Job ID = 10536525 sra ファイルのダウンロード中... Completed: 1096847K bytes transferred in 29 seconds (306322K bits/sec), in 1 file. 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 29647482 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3671217/SRR6696969.sra Written 29647482 spots total rm: cannot remove `[DSE]RX*': 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 `[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: 00:18:05 29647482 reads; of these: 29647482 (100.00%) were paired; of these: 7841674 (26.45%) aligned concordantly 0 times 19328148 (65.19%) aligned concordantly exactly 1 time 2477660 (8.36%) aligned concordantly >1 times ---- 7841674 pairs aligned concordantly 0 times; of these: 19869 (0.25%) aligned discordantly 1 time ---- 7821805 pairs aligned 0 times concordantly or discordantly; of these: 15643610 mates make up the pairs; of these: 15460020 (98.83%) aligned 0 times 153186 (0.98%) aligned exactly 1 time 30404 (0.19%) aligned >1 times 73.93% overall alignment rate Time searching: 00:18:05 Overall time: 00:18:05 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 20 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] 8560162 / 21810162 = 0.3925 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 @ Thu, 05 Apr 2018 10:30:14: # Command line: callpeak -t SRX3671217.bam -f BAM -g 12100000 -n SRX3671217.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3671217.20 # format = BAM # ChIP-seq file = ['SRX3671217.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 @ Thu, 05 Apr 2018 10:30:14: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:30:14: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:30:14: # Command line: callpeak -t SRX3671217.bam -f BAM -g 12100000 -n SRX3671217.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3671217.05 # format = BAM # ChIP-seq file = ['SRX3671217.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 @ Thu, 05 Apr 2018 10:30:14: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:30:14: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:30:14: # Command line: callpeak -t SRX3671217.bam -f BAM -g 12100000 -n SRX3671217.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3671217.10 # format = BAM # ChIP-seq file = ['SRX3671217.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 @ Thu, 05 Apr 2018 10:30:14: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:30:14: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:30:20: 1000000 INFO @ Thu, 05 Apr 2018 10:30:20: 1000000 INFO @ Thu, 05 Apr 2018 10:30:20: 1000000 INFO @ Thu, 05 Apr 2018 10:30:26: 2000000 INFO @ Thu, 05 Apr 2018 10:30:26: 2000000 INFO @ Thu, 05 Apr 2018 10:30:26: 2000000 INFO @ Thu, 05 Apr 2018 10:30:32: 3000000 INFO @ Thu, 05 Apr 2018 10:30:33: 3000000 INFO @ Thu, 05 Apr 2018 10:30:33: 3000000 INFO @ Thu, 05 Apr 2018 10:30:38: 4000000 INFO @ Thu, 05 Apr 2018 10:30:39: 4000000 INFO @ Thu, 05 Apr 2018 10:30:40: 4000000 INFO @ Thu, 05 Apr 2018 10:30:45: 5000000 INFO @ Thu, 05 Apr 2018 10:30:46: 5000000 INFO @ Thu, 05 Apr 2018 10:30:46: 5000000 INFO @ Thu, 05 Apr 2018 10:30:51: 6000000 INFO @ Thu, 05 Apr 2018 10:30:53: 6000000 INFO @ Thu, 05 Apr 2018 10:30:53: 6000000 INFO @ Thu, 05 Apr 2018 10:30:57: 7000000 INFO @ Thu, 05 Apr 2018 10:30:59: 7000000 INFO @ Thu, 05 Apr 2018 10:30:59: 7000000 INFO @ Thu, 05 Apr 2018 10:31:03: 8000000 INFO @ Thu, 05 Apr 2018 10:31:06: 8000000 INFO @ Thu, 05 Apr 2018 10:31:06: 8000000 INFO @ Thu, 05 Apr 2018 10:31:09: 9000000 INFO @ Thu, 05 Apr 2018 10:31:12: 9000000 INFO @ Thu, 05 Apr 2018 10:31:13: 9000000 INFO @ Thu, 05 Apr 2018 10:31:15: 10000000 INFO @ Thu, 05 Apr 2018 10:31:19: 10000000 INFO @ Thu, 05 Apr 2018 10:31:19: 10000000 INFO @ Thu, 05 Apr 2018 10:31:21: 11000000 INFO @ Thu, 05 Apr 2018 10:31:25: 11000000 INFO @ Thu, 05 Apr 2018 10:31:26: 11000000 INFO @ Thu, 05 Apr 2018 10:31:27: 12000000 INFO @ Thu, 05 Apr 2018 10:31:32: 12000000 INFO @ Thu, 05 Apr 2018 10:31:32: 12000000 INFO @ Thu, 05 Apr 2018 10:31:33: 13000000 INFO @ Thu, 05 Apr 2018 10:31:38: 13000000 INFO @ Thu, 05 Apr 2018 10:31:38: 13000000 INFO @ Thu, 05 Apr 2018 10:31:39: 14000000 INFO @ Thu, 05 Apr 2018 10:31:44: 14000000 INFO @ Thu, 05 Apr 2018 10:31:45: 14000000 INFO @ Thu, 05 Apr 2018 10:31:46: 15000000 INFO @ Thu, 05 Apr 2018 10:31:51: 15000000 INFO @ Thu, 05 Apr 2018 10:31:51: 15000000 INFO @ Thu, 05 Apr 2018 10:31:52: 16000000 INFO @ Thu, 05 Apr 2018 10:31:58: 17000000 INFO @ Thu, 05 Apr 2018 10:31:58: 16000000 INFO @ Thu, 05 Apr 2018 10:31:58: 16000000 INFO @ Thu, 05 Apr 2018 10:32:04: 18000000 INFO @ Thu, 05 Apr 2018 