Job ID = 10536532 sra ファイルのダウンロード中... Completed: 1225777K bytes transferred in 32 seconds (305685K 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... Written 33385008 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3671223/SRR6696975.sra Written 33385008 spots total 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: 00:20:36 33385008 reads; of these: 33385008 (100.00%) were paired; of these: 9877064 (29.59%) aligned concordantly 0 times 20343204 (60.94%) aligned concordantly exactly 1 time 3164740 (9.48%) aligned concordantly >1 times ---- 9877064 pairs aligned concordantly 0 times; of these: 28752 (0.29%) aligned discordantly 1 time ---- 9848312 pairs aligned 0 times concordantly or discordantly; of these: 19696624 mates make up the pairs; of these: 19486650 (98.93%) aligned 0 times 171425 (0.87%) aligned exactly 1 time 38549 (0.20%) aligned >1 times 70.82% overall alignment rate Time searching: 00:20:36 Overall time: 00:20:36 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 20 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] 13090368 / 23512783 = 0.5567 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 @ Thu, 05 Apr 2018 10:35:23: # Command line: callpeak -t SRX3671223.bam -f BAM -g 12100000 -n SRX3671223.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3671223.05 # format = BAM # ChIP-seq file = ['SRX3671223.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 @ Thu, 05 Apr 2018 10:35:23: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:35:23: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:35:23: # Command line: callpeak -t SRX3671223.bam -f BAM -g 12100000 -n SRX3671223.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3671223.10 # format = BAM # ChIP-seq file = ['SRX3671223.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 @ Thu, 05 Apr 2018 10:35:23: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:35:23: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:35:23: # Command line: callpeak -t SRX3671223.bam -f BAM -g 12100000 -n SRX3671223.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3671223.20 # format = BAM # ChIP-seq file = ['SRX3671223.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 @ Thu, 05 Apr 2018 10:35:23: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:35:23: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:35:29: 1000000 INFO @ Thu, 05 Apr 2018 10:35:29: 1000000 INFO @ Thu, 05 Apr 2018 10:35:29: 1000000 INFO @ Thu, 05 Apr 2018 10:35:34: 2000000 INFO @ Thu, 05 Apr 2018 10:35:34: 2000000 INFO @ Thu, 05 Apr 2018 10:35:34: 2000000 INFO @ Thu, 05 Apr 2018 10:35:39: 3000000 INFO @ Thu, 05 Apr 2018 10:35:39: 3000000 INFO @ Thu, 05 Apr 2018 10:35:40: 3000000 INFO @ Thu, 05 Apr 2018 10:35:45: 4000000 INFO @ Thu, 05 Apr 2018 10:35:45: 4000000 INFO @ Thu, 05 Apr 2018 10:35:46: 4000000 INFO @ Thu, 05 Apr 2018 10:35:51: 5000000 INFO @ Thu, 05 Apr 2018 10:35:51: 5000000 INFO @ Thu, 05 Apr 2018 10:35:52: 5000000 INFO @ Thu, 05 Apr 2018 10:35:56: 6000000 INFO @ Thu, 05 Apr 2018 10:35:56: 6000000 INFO @ Thu, 05 Apr 2018 10:35:58: 6000000 INFO @ Thu, 05 Apr 2018 10:36:02: 7000000 INFO @ Thu, 05 Apr 2018 10:36:02: 7000000 INFO @ Thu, 05 Apr 2018 10:36:04: 7000000 INFO @ Thu, 05 Apr 2018 10:36:08: 8000000 INFO @ Thu, 05 Apr 2018 10:36:08: 8000000 INFO @ Thu, 05 Apr 2018 10:36:10: 8000000 INFO @ Thu, 05 Apr 2018 10:36:13: 9000000 INFO @ Thu, 05 Apr 2018 10:36:13: 9000000 INFO @ Thu, 05 Apr 2018 10:36:16: 9000000 INFO @ Thu, 05 Apr 2018 10:36:19: 10000000 INFO @ Thu, 05 Apr 2018 10:36:19: 10000000 INFO @ Thu, 05 Apr 2018 10:36:22: 10000000 INFO @ Thu, 05 Apr 2018 10:36:25: 11000000 INFO @ Thu, 05 Apr 2018 10:36:25: 11000000 INFO @ Thu, 05 Apr 2018 10:36:28: 11000000 INFO @ Thu, 05 Apr 2018 10:36:30: 12000000 INFO @ Thu, 05 Apr 2018 10:36:30: 12000000 INFO @ Thu, 05 Apr 2018 10:36:34: 12000000 INFO @ Thu, 05 Apr 2018 10:36:36: 13000000 INFO @ Thu, 05 Apr 2018 10:36:36: 13000000 INFO @ Thu, 05 Apr 2018 10:36:40: 13000000 INFO @ Thu, 05 Apr 2018 10:36:42: 14000000 INFO @ Thu, 05 Apr 2018 10:36:42: 14000000 INFO @ Thu, 05 Apr 2018 10:36:46: 14000000 INFO @ Thu, 05 Apr 2018 10:36:47: 15000000 INFO @ Thu, 05 Apr 2018 10:36:47: 15000000 INFO @ Thu, 05 Apr 2018 10:36:52: 