Job ID = 9161991 sra ファイルのダウンロード中... Completed: 1542895K bytes transferred in 17 seconds (723383K 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 23998691 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1423723/SRR2931012.sra Written 23998691 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: 00:15:13 23998691 reads; of these: 23998691 (100.00%) were paired; of these: 5869252 (24.46%) aligned concordantly 0 times 16268476 (67.79%) aligned concordantly exactly 1 time 1860963 (7.75%) aligned concordantly >1 times ---- 5869252 pairs aligned concordantly 0 times; of these: 56674 (0.97%) aligned discordantly 1 time ---- 5812578 pairs aligned 0 times concordantly or discordantly; of these: 11625156 mates make up the pairs; of these: 11361501 (97.73%) aligned 0 times 211546 (1.82%) aligned exactly 1 time 52109 (0.45%) aligned >1 times 76.33% overall alignment rate Time searching: 00:15:13 Overall time: 00:15:13 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] 12919224 / 18148229 = 0.7119 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 05:35:05: # Command line: callpeak -t SRX1423723.bam -f BAM -g 12100000 -n SRX1423723.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1423723.20 # format = BAM # ChIP-seq file = ['SRX1423723.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 05:35:05: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:35:05: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:35:05: # Command line: callpeak -t SRX1423723.bam -f BAM -g 12100000 -n SRX1423723.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1423723.10 # format = BAM # ChIP-seq file = ['SRX1423723.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 05:35:05: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:35:05: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:35:05: # Command line: callpeak -t SRX1423723.bam -f BAM -g 12100000 -n SRX1423723.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1423723.05 # format = BAM # ChIP-seq file = ['SRX1423723.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 05:35:05: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:35:05: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:35:11: 1000000 INFO @ Wed, 28 Jun 2017 05:35:12: 1000000 INFO @ Wed, 28 Jun 2017 05:35:12: 1000000 INFO @ Wed, 28 Jun 2017 05:35:18: 2000000 INFO @ Wed, 28 Jun 2017 05:35:19: 2000000 INFO @ Wed, 28 Jun 2017 05:35:19: 2000000 INFO @ Wed, 28 Jun 2017 05:35:24: 3000000 INFO @ Wed, 28 Jun 2017 05:35:25: 3000000 INFO @ Wed, 28 Jun 2017 05:35:25: 3000000 INFO @ Wed, 28 Jun 2017 05:35:30: 4000000 INFO @ Wed, 28 Jun 2017 05:35:32: 4000000 INFO @ Wed, 28 Jun 2017 05:35:32: 4000000 INFO @ Wed, 28 Jun 2017 05:35:36: 5000000 INFO @ Wed, 28 Jun 2017 05:35:39: 5000000 INFO @ Wed, 28 Jun 2017 05:35:39: 5000000 INFO @ Wed, 28 Jun 2017 05:35:43: 6000000 INFO @ Wed, 28 Jun 2017 05:35:46: 6000000 INFO @ Wed, 28 Jun 2017 05:35:46: 6000000 INFO @ Wed, 28 Jun 2017 05:35:49: 7000000 INFO @ Wed, 28 Jun 2017 05:35:53: 7000000 INFO @ Wed, 28 Jun 2017 05:35:53: 7000000 INFO @ Wed, 28 Jun 2017 05:35:55: 8000000 INFO @ Wed, 28 Jun 2017 05:36:00: 8000000 INFO @ Wed, 28 Jun 2017 05:36:00: 8000000 INFO @ Wed, 28 Jun 2017 05:36:02: 9000000 INFO @ Wed, 28 Jun 2017 05:36:07: 9000000 INFO @ Wed, 28 Jun 2017 05:36:07: 9000000 INFO @ Wed, 28 Jun 2017 05:36:08: 10000000 INFO @ Wed, 28 Jun 2017 05:36:13: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:36:13: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:36:13: #1 total tags in treatment: 5227584 INFO @ Wed, 28 Jun 2017 05:36:13: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:36:13: #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 05:36:13: #1 tags after filtering in treatment: 4133655 INFO @ Wed, 28 Jun 2017 05:36:13: #1 Redundant rate of treatment: 0.21 INFO @ Wed, 28 Jun 2017 05:36:13: #1 finished! INFO @ Wed, 28 Jun 2017 05:36:13: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:36:13: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:36:13: #2 number of paired peaks: 74 WARNING @ Wed, 28 Jun 2017 05:36:13: Too few paired peaks (74) 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 05:36:13: Process for pairing-model is terminated! cat: SRX1423723.05_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 `SRX1423723.05_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 `SRX1423723.05_*.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 `SRX1423723.05_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 @ Wed, 28 Jun 2017 05:36:14: 10000000 INFO @ Wed, 28 Jun 2017 05:36:14: 10000000 INFO @ Wed, 28 Jun 2017 05:36:19: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:36:19: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:36:19: #1 total tags in treatment: 5227584 INFO @ Wed, 28 Jun 2017 05:36:19: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:36:19: #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 05:36:19: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:36:19: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:36:19: #1 total tags in treatment: 5227584 INFO @ Wed, 28 Jun 2017 05:36:19: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:36:19: #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 05:36:20: #1 tags after filtering in treatment: 4133655 INFO @ Wed, 28 Jun 2017 05:36:20: #1 Redundant rate of treatment: 0.21 INFO @ Wed, 28 Jun 2017 05:36:20: #1 finished! INFO @ Wed, 28 Jun 2017 05:36:20: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:36:20: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:36:20: #1 tags after filtering in treatment: 4133655 INFO @ Wed, 28 Jun 2017 05:36:20: #1 Redundant rate of treatment: 0.21 INFO @ Wed, 28 Jun 2017 05:36:20: #1 finished! INFO @ Wed, 28 Jun 2017 05:36:20: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:36:20: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:36:20: #2 number of paired peaks: 74 WARNING @ Wed, 28 Jun 2017 05:36:20: Too few paired peaks (74) 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 05:36:20: Process for pairing-model is terminated! INFO @ Wed, 28 Jun 2017 05:36:20: #2 number of paired peaks: 74 WARNING @ Wed, 28 Jun 2017 05:36:20: Too few paired peaks (74) 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 05:36:20: Process for pairing-model is terminated! cat: SRX1423723.20_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: SRX1423723.10_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 `SRX1423723.20_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 `SRX1423723.20_*.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 `SRX1423723.20_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): 0 millis CompletedMACS2peakCalling needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX1423723.10_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 `SRX1423723.10_*.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 `SRX1423723.10_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。