Job ID = 11245014 sra ファイルのダウンロード中... Completed: 519761K bytes transferred in 18 seconds (236335K 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 9315685 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554727/SRR7696400.sra Written 9315685 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554727/SRR7696400.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: 00:06:51 9315685 reads; of these: 9315685 (100.00%) were paired; of these: 759676 (8.15%) aligned concordantly 0 times 8122463 (87.19%) aligned concordantly exactly 1 time 433546 (4.65%) aligned concordantly >1 times ---- 759676 pairs aligned concordantly 0 times; of these: 237412 (31.25%) aligned discordantly 1 time ---- 522264 pairs aligned 0 times concordantly or discordantly; of these: 1044528 mates make up the pairs; of these: 869400 (83.23%) aligned 0 times 135760 (13.00%) aligned exactly 1 time 39368 (3.77%) aligned >1 times 95.33% overall alignment rate Time searching: 00:06:51 Overall time: 00:06:51 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] 342787 / 8741758 = 0.0392 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 23:20:00: # Command line: callpeak -t SRX4554727.bam -f BAM -g 12100000 -n SRX4554727.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4554727.10 # format = BAM # ChIP-seq file = ['SRX4554727.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 23:20:00: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:20:00: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:20:00: # Command line: callpeak -t SRX4554727.bam -f BAM -g 12100000 -n SRX4554727.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4554727.05 # format = BAM # ChIP-seq file = ['SRX4554727.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 23:20:00: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:20:00: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:20:00: # Command line: callpeak -t SRX4554727.bam -f BAM -g 12100000 -n SRX4554727.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4554727.20 # format = BAM # ChIP-seq file = ['SRX4554727.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 23:20:00: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:20:00: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:20:08: 1000000 INFO @ Tue, 09 Oct 2018 23:20:08: 1000000 INFO @ Tue, 09 Oct 2018 23:20:09: 1000000 INFO @ Tue, 09 Oct 2018 23:20:16: 2000000 INFO @ Tue, 09 Oct 2018 23:20:16: 2000000 INFO @ Tue, 09 Oct 2018 23:20:16: 2000000 INFO @ Tue, 09 Oct 2018 23:20:24: 3000000 INFO @ Tue, 09 Oct 2018 23:20:24: 3000000 INFO @ Tue, 09 Oct 2018 23:20:24: 3000000 INFO @ Tue, 09 Oct 2018 23:20:32: 4000000 INFO @ Tue, 09 Oct 2018 23:20:32: 4000000 INFO @ Tue, 09 Oct 2018 23:20:32: 4000000 INFO @ Tue, 09 Oct 2018 23:20:39: 5000000 INFO @ Tue, 09 Oct 2018 23:20:40: 5000000 INFO @ Tue, 09 Oct 2018 23:20:40: 5000000 INFO @ Tue, 09 Oct 2018 23:20:47: 6000000 INFO @ Tue, 09 Oct 2018 23:20:48: 6000000 INFO @ Tue, 09 Oct 2018 23:20:48: 6000000 INFO @ Tue, 09 Oct 2018 23:20:55: 7000000 INFO @ Tue, 09 Oct 2018 23:20:56: 7000000 INFO @ Tue, 09 Oct 2018 23:20:56: 7000000 INFO @ Tue, 09 Oct 2018 23:21:02: 8000000 INFO @ Tue, 09 Oct 2018 23:21:04: 8000000 INFO @ Tue, 09 Oct 2018 23:21:04: 8000000 INFO @ Tue, 09 Oct 2018 23:21:10: 9000000 INFO @ Tue, 09 Oct 2018 23:21:11: 9000000 INFO @ Tue, 09 Oct 2018 23:21:11: 9000000 INFO @ Tue, 09 Oct 2018 23:21:18: 10000000 INFO @ Tue, 09 Oct 2018 23:21:19: 10000000 INFO @ Tue, 09 Oct 2018 23:21:19: 10000000 INFO @ Tue, 09 Oct 2018 23:21:26: 11000000 INFO @ Tue, 09 Oct 2018 23:21:26: 11000000 INFO @ Tue, 09 Oct 2018 23:21:26: 11000000 INFO @ Tue, 09 Oct 2018 23:21:34: 12000000 INFO @ Tue, 09 Oct 2018 23:21:34: 12000000 INFO @ Tue, 09 Oct 2018 23:21:34: 12000000 INFO @ Tue, 09 Oct 2018 23:21:42: 13000000 INFO @ Tue, 09 Oct 2018 23:21:42: 13000000 INFO @ Tue, 09 Oct 2018 23:21:42: 