Job ID = 10045043 sra ファイルのダウンロード中... Completed: 431041K bytes transferred in 22 seconds (155262K bits/sec), in 2 files, 3 directories. 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 8850429 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2704971/SRR5413020.sra Written 8850429 spots total Written 9100400 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2704971/SRR5413019.sra Written 9100400 spots total 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: 00:07:28 17950829 reads; of these: 17950829 (100.00%) were paired; of these: 4774693 (26.60%) aligned concordantly 0 times 10481773 (58.39%) aligned concordantly exactly 1 time 2694363 (15.01%) aligned concordantly >1 times ---- 4774693 pairs aligned concordantly 0 times; of these: 441027 (9.24%) aligned discordantly 1 time ---- 4333666 pairs aligned 0 times concordantly or discordantly; of these: 8667332 mates make up the pairs; of these: 7361252 (84.93%) aligned 0 times 877520 (10.12%) aligned exactly 1 time 428560 (4.94%) aligned >1 times 79.50% overall alignment rate Time searching: 00:07:28 Overall time: 00:07:28 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] 5366099 / 13296142 = 0.4036 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, 02 Oct 2017 14:51:33: # Command line: callpeak -t SRX2704971.bam -f BAM -g 12100000 -n SRX2704971.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2704971.05 # format = BAM # ChIP-seq file = ['SRX2704971.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, 02 Oct 2017 14:51:33: #1 read tag files... INFO @ Mon, 02 Oct 2017 14:51:33: #1 read treatment tags... INFO @ Mon, 02 Oct 2017 14:51:33: # Command line: callpeak -t SRX2704971.bam -f BAM -g 12100000 -n SRX2704971.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2704971.20 # format = BAM # ChIP-seq file = ['SRX2704971.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, 02 Oct 2017 14:51:33: #1 read tag files... INFO @ Mon, 02 Oct 2017 14:51:33: #1 read treatment tags... INFO @ Mon, 02 Oct 2017 14:51:33: # Command line: callpeak -t SRX2704971.bam -f BAM -g 12100000 -n SRX2704971.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2704971.10 # format = BAM # ChIP-seq file = ['SRX2704971.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, 02 Oct 2017 14:51:33: #1 read tag files... INFO @ Mon, 02 Oct 2017 14:51:33: #1 read treatment tags... INFO @ Mon, 02 Oct 2017 14:51:37: 1000000 INFO @ Mon, 02 Oct 2017 14:51:37: 1000000 INFO @ Mon, 02 Oct 2017 14:51:37: 1000000 INFO @ Mon, 02 Oct 2017 14:51:42: 2000000 INFO @ Mon, 02 Oct 2017 14:51:42: 2000000 INFO @ Mon, 02 Oct 2017 14:51:42: 2000000 INFO @ Mon, 02 Oct 2017 14:51:47: 3000000 INFO @ Mon, 02 Oct 2017 14:51:47: 3000000 INFO @ Mon, 02 Oct 2017 14:51:48: 3000000 INFO @ Mon, 02 Oct 2017 14:51:51: 4000000 INFO @ Mon, 02 Oct 2017 14:51:52: 4000000 INFO @ Mon, 02 Oct 2017 14:51:53: 4000000 INFO @ Mon, 02 Oct 2017 14:51:56: 5000000 INFO @ Mon, 02 Oct 2017 14:51:57: 5000000 INFO @ Mon, 02 Oct 2017 14:51:59: 5000000 INFO @ Mon, 02 Oct 2017 14:52:00: 6000000 INFO @ Mon, 02 Oct 2017 14:52:02: 6000000 INFO @ Mon, 02 Oct 2017 14:52:03: 6000000 INFO @ Mon, 02 Oct 2017 14:52:05: 7000000 INFO @ Mon, 02 Oct 2017 14:52:07: 7000000 INFO @ Mon, 02 Oct 2017 14:52:08: 7000000 INFO @ Mon, 02 Oct 2017 14:52:10: 8000000 INFO @ Mon, 02 Oct 2017 14:52:11: 8000000 INFO @ Mon, 02 Oct 2017 14:52:13: 8000000 INFO @ Mon, 02 Oct 2017 14:52:14: 9000000 INFO @ Mon, 02 Oct 2017 14:52:16: 9000000 INFO @ Mon, 02 Oct 2017 14:52:18: 9000000 INFO @ Mon, 02 Oct 2017 14:52:19: 10000000 INFO @ Mon, 02 Oct 2017 14:52:21: 10000000 INFO @ Mon, 02 Oct 2017 14:52:23: 11000000 INFO @ Mon, 02 Oct 2017 14:52:23: 10000000 INFO @ Mon, 02 Oct 2017 14:52:26: 11000000 INFO @ Mon, 02 Oct 2017 14:52:27: 12000000 INFO @ Mon, 02 Oct 2017 14:52:28: 11000000 INFO @ Mon, 02 Oct 2017 14:52:30: 12000000 INFO @ Mon, 02 Oct 2017 14:52:32: 13000000 INFO @ Mon, 02 Oct 2017 14:52:33: 12000000 INFO @ Mon, 02 Oct 2017 14:52:35: 13000000 INFO @ Mon, 02 Oct 2017 14:52:36: 14000000 INFO @ Mon, 02 Oct 2017 14:52:38: 13000000 INFO @ Mon, 02 Oct 2017 14:52:40: 14000000 