Job ID = 9162511 sra ファイルのダウンロード中... Completed: 704429K bytes transferred in 7 seconds (769997K 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 10599166 spots for /home/okishinya/chipatlas/results/sacCer3/SRX360907/SRR1003629.sra Written 10599166 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: 00:08:49 10599166 reads; of these: 10599166 (100.00%) were paired; of these: 1078759 (10.18%) aligned concordantly 0 times 7477136 (70.54%) aligned concordantly exactly 1 time 2043271 (19.28%) aligned concordantly >1 times ---- 1078759 pairs aligned concordantly 0 times; of these: 11517 (1.07%) aligned discordantly 1 time ---- 1067242 pairs aligned 0 times concordantly or discordantly; of these: 2134484 mates make up the pairs; of these: 1941788 (90.97%) aligned 0 times 148717 (6.97%) aligned exactly 1 time 43979 (2.06%) aligned >1 times 90.84% overall alignment rate Time searching: 00:08:49 Overall time: 00:08:49 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] 3531919 / 9526651 = 0.3707 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 08:14:23: # Command line: callpeak -t SRX360907.bam -f BAM -g 12100000 -n SRX360907.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX360907.05 # format = BAM # ChIP-seq file = ['SRX360907.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 08:14:23: #1 read tag files... INFO @ Wed, 28 Jun 2017 08:14:23: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 08:14:23: # Command line: callpeak -t SRX360907.bam -f BAM -g 12100000 -n SRX360907.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX360907.20 # format = BAM # ChIP-seq file = ['SRX360907.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 08:14:23: #1 read tag files... INFO @ Wed, 28 Jun 2017 08:14:23: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 08:14:23: # Command line: callpeak -t SRX360907.bam -f BAM -g 12100000 -n SRX360907.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX360907.10 # format = BAM # ChIP-seq file = ['SRX360907.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 08:14:23: #1 read tag files... INFO @ Wed, 28 Jun 2017 08:14:23: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 08:14:31: 1000000 INFO @ Wed, 28 Jun 2017 08:14:32: 1000000 INFO @ Wed, 28 Jun 2017 08:14:32: 1000000 INFO @ Wed, 28 Jun 2017 08:14:39: 2000000 INFO @ Wed, 28 Jun 2017 08:14:40: 2000000 INFO @ Wed, 28 Jun 2017 08:14:40: 2000000 INFO @ Wed, 28 Jun 2017 08:14:47: 3000000 INFO @ Wed, 28 Jun 2017 08:14:48: 3000000 INFO @ Wed, 28 Jun 2017 08:14:48: 3000000 INFO @ Wed, 28 Jun 2017 08:14:55: 4000000 INFO @ Wed, 28 Jun 2017 08:14:57: 4000000 INFO @ Wed, 28 Jun 2017 08:14:57: 4000000 INFO @ Wed, 28 Jun 2017 08:15:03: 5000000 INFO @ Wed, 28 Jun 2017 08:15:05: 5000000 INFO @ Wed, 28 Jun 2017 08:15:05: 5000000 INFO @ Wed, 28 Jun 2017 08:15:12: 6000000 INFO @ Wed, 28 Jun 2017 08:15:14: 6000000 INFO @ Wed, 28 Jun 2017 08:15:14: 6000000 INFO @ Wed, 28 Jun 2017 08:15:19: 7000000 INFO @ Wed, 28 Jun 2017 08:15:22: 7000000 INFO @ Wed, 28 Jun 2017 08:15:22: 7000000 INFO @ Wed, 28 Jun 2017 08:15:27: 8000000 INFO @ Wed, 28 Jun 2017 08:15:31: 8000000 INFO @ Wed, 28 Jun 2017 08:15:31: 8000000 INFO @ Wed, 28 Jun 2017 08:15:34: 9000000 INFO @ Wed, 28 Jun 2017 08:15:40: 9000000 INFO @ Wed, 28 Jun 2017 08:15:40: 9000000 INFO @ Wed, 28 Jun 2017 08:15:42: 10000000 INFO @ Wed, 28 Jun 2017 08:15:49: 10000000 INFO @ Wed, 28 Jun 2017 08:15:49: 10000000 INFO @ Wed, 28 Jun 2017 08:15:49: 11000000 INFO @ Wed, 28 Jun 2017 08:15:56: 12000000 INFO @ Wed, 28 Jun 2017 08:15:57: 11000000 INFO @ Wed, 28 Jun 2017 08:15:57: 11000000 INFO @ Wed, 28 Jun 2017 08:15:58: #1 tag size is determined as 51 bps INFO @ Wed, 28 Jun 2017 08:15:58: #1 tag size = 51 INFO @ Wed, 28 Jun 2017 08:15:58: #1 total tags in treatment: 5989161 INFO @ Wed, 28 Jun 2017 08:15:58: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 08:15:58: #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 08:15:58: #1 tags after filtering in treatment: 4603480 INFO @ Wed, 28 Jun 2017 08:15:58: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 28 Jun 2017 08:15:58: #1 finished! INFO @ Wed, 28 Jun 2017 08:15:58: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 08:15:58: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 08:15:58: #2 number of paired peaks: 28 WARNING @ Wed, 28 Jun 2017 08:15:58: Too few paired peaks (28) 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 08:15:58: Process for pairing-model is terminated! cat: SRX360907.10_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 `SRX360907.10_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 `SRX360907.10_*.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 `SRX360907.10_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 08:16:03: 12000000 INFO @ Wed, 28 Jun 2017 08:16:03: 12000000 INFO @ Wed, 28 Jun 2017 08:16:05: #1 tag size is determined as 51 bps INFO @ Wed, 28 Jun 2017 08:16:05: #1 tag size = 51 INFO @ Wed, 28 Jun 2017 08:16:05: #1 total tags in treatment: 5989161 INFO @ Wed, 28 Jun 2017 08:16:05: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 08:16:05: #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 08:16:05: #1 tag size is determined as 51 bps INFO @ Wed, 28 Jun 2017 08:16:05: #1 tag size = 51 INFO @ Wed, 28 Jun 2017 08:16:05: #1 total tags in treatment: 5989161 INFO @ Wed, 28 Jun 2017 08:16:05: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 08:16:05: #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 08:16:05: #1 tags after filtering in treatment: 4603480 INFO @ Wed, 28 Jun 2017 08:16:05: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 28 Jun 2017 08:16:05: #1 finished! INFO @ Wed, 28 Jun 2017 08:16:05: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 08:16:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 08:16:05: #1 tags after filtering in treatment: 4603480 INFO @ Wed, 28 Jun 2017 08:16:05: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 28 Jun 2017 08:16:05: #1 finished! INFO @ Wed, 28 Jun 2017 08:16:05: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 08:16:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 08:16:05: #2 number of paired peaks: 28 WARNING @ Wed, 28 Jun 2017 08:16:05: Too few paired peaks (28) 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 08:16:05: Process for pairing-model is terminated! INFO @ Wed, 28 Jun 2017 08:16:05: #2 number of paired peaks: 28 WARNING @ Wed, 28 Jun 2017 08:16:05: Too few paired peaks (28) 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 08:16:05: Process for pairing-model is terminated! cat: SRX360907.20_peaks.narrowPeak: そのようなファイルやディレクトリはありません cat: SRX360907.05_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) pass1 - making usageList (0 chroms): 1 millis rm: cannot remove `SRX360907.20_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 `SRX360907.20_*.xls': そのようなファイルやディレクトリはありません needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX360907.20_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 rm: cannot remove `SRX360907.05_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 `SRX360907.05_*.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 `SRX360907.05_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。