Job ID = 11244951 sra ファイルのダウンロード中... Completed: 383008K bytes transferred in 7 seconds (419808K 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 11753012 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554681/SRR7696354.sra Written 11753012 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554681/SRR7696354.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: 00:07:11 11753012 reads; of these: 11753012 (100.00%) were paired; of these: 2065747 (17.58%) aligned concordantly 0 times 6837236 (58.17%) aligned concordantly exactly 1 time 2850029 (24.25%) aligned concordantly >1 times ---- 2065747 pairs aligned concordantly 0 times; of these: 220225 (10.66%) aligned discordantly 1 time ---- 1845522 pairs aligned 0 times concordantly or discordantly; of these: 3691044 mates make up the pairs; of these: 3185134 (86.29%) aligned 0 times 220436 (5.97%) aligned exactly 1 time 285474 (7.73%) aligned >1 times 86.45% overall alignment rate Time searching: 00:07:11 Overall time: 00:07:11 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] 1119901 / 9859125 = 0.1136 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 @ Tue, 09 Oct 2018 23:08:46: # Command line: callpeak -t SRX4554681.bam -f BAM -g 12100000 -n SRX4554681.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4554681.20 # format = BAM # ChIP-seq file = ['SRX4554681.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 @ Tue, 09 Oct 2018 23:08:46: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:08:46: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:08:46: # Command line: callpeak -t SRX4554681.bam -f BAM -g 12100000 -n SRX4554681.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4554681.05 # format = BAM # ChIP-seq file = ['SRX4554681.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 @ Tue, 09 Oct 2018 23:08:46: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:08:46: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:08:46: # Command line: callpeak -t SRX4554681.bam -f BAM -g 12100000 -n SRX4554681.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4554681.10 # format = BAM # ChIP-seq file = ['SRX4554681.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 @ Tue, 09 Oct 2018 23:08:46: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:08:46: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:08:52: 1000000 INFO @ Tue, 09 Oct 2018 23:08:52: 1000000 INFO @ Tue, 09 Oct 2018 23:08:52: 1000000 INFO @ Tue, 09 Oct 2018 23:08:57: 2000000 INFO @ Tue, 09 Oct 2018 23:08:59: 2000000 INFO @ Tue, 09 Oct 2018 23:08:59: 2000000 INFO @ Tue, 09 Oct 2018 23:09:03: 3000000 INFO @ Tue, 09 Oct 2018 23:09:05: 3000000 INFO @ Tue, 09 Oct 2018 23:09:05: 3000000 INFO @ Tue, 09 Oct 2018 23:09:08: 4000000 INFO @ Tue, 09 Oct 2018 23:09:11: 4000000 INFO @ Tue, 09 Oct 2018 23:09:11: 4000000 INFO @ Tue, 09 Oct 2018 23:09:14: 5000000 INFO @ Tue, 09 Oct 2018 23:09:17: 5000000 INFO @ Tue, 09 Oct 2018 23:09:17: 5000000 INFO @ Tue, 09 Oct 2018 23:09:19: 6000000 INFO @ Tue, 09 Oct 2018 23:09:23: 6000000 INFO @ Tue, 09 Oct 2018 23:09:23: 6000000 INFO @ Tue, 09 Oct 2018 23:09:25: 7000000 INFO @ Tue, 09 Oct 2018 23:09:29: 7000000 INFO @ Tue, 09 Oct 2018 23:09:29: 7000000 INFO @ Tue, 09 Oct 2018 23:09:30: 8000000 INFO @ Tue, 09 Oct 2018 23:09:35: 8000000 INFO @ Tue, 09 Oct 2018 23:09:35: 8000000 INFO @ Tue, 09 Oct 2018 23:09:36: 9000000 INFO @ Tue, 09 Oct 2018 23:09:41: 9000000 INFO @ Tue, 09 Oct 2018 23:09:41: 10000000 INFO @ Tue, 09 Oct 2018 23:09:41: 9000000 INFO @ Tue, 09 Oct 2018 23:09:47: 11000000 INFO @ Tue, 09 Oct 2018 23:09:48: 10000000 INFO @ Tue, 09 Oct 2018 23:09:48: 10000000 INFO @ Tue, 09 Oct 2018 23:09:52: 12000000 INFO @ Tue, 09 Oct 2018 23:09:54: 11000000 INFO @ Tue, 09 Oct 2018 23:09:54: 11000000 INFO @ Tue, 09 Oct 2018 23:09:58: 13000000 INFO @ Tue, 09 Oct 2018 23:10:00: 12000000 INFO @ Tue, 09 Oct 2018 23:10:00: 12000000 INFO @ Tue, 09 Oct 2018 23:10:03: 14000000 INFO @ Tue, 09 Oct 2018 23:10:06: 13000000 INFO @ Tue, 09 Oct 2018 23:10:06: 13000000 