INFO @ Mon, 02 Oct 2017 14:52:41: 15000000 INFO @ Mon, 02 Oct 2017 14:52:43: 14000000 INFO @ Mon, 02 Oct 2017 14:52:45: 15000000 INFO @ Mon, 02 Oct 2017 14:52:45: 16000000 INFO @ Mon, 02 Oct 2017 14:52:49: 15000000 INFO @ Mon, 02 Oct 2017 14:52:49: 17000000 INFO @ Mon, 02 Oct 2017 14:52:50: 16000000 INFO @ Mon, 02 Oct 2017 14:52:53: #1 tag size is determined as 25 bps INFO @ Mon, 02 Oct 2017 14:52:53: #1 tag size = 25 INFO @ Mon, 02 Oct 2017 14:52:53: #1 total tags in treatment: 7810972 INFO @ Mon, 02 Oct 2017 14:52:53: #1 user defined the maximum tags... INFO @ Mon, 02 Oct 2017 14:52:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 02 Oct 2017 14:52:53: #1 tags after filtering in treatment: 3361761 INFO @ Mon, 02 Oct 2017 14:52:53: #1 Redundant rate of treatment: 0.57 INFO @ Mon, 02 Oct 2017 14:52:53: #1 finished! INFO @ Mon, 02 Oct 2017 14:52:53: #2 Build Peak Model... INFO @ Mon, 02 Oct 2017 14:52:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 02 Oct 2017 14:52:53: #2 number of paired peaks: 25 WARNING @ Mon, 02 Oct 2017 14:52:53: Too few paired peaks (25) 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, 02 Oct 2017 14:52:53: Process for pairing-model is terminated! cat: SRX2704971.05_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): 4 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2704971.05_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 `SRX2704971.05_*.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 `SRX2704971.05_peaks.narrowPeak': そのようなファイルやディレクトリはありません INFO @ Mon, 02 Oct 2017 14:52:54: 16000000 CompletedMACS2peakCalling INFO @ Mon, 02 Oct 2017 14:52:54: 17000000 INFO @ Mon, 02 Oct 2017 14:52:58: #1 tag size is determined as 25 bps INFO @ Mon, 02 Oct 2017 14:52:58: #1 tag size = 25 INFO @ Mon, 02 Oct 2017 14:52:58: #1 total tags in treatment: 7810972 INFO @ Mon, 02 Oct 2017 14:52:58: #1 user defined the maximum tags... INFO @ Mon, 02 Oct 2017 14:52:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 02 Oct 2017 14:52:58: #1 tags after filtering in treatment: 3361761 INFO @ Mon, 02 Oct 2017 14:52:58: #1 Redundant rate of treatment: 0.57 INFO @ Mon, 02 Oct 2017 14:52:58: #1 finished! INFO @ Mon, 02 Oct 2017 14:52:58: #2 Build Peak Model... INFO @ Mon, 02 Oct 2017 14:52:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 02 Oct 2017 14:52:58: 17000000 INFO @ Mon, 02 Oct 2017 14:52:59: #2 number of paired peaks: 25 WARNING @ Mon, 02 Oct 2017 14:52:59: Too few paired peaks (25) 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, 02 Oct 2017 14:52:59: Process for pairing-model is terminated! cat: SRX2704971.20_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): 4 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2704971.20_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 `SRX2704971.20_*.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 `SRX2704971.20_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, 02 Oct 2017 14:53:02: #1 tag size is determined as 25 bps INFO @ Mon, 02 Oct 2017 14:53:02: #1 tag size = 25 INFO @ Mon, 02 Oct 2017 14:53:02: #1 total tags in treatment: 7810972 INFO @ Mon, 02 Oct 2017 14:53:02: #1 user defined the maximum tags... INFO @ Mon, 02 Oct 2017 14:53:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 02 Oct 2017 14:53:02: #1 tags after filtering in treatment: 3361761 INFO @ Mon, 02 Oct 2017 14:53:02: #1 Redundant rate of treatment: 0.57 INFO @ Mon, 02 Oct 2017 14:53:02: #1 finished! INFO @ Mon, 02 Oct 2017 14:53:02: #2 Build Peak Model... INFO @ Mon, 02 Oct 2017 14:53:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 02 Oct 2017 14:53:03: #2 number of paired peaks: 25 WARNING @ Mon, 02 Oct 2017 14:53:03: Too few paired peaks (25) 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, 02 Oct 2017 14:53:03: Process for pairing-model is terminated! cat: SRX2704971.10_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2704971.10_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 `SRX2704971.10_*.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 `SRX2704971.10_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。