Job ID = 9162102 sra ファイルのダウンロード中... Completed: 491066K bytes transferred in 7 seconds (553664K 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 11148538 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1631838/SRR3225771.sra Written 11148538 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: 00:09:36 11148538 reads; of these: 11148538 (100.00%) were paired; of these: 804631 (7.22%) aligned concordantly 0 times 8529919 (76.51%) aligned concordantly exactly 1 time 1813988 (16.27%) aligned concordantly >1 times ---- 804631 pairs aligned concordantly 0 times; of these: 405225 (50.36%) aligned discordantly 1 time ---- 399406 pairs aligned 0 times concordantly or discordantly; of these: 798812 mates make up the pairs; of these: 510285 (63.88%) aligned 0 times 76328 (9.56%) aligned exactly 1 time 212199 (26.56%) aligned >1 times 97.71% overall alignment rate Time searching: 00:09:36 Overall time: 00:09:36 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 12 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] 576831 / 10717747 = 0.0538 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 06:06:58: # Command line: callpeak -t SRX1631838.bam -f BAM -g 12100000 -n SRX1631838.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1631838.20 # format = BAM # ChIP-seq file = ['SRX1631838.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 06:06:58: #1 read tag files... INFO @ Wed, 28 Jun 2017 06:06:58: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 06:06:58: # Command line: callpeak -t SRX1631838.bam -f BAM -g 12100000 -n SRX1631838.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1631838.10 # format = BAM # ChIP-seq file = ['SRX1631838.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 06:06:58: #1 read tag files... INFO @ Wed, 28 Jun 2017 06:06:58: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 06:06:58: # Command line: callpeak -t SRX1631838.bam -f BAM -g 12100000 -n SRX1631838.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1631838.05 # format = BAM # ChIP-seq file = ['SRX1631838.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 06:06:58: #1 read tag files... INFO @ Wed, 28 Jun 2017 06:06:58: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 06:07:05: 1000000 INFO @ Wed, 28 Jun 2017 06:07:05: 1000000 INFO @ Wed, 28 Jun 2017 06:07:05: 1000000 INFO @ Wed, 28 Jun 2017 06:07:11: 2000000 INFO @ Wed, 28 Jun 2017 06:07:12: 2000000 INFO @ Wed, 28 Jun 2017 06:07:12: 2000000 INFO @ Wed, 28 Jun 2017 06:07:17: 3000000 INFO @ Wed, 28 Jun 2017 06:07:18: 3000000 INFO @ Wed, 28 Jun 2017 06:07:19: 3000000 INFO @ Wed, 28 Jun 2017 06:07:24: 4000000 INFO @ Wed, 28 Jun 2017 06:07:25: 4000000 INFO @ Wed, 28 Jun 2017 06:07:25: 4000000 INFO @ Wed, 28 Jun 2017 06:07:30: 5000000 INFO @ Wed, 28 Jun 2017 06:07:32: 5000000 INFO @ Wed, 28 Jun 2017 06:07:32: 5000000 INFO @ Wed, 28 Jun 2017 06:07:37: 6000000 INFO @ Wed, 28 Jun 2017 06:07:39: 6000000 INFO @ Wed, 28 Jun 2017 06:07:39: 6000000 INFO @ Wed, 28 Jun 2017 06:07:43: 7000000 INFO @ Wed, 28 Jun 2017 06:07:46: 7000000 INFO @ Wed, 28 Jun 2017 06:07:46: 7000000 INFO @ Wed, 28 Jun 2017 06:07:50: 8000000 INFO @ Wed, 28 Jun 2017 06:07:53: 8000000 INFO @ Wed, 28 Jun 2017 06:07:53: 8000000 INFO @ Wed, 28 Jun 2017 06:07:56: 9000000 INFO @ Wed, 28 Jun 2017 06:08:00: 9000000 INFO @ Wed, 28 Jun 2017 06:08:00: 9000000 INFO @ Wed, 28 Jun 2017 06:08:03: 10000000 INFO @ Wed, 28 Jun 2017 06:08:07: 10000000 INFO @ Wed, 28 Jun 2017 06:08:07: 10000000 INFO @ Wed, 28 Jun 2017 06:08:10: 11000000 INFO @ Wed, 28 Jun 2017 06:08:14: 11000000 INFO @ Wed, 28 Jun 2017 06:08:14: 11000000 INFO @ Wed, 28 Jun 2017 06:08:16: 12000000 INFO @ Wed, 28 Jun 2017 06:08:21: 12000000 INFO @ Wed, 28 Jun 2017 06:08:21: 12000000 INFO @ Wed, 28 Jun 2017 06:08:23: 13000000 INFO @ Wed, 28 Jun 2017 06:08:28: 13000000 INFO @ Wed, 28 Jun 2017 06:08:28: 13000000 INFO @ Wed, 28 Jun 2017 06:08:29: 14000000 INFO @ Wed, 28 Jun 2017 06:08:34: 14000000 INFO @ Wed, 28 Jun 2017 06:08:35: 14000000 INFO @ Wed, 28 Jun 2017 06:08:36: 15000000 INFO @ Wed, 28 Jun 2017 06:08:42: 15000000 INFO @ Wed, 28 Jun 2017 06:08:42: 