INFO @ Tue, 09 Oct 2018 23:10:09: 15000000 INFO @ Tue, 09 Oct 2018 23:10:12: 14000000 INFO @ Tue, 09 Oct 2018 23:10:12: 14000000 INFO @ Tue, 09 Oct 2018 23:10:14: 16000000 INFO @ Tue, 09 Oct 2018 23:10:18: 15000000 INFO @ Tue, 09 Oct 2018 23:10:18: 15000000 INFO @ Tue, 09 Oct 2018 23:10:20: 17000000 INFO @ Tue, 09 Oct 2018 23:10:24: 16000000 INFO @ Tue, 09 Oct 2018 23:10:24: 16000000 INFO @ Tue, 09 Oct 2018 23:10:25: 18000000 INFO @ Tue, 09 Oct 2018 23:10:26: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:10:26: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:10:26: #1 total tags in treatment: 8577422 INFO @ Tue, 09 Oct 2018 23:10:26: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:10:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:10:26: #1 tags after filtering in treatment: 5015985 INFO @ Tue, 09 Oct 2018 23:10:26: #1 Redundant rate of treatment: 0.42 INFO @ Tue, 09 Oct 2018 23:10:26: #1 finished! INFO @ Tue, 09 Oct 2018 23:10:26: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:10:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:10:26: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:10:26: 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 @ Tue, 09 Oct 2018 23:10:26: Process for pairing-model is terminated! cat: SRX4554681.05_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 `SRX4554681.05_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 `SRX4554681.05_*.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 `SRX4554681.05_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 @ Tue, 09 Oct 2018 23:10:30: 17000000 INFO @ Tue, 09 Oct 2018 23:10:30: 17000000 INFO @ Tue, 09 Oct 2018 23:10:36: 18000000 INFO @ Tue, 09 Oct 2018 23:10:36: 18000000 INFO @ Tue, 09 Oct 2018 23:10:37: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:10:37: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:10:37: #1 total tags in treatment: 8577422 INFO @ Tue, 09 Oct 2018 23:10:37: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:10:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:10:37: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:10:37: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:10:37: #1 total tags in treatment: 8577422 INFO @ Tue, 09 Oct 2018 23:10:37: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:10:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:10:37: #1 tags after filtering in treatment: 5015985 INFO @ Tue, 09 Oct 2018 23:10:37: #1 Redundant rate of treatment: 0.42 INFO @ Tue, 09 Oct 2018 23:10:37: #1 finished! INFO @ Tue, 09 Oct 2018 23:10:37: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:10:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:10:37: #1 tags after filtering in treatment: 5015985 INFO @ Tue, 09 Oct 2018 23:10:37: #1 Redundant rate of treatment: 0.42 INFO @ Tue, 09 Oct 2018 23:10:37: #1 finished! INFO @ Tue, 09 Oct 2018 23:10:37: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:10:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:10:37: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:10:37: 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 @ Tue, 09 Oct 2018 23:10:37: Process for pairing-model is terminated! cat: SRX4554681.10_peaks.narrowPeak: そのようなファイルやディレクトリはありません INFO @ Tue, 09 Oct 2018 23:10:37: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:10:37: 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 @ Tue, 09 Oct 2018 23:10:37: Process for pairing-model is terminated! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4554681.10_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 `SRX4554681.10_*.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 `SRX4554681.10_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 cat: SRX4554681.20_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 `SRX4554681.20_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 `SRX4554681.20_*.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 `SRX4554681.20_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。