15000000 INFO @ Thu, 05 Apr 2018 10:36:53: 16000000 INFO @ Thu, 05 Apr 2018 10:36:53: 16000000 INFO @ Thu, 05 Apr 2018 10:36:58: 16000000 INFO @ Thu, 05 Apr 2018 10:36:59: 17000000 INFO @ Thu, 05 Apr 2018 10:36:59: 17000000 INFO @ Thu, 05 Apr 2018 10:37:04: 17000000 INFO @ Thu, 05 Apr 2018 10:37:04: 18000000 INFO @ Thu, 05 Apr 2018 10:37:04: 18000000 INFO @ Thu, 05 Apr 2018 10:37:10: 19000000 INFO @ Thu, 05 Apr 2018 10:37:10: 19000000 INFO @ Thu, 05 Apr 2018 10:37:10: 18000000 INFO @ Thu, 05 Apr 2018 10:37:16: 20000000 INFO @ Thu, 05 Apr 2018 10:37:16: 20000000 INFO @ Thu, 05 Apr 2018 10:37:16: 19000000 INFO @ Thu, 05 Apr 2018 10:37:21: 21000000 INFO @ Thu, 05 Apr 2018 10:37:21: 21000000 INFO @ Thu, 05 Apr 2018 10:37:22: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:37:22: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:37:22: #1 total tags in treatment: 10420245 INFO @ Thu, 05 Apr 2018 10:37:22: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:37:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 10:37:22: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:37:22: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:37:22: #1 total tags in treatment: 10420245 INFO @ Thu, 05 Apr 2018 10:37:22: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:37:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 10:37:22: 20000000 INFO @ Thu, 05 Apr 2018 10:37:22: #1 tags after filtering in treatment: 5213097 INFO @ Thu, 05 Apr 2018 10:37:22: #1 Redundant rate of treatment: 0.50 INFO @ Thu, 05 Apr 2018 10:37:22: #1 finished! INFO @ Thu, 05 Apr 2018 10:37:22: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:37:22: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:37:22: #1 tags after filtering in treatment: 5213097 INFO @ Thu, 05 Apr 2018 10:37:22: #1 Redundant rate of treatment: 0.50 INFO @ Thu, 05 Apr 2018 10:37:22: #1 finished! INFO @ Thu, 05 Apr 2018 10:37:22: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:37:22: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:37:23: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:37:23: 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 @ Thu, 05 Apr 2018 10:37:23: Process for pairing-model is terminated! cat: SRX3671223.10_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 `SRX3671223.10_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 `SRX3671223.10_*.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 `SRX3671223.10_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 @ Thu, 05 Apr 2018 10:37:23: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:37:23: 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 @ Thu, 05 Apr 2018 10:37:23: Process for pairing-model is terminated! cat: SRX3671223.20_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 `SRX3671223.20_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 `SRX3671223.20_*.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 `SRX3671223.20_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 @ Thu, 05 Apr 2018 10:37:27: 21000000 INFO @ Thu, 05 Apr 2018 10:37:28: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:37:28: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:37:28: #1 total tags in treatment: 10420245 INFO @ Thu, 05 Apr 2018 10:37:28: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:37:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 10:37:28: #1 tags after filtering in treatment: 5213097 INFO @ Thu, 05 Apr 2018 10:37:28: #1 Redundant rate of treatment: 0.50 INFO @ Thu, 05 Apr 2018 10:37:28: #1 finished! INFO @ Thu, 05 Apr 2018 10:37:28: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:37:28: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:37:28: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:37:28: 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 @ Thu, 05 Apr 2018 10:37:28: Process for pairing-model is terminated! cat: SRX3671223.05_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): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3671223.05_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 `SRX3671223.05_*.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 `SRX3671223.05_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。