Job ID = 11193125 sra ファイルのダウンロード中... Completed: 446369K bytes transferred in 14 seconds (252609K 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... Read 13898741 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4337717/SRR7467886.sra Written 13898741 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4337717/SRR7467886.sra 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: 00:08:46 13898741 reads; of these: 13898741 (100.00%) were paired; of these: 6030795 (43.39%) aligned concordantly 0 times 5977994 (43.01%) aligned concordantly exactly 1 time 1889952 (13.60%) aligned concordantly >1 times ---- 6030795 pairs aligned concordantly 0 times; of these: 619825 (10.28%) aligned discordantly 1 time ---- 5410970 pairs aligned 0 times concordantly or discordantly; of these: 10821940 mates make up the pairs; of these: 8611546 (79.57%) aligned 0 times 1581515 (14.61%) aligned exactly 1 time 628879 (5.81%) aligned >1 times 69.02% overall alignment rate Time searching: 00:08:46 Overall time: 00:08:46 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 8 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] 1509837 / 8393569 = 0.1799 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 @ Sat, 15 Sep 2018 11:13:10: # Command line: callpeak -t SRX4337717.bam -f BAM -g 12100000 -n SRX4337717.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4337717.10 # format = BAM # ChIP-seq file = ['SRX4337717.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 @ Sat, 15 Sep 2018 11:13:10: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:13:10: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:13:10: # Command line: callpeak -t SRX4337717.bam -f BAM -g 12100000 -n SRX4337717.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4337717.20 # format = BAM # ChIP-seq file = ['SRX4337717.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 @ Sat, 15 Sep 2018 11:13:10: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:13:10: # Command line: callpeak -t SRX4337717.bam -f BAM -g 12100000 -n SRX4337717.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4337717.05 # format = BAM # ChIP-seq file = ['SRX4337717.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 @ Sat, 15 Sep 2018 11:13:10: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:13:10: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:13:10: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:13:17: 1000000 INFO @ Sat, 15 Sep 2018 11:13:18: 1000000 INFO @ Sat, 15 Sep 2018 11:13:18: 1000000 INFO @ Sat, 15 Sep 2018 11:13:23: 2000000 INFO @ Sat, 15 Sep 2018 11:13:25: 2000000 INFO @ Sat, 15 Sep 2018 11:13:25: 2000000 INFO @ Sat, 15 Sep 2018 11:13:30: 3000000 INFO @ Sat, 15 Sep 2018 11:13:31: 3000000 INFO @ Sat, 15 Sep 2018 11:13:31: 3000000 INFO @ Sat, 15 Sep 2018 11:13:36: 4000000 INFO @ Sat, 15 Sep 2018 11:13:37: 4000000 INFO @ Sat, 15 Sep 2018 11:13:37: 4000000 INFO @ Sat, 15 Sep 2018 11:13:42: 5000000 INFO @ Sat, 15 Sep 2018 11:13:44: 5000000 INFO @ Sat, 15 Sep 2018 11:13:44: 5000000 INFO @ Sat, 15 Sep 2018 11:13:48: 6000000 INFO @ Sat, 15 Sep 2018 11:13:51: 6000000 INFO @ Sat, 15 Sep 2018 11:13:51: 6000000 INFO @ Sat, 15 Sep 2018 11:13:54: 7000000 INFO @ Sat, 15 Sep 2018 11:13:58: 7000000 INFO @ Sat, 15 Sep 2018 11:13:58: 7000000 INFO @ Sat, 15 Sep 2018 11:14:00: 8000000 INFO @ Sat, 15 Sep 2018 11:14:06: 9000000 INFO @ Sat, 15 Sep 2018 11:14:06: 8000000 INFO @ Sat, 15 Sep 2018 11:14:06: 8000000 INFO @ Sat, 15 Sep 2018 11:14:11: 10000000 INFO @ Sat, 15 Sep 2018 11:14:13: 9000000 INFO @ Sat, 15 Sep 2018 11:14:13: 9000000 INFO @ Sat, 15 Sep 2018 11:14:17: 11000000 INFO @ Sat, 15 Sep 2018 11:14:20: 10000000 INFO @ Sat, 15 Sep 2018 11:14:20: 10000000 INFO @ Sat, 15 Sep 2018 11:14:23: 12000000 INFO @ Sat, 15 Sep 2018 11:14:28: 11000000 INFO @ Sat, 15 Sep 2018 11:14:28: 11000000 INFO @ Sat, 15 Sep 2018 11:14:30: 13000000 INFO @ Sat, 15 Sep 2018 11:14:36: 12000000 INFO @ Sat, 15 Sep 2018 11:14:36: 12000000 INFO @ Sat, 15 Sep 2018 