100000 -n SRX3671146.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3671146.20 # format = BAM # ChIP-seq file = ['SRX3671146.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 09:51:55: # Command line: callpeak -t SRX3671146.bam -f BAM -g 12100000 -n SRX3671146.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3671146.05 # format = BAM # ChIP-seq file = ['SRX3671146.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 09:51:55: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:51:55: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:51:55: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:51:55: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:51:55: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:51:55: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:52:02: 1000000 INFO @ Thu, 05 Apr 2018 09:52:02: 1000000 INFO @ Thu, 05 Apr 2018 09:52:02: 1000000 INFO @ Thu, 05 Apr 2018 09:52:09: 2000000 INFO @ Thu, 05 Apr 2018 09:52:09: 2000000 INFO @ Thu, 05 Apr 2018 09:52:09: 2000000 INFO @ Thu, 05 Apr 2018 09:52:15: 3000000 INFO @ Thu, 05 Apr 2018 09:52:15: 3000000 INFO @ Thu, 05 Apr 2018 09:52:15: 3000000 INFO @ Thu, 05 Apr 2018 09:52:22: 4000000 INFO @ Thu, 05 Apr 2018 09:52:22: 4000000 INFO @ Thu, 05 Apr 2018 09:52:22: 4000000 INFO @ Thu, 05 Apr 2018 09:52:28: 5000000 INFO @ Thu, 05 Apr 2018 09:52:28: 5000000 INFO @ Thu, 05 Apr 2018 09:52:29: 5000000 INFO @ Thu, 05 Apr 2018 09:52:35: 6000000 INFO @ Thu, 05 Apr 2018 09:52:35: 6000000 INFO @ Thu, 05 Apr 2018 09:52:35: 6000000 INFO @ Thu, 05 Apr 2018 09:52:42: 7000000 INFO @ Thu, 05 Apr 2018 09:52:42: 7000000 INFO @ Thu, 05 Apr 2018 09:52:42: 7000000 INFO @ Thu, 05 Apr 2018 09:52:49: 8000000 INFO @ Thu, 05 Apr 2018 09:52:49: 8000000 INFO @ Thu, 05 Apr 2018 09:52:50: 8000000 INFO @ Thu, 05 Apr 2018 09:52:56: 9000000 INFO @ Thu, 05 Apr 2018 09:52:56: 9000000 INFO @ Thu, 05 Apr 2018 09:52:56: 9000000 INFO @ Thu, 05 Apr 2018 09:53:02: 10000000 INFO @ Thu, 05 Apr 2018 09:53:02: 10000000 INFO @ Thu, 05 Apr 2018 09:53:02: 10000000 INFO @ Thu, 05 Apr 2018 09:53:09: 11000000 INFO @ Thu, 05 Apr 2018 09:53:09: 11000000 INFO @ Thu, 05 Apr 2018 09:53:09: 11000000 INFO @ Thu, 05 Apr 2018 09:53:16: 12000000 INFO @ Thu, 05 Apr 2018 09:53:16: 12000000 INFO @ Thu, 05 Apr 2018 09:53:16: 12000000 INFO @ Thu, 05 Apr 2018 09:53:22: 13000000 INFO @ Thu, 05 Apr 2018 09:53:23: 13000000 INFO @ Thu, 05 Apr 2018 09:53:23: 13000000 INFO @ Thu, 05 Apr 2018 09:53:30: 14000000 INFO @ Thu, 05 Apr 2018 09:53:30: 14000000 INFO @ Thu, 05 Apr 2018 09:53:30: 14000000 INFO @ Thu, 05 Apr 2018 09:53:37: 15000000 INFO @ Thu, 05 Apr 2018 09:53:37: 15000000 INFO @ Thu, 05 Apr 2018 09:53:37: 15000000 INFO @ Thu, 05 Apr 2018 09:53:43: 16000000 INFO @ Thu, 05 Apr 2018 09:53:44: 16000000 INFO @ Thu, 05 Apr 2018 09:53:44: 16000000 INFO @ Thu, 05 Apr 2018 09:53:50: 17000000 INFO @ Thu, 05 Apr 2018 09:53:51: 17000000 INFO @ Thu, 05 Apr 2018 09:53:51: 17000000 INFO @ Thu, 05 Apr 2018 09:53:56: 18000000 INFO @ Thu, 05 Apr 2018 09:53:57: 18000000 INFO @ Thu, 05 Apr 2018 09:53:57: 18000000 INFO @ Thu, 05 Apr 2018 09:54:02: 19000000 INFO @ Thu, 05 Apr 2018 09:54:04: 19000000 INFO @ Thu, 05 Apr 2018 09:54:04: 19000000 INFO @ Thu, 05 Apr 2018 09:54:08: 20000000 INFO @ Thu, 05 Apr 2018 09:54:10: 20000000 INFO @ Thu, 05 Apr 2018 09:54:10: 20000000 INFO @ Thu, 05 Apr 2018 09:54:15: 21000000 INFO @ Thu, 05 Apr 2018 09:54:17: 21000000 INFO @ Thu, 05 Apr 2018 09:54:17: 21000000 INFO @ Thu, 05 Apr 2018 09:54:21: 22000000 INFO @ Thu, 05 Apr 2018 09:54:24: 22000000 INFO @ Thu, 05 Apr 2018 09:54:24: 22000000 INFO @ Thu, 05 Apr 2018 09:54:27: 23000000 INFO @ Thu, 05 Apr 2018 09:54:30: 23000000 INFO @ Thu, 05 Apr 2018 09:54:30: 23000000 INFO @ Thu, 05 Apr 2018 09:54:34: 24000000 INFO @ Thu, 05 Apr 2018 09:54:37: 24000000 INFO @ Thu, 05 Apr 2018 09:54:37: 24000000 INFO @ Thu, 05 Apr 2018 09:54:41: 25000000 INFO @ Thu, 05 Apr 2018 09:54:45: 25000000 INFO @ Thu, 05 Apr 2018 09:54:45: 25000000 INFO @ Thu, 05 Apr 2018 09:54:48: 26000000 INFO @ Thu, 05 Apr 2018 09:54:52: 26000000 INFO @ Thu, 05 Apr 2018 09:54:52: 26000000 INFO @ Thu, 05 Apr 2018 09:54:56: 27000000 INFO @ Thu, 05 Apr 2018 09:55:00: 27000000 INFO @ Thu, 05 Apr 2018 09:55:00: 27000000 INFO @ Thu, 05 Apr 2018 09:55:03: 28000000 INFO @ Thu, 05 Apr 2018 09:55:07: 28000000 INFO @ Thu, 05 Apr 2018 09:55:07: 28000000 INFO @ Thu, 05 Apr 