Job ID = 11296946 sra ファイルのダウンロード中... Completed: 231599K bytes transferred in 5 seconds (332328K 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: SINGLE fastq に変換中... Read 11079266 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3856367/SRR6908186.sra Written 11079266 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3856367/SRR6908186.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: 00:02:03 11079266 reads; of these: 11079266 (100.00%) were unpaired; of these: 765239 (6.91%) aligned 0 times 7082359 (63.92%) aligned exactly 1 time 3231668 (29.17%) aligned >1 times 93.09% overall alignment rate Time searching: 00:02:03 Overall time: 00:02:03 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_rmdupse_core] 6241250 / 10314027 = 0.6051 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 18:03:47: # Command line: callpeak -t SRX3856367.bam -f BAM -g 12100000 -n SRX3856367.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3856367.10 # format = BAM # ChIP-seq file = ['SRX3856367.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 18:03:47: #1 read tag files... INFO @ Mon, 05 Nov 2018 18:03:47: #1 read treatment tags... INFO @ Mon, 05 Nov 2018 18:03:47: # Command line: callpeak -t SRX3856367.bam -f BAM -g 12100000 -n SRX3856367.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3856367.20 # format = BAM # ChIP-seq file = ['SRX3856367.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 18:03:47: #1 read tag files... INFO @ Mon, 05 Nov 2018 18:03:47: #1 read treatment tags... INFO @ Mon, 05 Nov 2018 18:03:47: # Command line: callpeak -t SRX3856367.bam -f BAM -g 12100000 -n SRX3856367.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3856367.05 # format = BAM # ChIP-seq file = ['SRX3856367.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 18:03:47: #1 read tag files... INFO @ Mon, 05 Nov 2018 18:03:47: #1 read treatment tags... INFO @ Mon, 05 Nov 2018 18:03:54: 1000000 INFO @ Mon, 05 Nov 2018 18:03:55: 1000000 INFO @ Mon, 05 Nov 2018 18:03:55: 1000000 INFO @ Mon, 05 Nov 2018 18:04:01: 2000000 INFO @ Mon, 05 Nov 2018 18:04:02: 2000000 INFO @ Mon, 05 Nov 2018 18:04:02: 2000000 INFO @ Mon, 05 Nov 2018 18:04:09: 3000000 INFO @ Mon, 05 Nov 2018 18:04:10: 3000000 INFO @ Mon, 05 Nov 2018 18:04:10: 3000000 INFO @ Mon, 05 Nov 2018 18:04:16: 4000000 INFO @ Mon, 05 Nov 2018 18:04:16: #1 tag size is determined as 50 bps INFO @ Mon, 05 Nov 2018 18:04:16: #1 tag size = 50 INFO @ Mon, 05 Nov 2018 18:04:16: #1 total tags in treatment: 4072777 INFO @ Mon, 05 Nov 2018 18:04:16: #1 user defined the maximum tags... INFO @ Mon, 05 Nov 2018 18:04:16: #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 18:04:16: #1 tags after filtering in treatment: 4072777 INFO @ Mon, 05 Nov 2018 18:04:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Nov 2018 18:04:16: #1 finished! INFO @ Mon, 05 Nov 2018 18:04:16: #2 Build Peak Model... INFO @ Mon, 05 Nov 2018 18:04:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 05 Nov 2018 18:04:16: #2 number of paired peaks: 29 WARNING @ Mon, 05 Nov 2018 18:04:16: 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 @ Mon, 05 Nov 2018 18:04:16: Process for pairing-model is terminated! cat: SRX3856367.05_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 `SRX3856367.05_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 `SRX3856367.05_*.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 `SRX3856367.05_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 @ Mon, 05 Nov 2018 18:04:18: 4000000 INFO @ Mon, 05 Nov 2018 18:04:18: 4000000 INFO @ Mon, 05 Nov 2018 18:04:18: #1 tag size is determined as 50 bps INFO @ Mon, 05 Nov 2018 18:04:18: #1 tag size = 50 INFO @ Mon, 05 Nov 2018 18:04:18: #1 total tags in treatment: 4072777 INFO @ Mon, 05 Nov 2018 18:04:18: #1 user defined the maximum tags... INFO @ Mon, 05 Nov 2018 18:04:18: #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 18:04:18: #1 tag size is determined as 50 bps INFO @ Mon, 05 Nov 2018 18:04:18: #1 tag size = 50 INFO @ Mon, 05 Nov 2018 18:04:18: #1 total tags in treatment: 4072777 INFO @ Mon, 05 Nov 2018 18:04:18: #1 user defined the maximum tags... INFO @ Mon, 05 Nov 2018 18:04:18: #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 18:04:18: #1 tags after filtering in treatment: 4072777 INFO @ Mon, 05 Nov 2018 18:04:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Nov 2018 18:04:18: #1 finished! INFO @ Mon, 05 Nov 2018 18:04:18: #2 Build Peak Model... INFO @ Mon, 05 Nov 2018 18:04:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 05 Nov 2018 18:04:18: #1 tags after filtering in treatment: 4072777 INFO @ Mon, 05 Nov 2018 18:04:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Nov 2018 18:04:18: #1 finished! INFO @ Mon, 05 Nov 2018 18:04:18: #2 Build Peak Model... INFO @ Mon, 05 Nov 2018 18:04:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 05 Nov 2018 18:04:19: #2 number of paired peaks: 29 WARNING @ Mon, 05 Nov 2018 18:04:19: 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 @ Mon, 05 Nov 2018 18:04:19: Process for pairing-model is terminated! INFO @ Mon, 05 Nov 2018 18:04:19: #2 number of paired peaks: 29 WARNING @ Mon, 05 Nov 2018 18:04:19: 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 @ Mon, 05 Nov 2018 18:04:19: Process for pairing-model is terminated! cat: SRX3856367.10_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) cat: SRX3856367.20_peaks.narrowPeak: そのようなファイルやディレクトリはありません rm: cannot remove `SRX3856367.10_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 `SRX3856367.10_*.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 `SRX3856367.10_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 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3856367.20_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 `SRX3856367.20_*.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 `SRX3856367.20_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。