Job ID = 9161992 sra ファイルのダウンロード中... Completed: 1460938K bytes transferred in 17 seconds (697609K bits/sec), in 1 file, 2 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 23412718 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1423724/SRR2931013.sra Written 23412718 spots total 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: 00:16:52 23412718 reads; of these: 23412718 (100.00%) were paired; of these: 6915141 (29.54%) aligned concordantly 0 times 14808302 (63.25%) aligned concordantly exactly 1 time 1689275 (7.22%) aligned concordantly >1 times ---- 6915141 pairs aligned concordantly 0 times; of these: 32905 (0.48%) aligned discordantly 1 time ---- 6882236 pairs aligned 0 times concordantly or discordantly; of these: 13764472 mates make up the pairs; of these: 13444166 (97.67%) aligned 0 times 270059 (1.96%) aligned exactly 1 time 50247 (0.37%) aligned >1 times 71.29% overall alignment rate Time searching: 00:16:52 Overall time: 00:16:52 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 16 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] 12053554 / 16507556 = 0.7302 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 @ Wed, 28 Jun 2017 05:36:01: # Command line: callpeak -t SRX1423724.bam -f BAM -g 12100000 -n SRX1423724.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1423724.10 # format = BAM # ChIP-seq file = ['SRX1423724.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 @ Wed, 28 Jun 2017 05:36:01: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:36:01: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:36:01: # Command line: callpeak -t SRX1423724.bam -f BAM -g 12100000 -n SRX1423724.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1423724.05 # format = BAM # ChIP-seq file = ['SRX1423724.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 @ Wed, 28 Jun 2017 05:36:01: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:36:01: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:36:01: # Command line: callpeak -t SRX1423724.bam -f BAM -g 12100000 -n SRX1423724.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1423724.20 # format = BAM # ChIP-seq file = ['SRX1423724.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 @ Wed, 28 Jun 2017 05:36:01: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:36:01: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:36:06: 1000000 INFO @ Wed, 28 Jun 2017 05:36:06: 1000000 INFO @ Wed, 28 Jun 2017 05:36:06: 1000000 INFO @ Wed, 28 Jun 2017 05:36:12: 2000000 INFO @ Wed, 28 Jun 2017 05:36:12: 2000000 INFO @ Wed, 28 Jun 2017 05:36:13: 2000000 INFO @ Wed, 28 Jun 2017 05:36:18: 3000000 INFO @ Wed, 28 Jun 2017 05:36:18: 3000000 INFO @ Wed, 28 Jun 2017 05:36:20: 3000000 INFO @ Wed, 28 Jun 2017 05:36:24: 4000000 INFO @ Wed, 28 Jun 2017 05:36:25: 4000000 INFO @ Wed, 28 Jun 2017 05:36:27: 4000000 INFO @ Wed, 28 Jun 2017 05:36:30: 5000000 INFO @ Wed, 28 Jun 2017 05:36:32: 5000000 INFO @ Wed, 28 Jun 2017 05:36:33: 5000000 INFO @ Wed, 28 Jun 2017 05:36:36: 6000000 INFO @ Wed, 28 Jun 2017 05:36:37: 6000000 INFO @ Wed, 28 Jun 2017 05:36:39: 6000000 INFO @ Wed, 28 Jun 2017 05:36:41: 7000000 INFO @ Wed, 28 Jun 2017 05:36:43: 7000000 INFO @ Wed, 28 Jun 2017 05:36:44: 7000000 INFO @ Wed, 28 Jun 2017 05:36:47: 8000000 INFO @ Wed, 28 Jun 2017 05:36:49: 8000000 INFO @ Wed, 28 Jun 2017 05:36:50: 8000000 INFO @ Wed, 28 Jun 2017 05:36:52: 9000000 INFO @ Wed, 28 Jun 2017 05:36:54: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:36:54: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:36:54: #1 total tags in treatment: 4451852 INFO @ Wed, 28 Jun 2017 05:36:54: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:36:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 05:36:54: #1 tags after filtering in treatment: 3643267 INFO @ Wed, 28 Jun 2017 05:36:54: #1 Redundant rate of treatment: 0.18 INFO @ Wed, 28 Jun 2017 05:36:54: #1 finished! INFO @ Wed, 28 Jun 2017 05:36:54: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:36:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:36:54: #2 number of paired peaks: 76 WARNING @ Wed, 28 Jun 2017 05:36:54: Too few paired peaks (76) 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 @ Wed, 28 Jun 2017 05:36:54: Process for pairing-model is terminated! cat: SRX1423724.20_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 `SRX1423724.20_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 `SRX1423724.20_*.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 `SRX1423724.20_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 @ Wed, 28 Jun 2017 05:36:55: 9000000 INFO @ Wed, 28 Jun 2017 05:36:56: 9000000 INFO @ Wed, 28 Jun 2017 05:36:57: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:36:57: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:36:57: #1 total tags in treatment: 4451852 INFO @ Wed, 28 Jun 2017 05:36:57: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:36:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 05:36:57: #1 tags after filtering in treatment: 3643267 INFO @ Wed, 28 Jun 2017 05:36:57: #1 Redundant rate of treatment: 0.18 INFO @ Wed, 28 Jun 2017 05:36:57: #1 finished! INFO @ Wed, 28 Jun 2017 05:36:57: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:36:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:36:57: #2 number of paired peaks: 76 WARNING @ Wed, 28 Jun 2017 05:36:57: Too few paired peaks (76) 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 @ Wed, 28 Jun 2017 05:36:57: Process for pairing-model is terminated! cat: SRX1423724.10_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 `SRX1423724.10_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 `SRX1423724.10_*.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 `SRX1423724.10_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 @ Wed, 28 Jun 2017 05:36:57: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:36:57: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:36:57: #1 total tags in treatment: 4451852 INFO @ Wed, 28 Jun 2017 05:36:57: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:36:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 05:36:57: #1 tags after filtering in treatment: 3643267 INFO @ Wed, 28 Jun 2017 05:36:57: #1 Redundant rate of treatment: 0.18 INFO @ Wed, 28 Jun 2017 05:36:57: #1 finished! INFO @ Wed, 28 Jun 2017 05:36:57: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:36:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:36:58: #2 number of paired peaks: 76 WARNING @ Wed, 28 Jun 2017 05:36:58: Too few paired peaks (76) 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 @ Wed, 28 Jun 2017 05:36:58: Process for pairing-model is terminated! cat: SRX1423724.05_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 `SRX1423724.05_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 `SRX1423724.05_*.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 `SRX1423724.05_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。