11:14:37: 14000000 INFO @ Sat, 15 Sep 2018 11:14:44: 13000000 INFO @ Sat, 15 Sep 2018 11:14:44: 13000000 INFO @ Sat, 15 Sep 2018 11:14:44: 15000000 INFO @ Sat, 15 Sep 2018 11:14:51: 16000000 INFO @ Sat, 15 Sep 2018 11:14:52: 14000000 INFO @ Sat, 15 Sep 2018 11:14:52: 14000000 INFO @ Sat, 15 Sep 2018 11:14:52: #1 tag size is determined as 41 bps INFO @ Sat, 15 Sep 2018 11:14:52: #1 tag size = 41 INFO @ Sat, 15 Sep 2018 11:14:52: #1 total tags in treatment: 6513216 INFO @ Sat, 15 Sep 2018 11:14:52: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:14:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 11:14:52: #1 tags after filtering in treatment: 4521277 INFO @ Sat, 15 Sep 2018 11:14:52: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 15 Sep 2018 11:14:52: #1 finished! INFO @ Sat, 15 Sep 2018 11:14:52: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:14:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:14:52: #2 number of paired peaks: 28 WARNING @ Sat, 15 Sep 2018 11:14:52: Too few paired peaks (28) 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 @ Sat, 15 Sep 2018 11:14:52: Process for pairing-model is terminated! cat: SRX4337717.10_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 `SRX4337717.10_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 `SRX4337717.10_*.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 `SRX4337717.10_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 @ Sat, 15 Sep 2018 11:15:00: 15000000 INFO @ Sat, 15 Sep 2018 11:15:00: 15000000 INFO @ Sat, 15 Sep 2018 11:15:07: 16000000 INFO @ Sat, 15 Sep 2018 11:15:07: 16000000 INFO @ Sat, 15 Sep 2018 11:15:07: #1 tag size is determined as 41 bps INFO @ Sat, 15 Sep 2018 11:15:07: #1 tag size = 41 INFO @ Sat, 15 Sep 2018 11:15:07: #1 total tags in treatment: 6513216 INFO @ Sat, 15 Sep 2018 11:15:07: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:15:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 11:15:07: #1 tag size is determined as 41 bps INFO @ Sat, 15 Sep 2018 11:15:07: #1 tag size = 41 INFO @ Sat, 15 Sep 2018 11:15:07: #1 total tags in treatment: 6513216 INFO @ Sat, 15 Sep 2018 11:15:07: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:15:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 11:15:08: #1 tags after filtering in treatment: 4521277 INFO @ Sat, 15 Sep 2018 11:15:08: #1 tags after filtering in treatment: 4521277 INFO @ Sat, 15 Sep 2018 11:15:08: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 15 Sep 2018 11:15:08: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 15 Sep 2018 11:15:08: #1 finished! INFO @ Sat, 15 Sep 2018 11:15:08: #1 finished! INFO @ Sat, 15 Sep 2018 11:15:08: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:15:08: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:15:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:15:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:15:08: #2 number of paired peaks: 28 WARNING @ Sat, 15 Sep 2018 11:15:08: Too few paired peaks (28) 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 @ Sat, 15 Sep 2018 11:15:08: Process for pairing-model is terminated! INFO @ Sat, 15 Sep 2018 11:15:08: #2 number of paired peaks: 28 WARNING @ Sat, 15 Sep 2018 11:15:08: Too few paired peaks (28) 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 @ Sat, 15 Sep 2018 11:15:08: Process for pairing-model is terminated! cat: SRX4337717.20_peaks.narrowPeak: そのようなファイルやディレクトリはありません cat: SRX4337717.05_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 `SRX4337717.20_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 `SRX4337717.20_*.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 `SRX4337717.20_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 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4337717.05_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 `SRX4337717.05_*.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 `SRX4337717.05_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。