Job ID = 11296962 sra ファイルのダウンロード中... Completed: 209868K bytes transferred in 5 seconds (331221K 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 6796402 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3886538/SRR6942576.sra Written 6796402 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3886538/SRR6942576.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: 00:04:27 6796402 reads; of these: 6796402 (100.00%) were paired; of these: 251597 (3.70%) aligned concordantly 0 times 5786025 (85.13%) aligned concordantly exactly 1 time 758780 (11.16%) aligned concordantly >1 times ---- 251597 pairs aligned concordantly 0 times; of these: 95045 (37.78%) aligned discordantly 1 time ---- 156552 pairs aligned 0 times concordantly or discordantly; of these: 313104 mates make up the pairs; of these: 251119 (80.20%) aligned 0 times 37343 (11.93%) aligned exactly 1 time 24642 (7.87%) aligned >1 times 98.15% overall alignment rate Time searching: 00:04:27 Overall time: 00:04:27 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_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] 319904 / 6638725 = 0.0482 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 @ Mon, 05 Nov 2018 18:09:07: # Command line: callpeak -t SRX3886538.bam -f BAM -g 12100000 -n SRX3886538.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3886538.05 # format = BAM # ChIP-seq file = ['SRX3886538.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 @ Mon, 05 Nov 2018 18:09:07: #1 read tag files... INFO @ Mon, 05 Nov 2018 18:09:07: #1 read treatment tags... INFO @ Mon, 05 Nov 2018 18:09:07: # Command line: callpeak -t SRX3886538.bam -f BAM -g 12100000 -n SRX3886538.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3886538.10 # format = BAM # ChIP-seq file = ['SRX3886538.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 @ Mon, 05 Nov 2018 18:09:07: #1 read tag files... INFO @ Mon, 05 Nov 2018 18:09:07: #1 read treatment tags... INFO @ Mon, 05 Nov 2018 18:09:07: # Command line: callpeak -t SRX3886538.bam -f BAM -g 12100000 -n SRX3886538.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3886538.20 # format = BAM # ChIP-seq file = ['SRX3886538.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 @ Mon, 05 Nov 2018 18:09:07: #1 read tag files... INFO @ Mon, 05 Nov 2018 18:09:07: #1 read treatment tags... INFO @ Mon, 05 Nov 2018 18:09:14: 1000000 INFO @ Mon, 05 Nov 2018 18:09:14: 1000000 INFO @ Mon, 05 Nov 2018 18:09:14: 1000000 INFO @ Mon, 05 Nov 2018 18:09:21: 2000000 INFO @ Mon, 05 Nov 2018 18:09:21: 2000000 INFO @ Mon, 05 Nov 2018 18:09:21: 2000000 INFO @ Mon, 05 Nov 2018 18:09:28: 3000000 INFO @ Mon, 05 Nov 2018 18:09:28: 3000000 INFO @ Mon, 05 Nov 2018 18:09:29: 3000000 INFO @ Mon, 05 Nov 2018 18:09:35: 4000000 INFO @ Mon, 05 Nov 2018 18:09:35: 4000000 INFO @ Mon, 05 Nov 2018 18:09:36: 4000000 INFO @ Mon, 05 Nov 2018 18:09:42: 5000000 INFO @ Mon, 05 Nov 2018 18:09:42: 5000000 INFO @ Mon, 05 Nov 2018 18:09:43: 5000000 INFO @ Mon, 05 Nov 2018 18:09:49: 6000000 INFO @ Mon, 05 Nov 2018 18:09:49: 6000000 INFO @ Mon, 05 Nov 2018 18:09:50: 6000000 INFO @ Mon, 05 Nov 2018 18:09:56: 7000000 INFO @ Mon, 05 Nov 2018 18:09:56: 7000000 INFO @ Mon, 05 Nov 2018 18:09:57: 7000000 INFO @ Mon, 05 Nov 2018 18:10:03: 8000000 INFO @ Mon, 05 Nov 2018 18:10:03: 8000000 INFO @ Mon, 05 Nov 2018 18:10:04: 8000000 INFO @ Mon, 05 Nov 2018 18:10:10: 9000000 INFO @ Mon, 05 Nov 2018 18:10:10: 9000000 INFO @ Mon, 05 Nov 2018 18:10:11: 9000000 INFO @ Mon, 05 Nov 2018 18:10:17: 10000000 INFO @ Mon, 05 Nov 2018 18:10:17: 10000000 INFO @ Mon, 05 Nov 2018 18:10:18: 10000000 INFO @ Mon, 05 Nov 2018 18:10:24: 11000000 INFO @ Mon, 05 Nov 2018 18:10:24: 