13000000 INFO @ Tue, 09 Oct 2018 23:21:49: 14000000 INFO @ Tue, 09 Oct 2018 23:21:49: 14000000 INFO @ Tue, 09 Oct 2018 23:21:50: 14000000 INFO @ Tue, 09 Oct 2018 23:21:57: 15000000 INFO @ Tue, 09 Oct 2018 23:21:57: 15000000 INFO @ Tue, 09 Oct 2018 23:21:58: 15000000 INFO @ Tue, 09 Oct 2018 23:22:05: 16000000 INFO @ Tue, 09 Oct 2018 23:22:05: 16000000 INFO @ Tue, 09 Oct 2018 23:22:06: 16000000 INFO @ Tue, 09 Oct 2018 23:22:13: 17000000 INFO @ Tue, 09 Oct 2018 23:22:13: 17000000 INFO @ Tue, 09 Oct 2018 23:22:13: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:22:13: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:22:13: #1 total tags in treatment: 8213914 INFO @ Tue, 09 Oct 2018 23:22:13: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:22:13: #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 23:22:13: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:22:13: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:22:13: #1 total tags in treatment: 8213914 INFO @ Tue, 09 Oct 2018 23:22:13: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:22:13: #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 23:22:13: #1 tags after filtering in treatment: 4958261 INFO @ Tue, 09 Oct 2018 23:22:13: #1 Redundant rate of treatment: 0.40 INFO @ Tue, 09 Oct 2018 23:22:13: #1 finished! INFO @ Tue, 09 Oct 2018 23:22:13: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:22:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:22:13: #1 tags after filtering in treatment: 4958261 INFO @ Tue, 09 Oct 2018 23:22:13: #1 Redundant rate of treatment: 0.40 INFO @ Tue, 09 Oct 2018 23:22:13: #1 finished! INFO @ Tue, 09 Oct 2018 23:22:13: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:22:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:22:14: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:22:14: 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 23:22:14: Process for pairing-model is terminated! cat: SRX4554727.20_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 `SRX4554727.20_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 `SRX4554727.20_*.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 `SRX4554727.20_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 @ Tue, 09 Oct 2018 23:22:14: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:22:14: 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 23:22:14: Process for pairing-model is terminated! cat: SRX4554727.10_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 `SRX4554727.10_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 `SRX4554727.10_*.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 `SRX4554727.10_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 @ Tue, 09 Oct 2018 23:22:14: 17000000 INFO @ Tue, 09 Oct 2018 23:22:15: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:22:15: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:22:15: #1 total tags in treatment: 8213914 INFO @ Tue, 09 Oct 2018 23:22:15: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:22:15: #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 23:22:15: #1 tags after filtering in treatment: 4958261 INFO @ Tue, 09 Oct 2018 23:22:15: #1 Redundant rate of treatment: 0.40 INFO @ Tue, 09 Oct 2018 23:22:15: #1 finished! INFO @ Tue, 09 Oct 2018 23:22:15: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:22:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:22:15: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:22:15: 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 23:22:15: Process for pairing-model is terminated! cat: SRX4554727.05_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 `SRX4554727.05_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 `SRX4554727.05_*.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 `SRX4554727.05_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。