Job ID = 11193126 sra ファイルのダウンロード中... Completed: 562965K bytes transferred in 14 seconds (315559K 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 17497156 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4337718/SRR7467885.sra Written 17497156 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4337718/SRR7467885.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 17497156 reads; of these: 17497156 (100.00%) were paired; of these: 9304270 (53.18%) aligned concordantly 0 times 6368607 (36.40%) aligned concordantly exactly 1 time 1824279 (10.43%) aligned concordantly >1 times ---- 9304270 pairs aligned concordantly 0 times; of these: 803133 (8.63%) aligned discordantly 1 time ---- 8501137 pairs aligned 0 times concordantly or discordantly; of these: 17002274 mates make up the pairs; of these: 14087548 (82.86%) aligned 0 times 2120362 (12.47%) aligned exactly 1 time 794364 (4.67%) aligned >1 times 59.74% 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] 2779115 / 8908619 = 0.3120 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 11:13:51: # Command line: callpeak -t SRX4337718.bam -f BAM -g 12100000 -n SRX4337718.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4337718.05 # format = BAM # ChIP-seq file = ['SRX4337718.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 11:13:51: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:13:51: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:13:51: # Command line: callpeak -t SRX4337718.bam -f BAM -g 12100000 -n SRX4337718.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4337718.10 # format = BAM # ChIP-seq file = ['SRX4337718.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 11:13:51: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:13:51: # Command line: callpeak -t SRX4337718.bam -f BAM -g 12100000 -n SRX4337718.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4337718.20 # format = BAM # ChIP-seq file = ['SRX4337718.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 11:13:51: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:13:51: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:13:51: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:13:57: 1000000 INFO @ Sat, 15 Sep 2018 11:13:57: 1000000 INFO @ Sat, 15 Sep 2018 11:13:57: 1000000 INFO @ Sat, 15 Sep 2018 11:14:02: 2000000 INFO @ Sat, 15 Sep 2018 11:14:02: 2000000 INFO @ Sat, 15 Sep 2018 11:14:02: 2000000 INFO @ Sat, 15 Sep 2018 11:14:07: 3000000 INFO @ Sat, 15 Sep 2018 11:14:08: 3000000 INFO @ Sat, 15 Sep 2018 11:14:08: 3000000 INFO @ Sat, 15 Sep 2018 11:14:12: 4000000 INFO @ Sat, 15 Sep 2018 11:14:12: 4000000 INFO @ Sat, 15 Sep 2018 11:14:13: 4000000 INFO @ Sat, 15 Sep 2018 11:14:16: 5000000 INFO @ Sat, 15 Sep 2018 11:14:17: 5000000 INFO @ Sat, 15 Sep 2018 11:14:18: 5000000 INFO @ Sat, 15 Sep 2018 11:14:22: 6000000 INFO @ Sat, 15 Sep 2018 11:14:23: 6000000 INFO @ Sat, 15 Sep 2018 11:14:24: 6000000 INFO @ Sat, 15 Sep 2018 11:14:27: 7000000 INFO @ Sat, 15 Sep 2018 11:14:28: 7000000 INFO @ Sat, 15 Sep 2018 11:14:30: 7000000 INFO @ Sat, 15 Sep 2018 11:14:32: 8000000 INFO @ Sat, 15 Sep 2018 11:14:33: 8000000 INFO @ Sat, 15 Sep 2018 11:14:35: 8000000 INFO @ Sat, 15 Sep 2018 11:14:38: 9000000 INFO @ Sat, 15 Sep 2018 11:14:38: 9000000 INFO @ Sat, 15 Sep 2018 11:14:41: 9000000 INFO @ Sat, 15 Sep 2018 11:14:43: 10000000 INFO @ Sat, 15 Sep 2018 11:14:43: 10000000 INFO @ Sat, 15 Sep 2018 11:14:47: 10000000 INFO @ Sat, 15 Sep 2018 11:14:48: 11000000 INFO @ Sat, 15 Sep 2018 11:14:49: 11000000 INFO @ Sat, 15 Sep 2018 11:14:52: 11000000 INFO @ Sat, 15 Sep 2018 11:14:54: 12000000 INFO @ Sat, 15 Sep 2018 11:14:54: 12000000 INFO @ Sat, 15 Sep 2018 11:14:58: 12000000 INFO @ Sat, 15 Sep 2018 11:14:59: 13000000 INFO @ Sat, 15 Sep 2018 