11000000 INFO @ Mon, 05 Nov 2018 18:10:25: 11000000 INFO @ Mon, 05 Nov 2018 18:10:31: 12000000 INFO @ Mon, 05 Nov 2018 18:10:31: 12000000 INFO @ Mon, 05 Nov 2018 18:10:32: 12000000 INFO @ Mon, 05 Nov 2018 18:10:35: #1 tag size is determined as 41 bps INFO @ Mon, 05 Nov 2018 18:10:35: #1 tag size = 41 INFO @ Mon, 05 Nov 2018 18:10:35: #1 total tags in treatment: 6226422 INFO @ Mon, 05 Nov 2018 18:10:35: #1 user defined the maximum tags... INFO @ Mon, 05 Nov 2018 18:10:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Nov 2018 18:10:35: #1 tags after filtering in treatment: 4680045 INFO @ Mon, 05 Nov 2018 18:10:35: #1 Redundant rate of treatment: 0.25 INFO @ Mon, 05 Nov 2018 18:10:35: #1 finished! INFO @ Mon, 05 Nov 2018 18:10:35: #2 Build Peak Model... INFO @ Mon, 05 Nov 2018 18:10:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 05 Nov 2018 18:10:36: #1 tag size is determined as 41 bps INFO @ Mon, 05 Nov 2018 18:10:36: #1 tag size = 41 INFO @ Mon, 05 Nov 2018 18:10:36: #1 total tags in treatment: 6226422 INFO @ Mon, 05 Nov 2018 18:10:36: #1 user defined the maximum tags... INFO @ Mon, 05 Nov 2018 18:10:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Nov 2018 18:10:36: #1 tags after filtering in treatment: 4680045 INFO @ Mon, 05 Nov 2018 18:10:36: #1 Redundant rate of treatment: 0.25 INFO @ Mon, 05 Nov 2018 18:10:36: #1 finished! INFO @ Mon, 05 Nov 2018 18:10:36: #2 Build Peak Model... INFO @ Mon, 05 Nov 2018 18:10:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 05 Nov 2018 18:10:36: #2 number of paired peaks: 28 WARNING @ Mon, 05 Nov 2018 18:10:36: 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 @ Mon, 05 Nov 2018 18:10:36: Process for pairing-model is terminated! cat: SRX3886538.20_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 `SRX3886538.20_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 `SRX3886538.20_*.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 `SRX3886538.20_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 INFO @ Mon, 05 Nov 2018 18:10:36: #2 number of paired peaks: 28 WARNING @ Mon, 05 Nov 2018 18:10:36: 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 @ Mon, 05 Nov 2018 18:10:36: Process for pairing-model is terminated! cat: SRX3886538.10_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 `SRX3886538.10_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 `SRX3886538.10_*.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 `SRX3886538.10_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 @ Mon, 05 Nov 2018 18:10:37: #1 tag size is determined as 41 bps INFO @ Mon, 05 Nov 2018 18:10:37: #1 tag size = 41 INFO @ Mon, 05 Nov 2018 18:10:37: #1 total tags in treatment: 6226422 INFO @ Mon, 05 Nov 2018 18:10:37: #1 user defined the maximum tags... INFO @ Mon, 05 Nov 2018 18:10:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Nov 2018 18:10:37: #1 tags after filtering in treatment: 4680045 INFO @ Mon, 05 Nov 2018 18:10:37: #1 Redundant rate of treatment: 0.25 INFO @ Mon, 05 Nov 2018 18:10:37: #1 finished! INFO @ Mon, 05 Nov 2018 18:10:37: #2 Build Peak Model... INFO @ Mon, 05 Nov 2018 18:10:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 05 Nov 2018 18:10:37: #2 number of paired peaks: 28 WARNING @ Mon, 05 Nov 2018 18:10:37: 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 @ Mon, 05 Nov 2018 18:10:37: Process for pairing-model is terminated! cat: SRX3886538.05_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 `SRX3886538.05_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 `SRX3886538.05_*.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 `SRX3886538.05_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。