15000000 INFO @ Wed, 28 Jun 2017 06:08:42: 16000000 INFO @ Wed, 28 Jun 2017 06:08:48: 17000000 INFO @ Wed, 28 Jun 2017 06:08:49: 16000000 INFO @ Wed, 28 Jun 2017 06:08:49: 16000000 INFO @ Wed, 28 Jun 2017 06:08:55: 18000000 INFO @ Wed, 28 Jun 2017 06:08:56: 17000000 INFO @ Wed, 28 Jun 2017 06:08:56: 17000000 INFO @ Wed, 28 Jun 2017 06:09:01: 19000000 INFO @ Wed, 28 Jun 2017 06:09:04: 18000000 INFO @ Wed, 28 Jun 2017 06:09:04: 18000000 INFO @ Wed, 28 Jun 2017 06:09:07: 20000000 INFO @ Wed, 28 Jun 2017 06:09:11: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 06:09:11: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 06:09:11: #1 total tags in treatment: 9776699 INFO @ Wed, 28 Jun 2017 06:09:11: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 06:09:11: #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 06:09:11: 19000000 INFO @ Wed, 28 Jun 2017 06:09:11: 19000000 INFO @ Wed, 28 Jun 2017 06:09:11: #1 tags after filtering in treatment: 7095991 INFO @ Wed, 28 Jun 2017 06:09:11: #1 Redundant rate of treatment: 0.27 INFO @ Wed, 28 Jun 2017 06:09:11: #1 finished! INFO @ Wed, 28 Jun 2017 06:09:11: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 06:09:11: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 06:09:12: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 06:09:12: 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 @ Wed, 28 Jun 2017 06:09:12: Process for pairing-model is terminated! cat: SRX1631838.10_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): 12 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX1631838.10_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 `SRX1631838.10_*.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 `SRX1631838.10_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 06:09:19: 20000000 INFO @ Wed, 28 Jun 2017 06:09:19: 20000000 INFO @ Wed, 28 Jun 2017 06:09:23: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 06:09:23: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 06:09:23: #1 total tags in treatment: 9776699 INFO @ Wed, 28 Jun 2017 06:09:23: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 06:09:23: #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 06:09:23: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 06:09:23: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 06:09:23: #1 total tags in treatment: 9776699 INFO @ Wed, 28 Jun 2017 06:09:23: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 06:09:23: #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 06:09:23: #1 tags after filtering in treatment: 7095991 INFO @ Wed, 28 Jun 2017 06:09:23: #1 Redundant rate of treatment: 0.27 INFO @ Wed, 28 Jun 2017 06:09:23: #1 finished! INFO @ Wed, 28 Jun 2017 06:09:23: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 06:09:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 06:09:24: #1 tags after filtering in treatment: 7095991 INFO @ Wed, 28 Jun 2017 06:09:24: #1 Redundant rate of treatment: 0.27 INFO @ Wed, 28 Jun 2017 06:09:24: #1 finished! INFO @ Wed, 28 Jun 2017 06:09:24: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 06:09:24: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 06:09:24: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 06:09:24: 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 @ Wed, 28 Jun 2017 06:09:24: Process for pairing-model is terminated! cat: SRX1631838.20_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX1631838.20_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 `SRX1631838.20_*.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 `SRX1631838.20_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 06:09:24: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 06:09:24: 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 @ Wed, 28 Jun 2017 06:09:24: Process for pairing-model is terminated! cat: SRX1631838.05_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 `SRX1631838.05_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 `SRX1631838.05_*.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 `SRX1631838.05_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。