10:32:04: 17000000 INFO @ Thu, 05 Apr 2018 10:32:04: 17000000 INFO @ Thu, 05 Apr 2018 10:32:09: 19000000 INFO @ Thu, 05 Apr 2018 10:32:11: 18000000 INFO @ Thu, 05 Apr 2018 10:32:11: 18000000 INFO @ Thu, 05 Apr 2018 10:32:15: 20000000 INFO @ Thu, 05 Apr 2018 10:32:18: 19000000 INFO @ Thu, 05 Apr 2018 10:32:18: 19000000 INFO @ Thu, 05 Apr 2018 10:32:21: 21000000 INFO @ Thu, 05 Apr 2018 10:32:24: 20000000 INFO @ Thu, 05 Apr 2018 10:32:24: 20000000 INFO @ Thu, 05 Apr 2018 10:32:27: 22000000 INFO @ Thu, 05 Apr 2018 10:32:31: 21000000 INFO @ Thu, 05 Apr 2018 10:32:31: 21000000 INFO @ Thu, 05 Apr 2018 10:32:33: 23000000 INFO @ Thu, 05 Apr 2018 10:32:37: 22000000 INFO @ Thu, 05 Apr 2018 10:32:38: 22000000 INFO @ Thu, 05 Apr 2018 10:32:39: 24000000 INFO @ Thu, 05 Apr 2018 10:32:44: 23000000 INFO @ Thu, 05 Apr 2018 10:32:44: 23000000 INFO @ Thu, 05 Apr 2018 10:32:45: 25000000 INFO @ Thu, 05 Apr 2018 10:32:51: 24000000 INFO @ Thu, 05 Apr 2018 10:32:51: 26000000 INFO @ Thu, 05 Apr 2018 10:32:51: 24000000 INFO @ Thu, 05 Apr 2018 10:32:56: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:32:56: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:32:56: #1 total tags in treatment: 13247443 INFO @ Thu, 05 Apr 2018 10:32:56: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:32:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 10:32:56: #1 tags after filtering in treatment: 5855408 INFO @ Thu, 05 Apr 2018 10:32:56: #1 Redundant rate of treatment: 0.56 INFO @ Thu, 05 Apr 2018 10:32:56: #1 finished! INFO @ Thu, 05 Apr 2018 10:32:56: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:32:56: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:32:56: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:32:56: 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 @ Thu, 05 Apr 2018 10:32:56: Process for pairing-model is terminated! cat: SRX3671217.20_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 `SRX3671217.20_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 `SRX3671217.20_*.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 `SRX3671217.20_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 @ Thu, 05 Apr 2018 10:32:57: 25000000 INFO @ Thu, 05 Apr 2018 10:32:58: 25000000 INFO @ Thu, 05 Apr 2018 10:33:03: 26000000 INFO @ Thu, 05 Apr 2018 10:33:04: 26000000 INFO @ Thu, 05 Apr 2018 10:33:07: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:33:07: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:33:07: #1 total tags in treatment: 13247443 INFO @ Thu, 05 Apr 2018 10:33:07: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:33:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 10:33:08: #1 tags after filtering in treatment: 5855408 INFO @ Thu, 05 Apr 2018 10:33:08: #1 Redundant rate of treatment: 0.56 INFO @ Thu, 05 Apr 2018 10:33:08: #1 finished! INFO @ Thu, 05 Apr 2018 10:33:08: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:33:08: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:33:08: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:33:08: 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 @ Thu, 05 Apr 2018 10:33:08: Process for pairing-model is terminated! cat: SRX3671217.10_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 `SRX3671217.10_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 `SRX3671217.10_*.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 `SRX3671217.10_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 @ Thu, 05 Apr 2018 10:33:08: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:33:08: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:33:08: #1 total tags in treatment: 13247443 INFO @ Thu, 05 Apr 2018 10:33:08: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:33:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 10:33:08: #1 tags after filtering in treatment: 5855408 INFO @ Thu, 05 Apr 2018 10:33:08: #1 Redundant rate of treatment: 0.56 INFO @ Thu, 05 Apr 2018 10:33:08: #1 finished! INFO @ Thu, 05 Apr 2018 10:33:08: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:33:08: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:33:09: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:33:09: 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 @ Thu, 05 Apr 2018 10:33:09: Process for pairing-model is terminated! cat: SRX3671217.05_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 `SRX3671217.05_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 `SRX3671217.05_*.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 `SRX3671217.05_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。