2018 09:55:11: 29000000 INFO @ Thu, 05 Apr 2018 09:55:14: 29000000 INFO @ Thu, 05 Apr 2018 09:55:14: 29000000 INFO @ Thu, 05 Apr 2018 09:55:18: 30000000 INFO @ Thu, 05 Apr 2018 09:55:22: 30000000 INFO @ Thu, 05 Apr 2018 09:55:22: 30000000 INFO @ Thu, 05 Apr 2018 09:55:25: 31000000 INFO @ Thu, 05 Apr 2018 09:55:29: 31000000 INFO @ Thu, 05 Apr 2018 09:55:29: 31000000 INFO @ Thu, 05 Apr 2018 09:55:33: 32000000 INFO @ Thu, 05 Apr 2018 09:55:37: 32000000 INFO @ Thu, 05 Apr 2018 09:55:37: 32000000 INFO @ Thu, 05 Apr 2018 09:55:40: 33000000 INFO @ Thu, 05 Apr 2018 09:55:44: 33000000 INFO @ Thu, 05 Apr 2018 09:55:44: 33000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 05 Apr 2018 09:55:48: 34000000 INFO @ Thu, 05 Apr 2018 09:55:53: 34000000 INFO @ Thu, 05 Apr 2018 09:55:53: 34000000 INFO @ Thu, 05 Apr 2018 09:55:57: 35000000 INFO @ Thu, 05 Apr 2018 09:56:02: 35000000 INFO @ Thu, 05 Apr 2018 09:56:02: 35000000 INFO @ Thu, 05 Apr 2018 09:56:06: 36000000 BigWig に変換しました。 INFO @ Thu, 05 Apr 2018 09:56:11: 36000000 INFO @ Thu, 05 Apr 2018 09:56:11: 36000000 INFO @ Thu, 05 Apr 2018 09:56:12: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:56:12: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:56:12: #1 total tags in treatment: 18050912 INFO @ Thu, 05 Apr 2018 09:56:12: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:56:12: #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 09:56:12: #1 tags after filtering in treatment: 11491058 INFO @ Thu, 05 Apr 2018 09:56:12: #1 Redundant rate of treatment: 0.36 INFO @ Thu, 05 Apr 2018 09:56:12: #1 finished! INFO @ Thu, 05 Apr 2018 09:56:12: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:56:12: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:56:13: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:56:13: 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 09:56:13: Process for pairing-model is terminated! cat: SRX3671146.05_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 `SRX3671146.05_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 `SRX3671146.05_*.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 `SRX3671146.05_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 09:56:16: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:56:16: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:56:16: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:56:16: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:56:16: #1 total tags in treatment: 18050912 INFO @ Thu, 05 Apr 2018 09:56:16: #1 total tags in treatment: 18050912 INFO @ Thu, 05 Apr 2018 09:56:16: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:56:16: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:56:16: #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 09:56:16: #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 09:56:16: #1 tags after filtering in treatment: 11491058 INFO @ Thu, 05 Apr 2018 09:56:16: #1 tags after filtering in treatment: 11491058 INFO @ Thu, 05 Apr 2018 09:56:16: #1 Redundant rate of treatment: 0.36 INFO @ Thu, 05 Apr 2018 09:56:16: #1 Redundant rate of treatment: 0.36 INFO @ Thu, 05 Apr 2018 09:56:16: #1 finished! INFO @ Thu, 05 Apr 2018 09:56:16: #1 finished! INFO @ Thu, 05 Apr 2018 09:56:16: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:56:16: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:56:16: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:56:16: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:56:17: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:56:17: 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 09:56:17: Process for pairing-model is terminated! INFO @ Thu, 05 Apr 2018 09:56:17: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:56:17: 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 09:56:17: Process for pairing-model is terminated! cat: SRX3671146.10_peaks.narrowPeak: そのようなファイルやディレクトリはありません cat: SRX3671146.20_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 `SRX3671146.10_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 `SRX3671146.10_*.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 `SRX3671146.10_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 `SRX3671146.20_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 `SRX3671146.20_*.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 `SRX3671146.20_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