11:14:59: 13000000 INFO @ Sat, 15 Sep 2018 11:15:04: 13000000 INFO @ Sat, 15 Sep 2018 11:15:04: 14000000 INFO @ Sat, 15 Sep 2018 11:15:04: 14000000 INFO @ Sat, 15 Sep 2018 11:15:09: 14000000 INFO @ Sat, 15 Sep 2018 11:15:10: 15000000 INFO @ Sat, 15 Sep 2018 11:15:10: 15000000 INFO @ Sat, 15 Sep 2018 11:15:11: #1 tag size is determined as 44 bps INFO @ Sat, 15 Sep 2018 11:15:11: #1 tag size = 44 INFO @ Sat, 15 Sep 2018 11:15:11: #1 total tags in treatment: 5791349 INFO @ Sat, 15 Sep 2018 11:15:11: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:15:11: #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 11:15:12: #1 tag size is determined as 44 bps INFO @ Sat, 15 Sep 2018 11:15:12: #1 tag size = 44 INFO @ Sat, 15 Sep 2018 11:15:12: #1 total tags in treatment: 5791349 INFO @ Sat, 15 Sep 2018 11:15:12: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:15:12: #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 11:15:12: #1 tags after filtering in treatment: 4086888 INFO @ Sat, 15 Sep 2018 11:15:12: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 15 Sep 2018 11:15:12: #1 finished! INFO @ Sat, 15 Sep 2018 11:15:12: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:15:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:15:12: #1 tags after filtering in treatment: 4086888 INFO @ Sat, 15 Sep 2018 11:15:12: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 15 Sep 2018 11:15:12: #1 finished! INFO @ Sat, 15 Sep 2018 11:15:12: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:15:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:15:12: #2 number of paired peaks: 29 WARNING @ Sat, 15 Sep 2018 11:15:12: Too few paired peaks (29) 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 11:15:12: Process for pairing-model is terminated! cat: SRX4337718.05_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 `SRX4337718.05_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 `SRX4337718.05_*.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 `SRX4337718.05_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 @ Sat, 15 Sep 2018 11:15:12: #2 number of paired peaks: 29 WARNING @ Sat, 15 Sep 2018 11:15:12: Too few paired peaks (29) 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 11:15:12: Process for pairing-model is terminated! cat: SRX4337718.10_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 `SRX4337718.10_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 `SRX4337718.10_*.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 `SRX4337718.10_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 11:15:15: 15000000 INFO @ Sat, 15 Sep 2018 11:15:17: #1 tag size is determined as 44 bps INFO @ Sat, 15 Sep 2018 11:15:17: #1 tag size = 44 INFO @ Sat, 15 Sep 2018 11:15:17: #1 total tags in treatment: 5791349 INFO @ Sat, 15 Sep 2018 11:15:17: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:15:17: #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 11:15:17: #1 tags after filtering in treatment: 4086888 INFO @ Sat, 15 Sep 2018 11:15:17: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 15 Sep 2018 11:15:17: #1 finished! INFO @ Sat, 15 Sep 2018 11:15:17: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:15:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:15:17: #2 number of paired peaks: 29 WARNING @ Sat, 15 Sep 2018 11:15:17: Too few paired peaks (29) 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 11:15:17: Process for pairing-model is terminated! cat: SRX4337718.20_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 `SRX4337718.20_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 `SRX4337718.20_*.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 `SRX4337718.20_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。