Job ID = 10608968 sra ファイルのダウンロード中... Completed: 2348963K bytes transferred in 136 seconds (140730K 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 18618899 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2741967/SRR5453801.sra Written 18618899 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: 00:24:54 18618899 reads; of these: 18618899 (100.00%) were paired; of these: 2464858 (13.24%) aligned concordantly 0 times 14572590 (78.27%) aligned concordantly exactly 1 time 1581451 (8.49%) aligned concordantly >1 times ---- 2464858 pairs aligned concordantly 0 times; of these: 983315 (39.89%) aligned discordantly 1 time ---- 1481543 pairs aligned 0 times concordantly or discordantly; of these: 2963086 mates make up the pairs; of these: 2006015 (67.70%) aligned 0 times 662461 (22.36%) aligned exactly 1 time 294610 (9.94%) aligned >1 times 94.61% overall alignment rate Time searching: 00:24:54 Overall time: 00:24:54 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] 480145 / 17050798 = 0.0282 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, 03 May 2018 23:34:38: # Command line: callpeak -t SRX2741967.bam -f BAM -g 12100000 -n SRX2741967.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2741967.10 # format = BAM # ChIP-seq file = ['SRX2741967.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, 03 May 2018 23:34:38: #1 read tag files... INFO @ Thu, 03 May 2018 23:34:38: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:34:38: # Command line: callpeak -t SRX2741967.bam -f BAM -g 12100000 -n SRX2741967.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2741967.20 # format = BAM # ChIP-seq file = ['SRX2741967.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, 03 May 2018 23:34:38: #1 read tag files... INFO @ Thu, 03 May 2018 23:34:38: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:34:38: # Command line: callpeak -t SRX2741967.bam -f BAM -g 12100000 -n SRX2741967.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2741967.05 # format = BAM # ChIP-seq file = ['SRX2741967.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, 03 May 2018 23:34:38: #1 read tag files... INFO @ Thu, 03 May 2018 23:34:38: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:34:46: 1000000 INFO @ Thu, 03 May 2018 23:34:46: 1000000 INFO @ Thu, 03 May 2018 23:34:46: 1000000 INFO @ Thu, 03 May 2018 23:34:53: 2000000 INFO @ Thu, 03 May 2018 23:34:53: 2000000 INFO @ Thu, 03 May 2018 23:34:53: 2000000 INFO @ Thu, 03 May 2018 23:35:00: 3000000 INFO @ Thu, 03 May 2018 23:35:00: 3000000 INFO @ Thu, 03 May 2018 23:35:00: 3000000 INFO @ Thu, 03 May 2018 23:35:07: 4000000 INFO @ Thu, 03 May 2018 23:35:08: 4000000 INFO @ Thu, 03 May 2018 23:35:08: 4000000 INFO @ Thu, 03 May 2018 23:35:15: 5000000 INFO @ Thu, 03 May 2018 23:35:15: 5000000 INFO @ Thu, 03 May 2018 23:35:15: 5000000 INFO @ Thu, 03 May 2018 23:35:22: 6000000 INFO @ Thu, 03 May 2018 23:35:23: 6000000 INFO @ Thu, 03 May 2018 23:35:23: 6000000 INFO @ Thu, 03 May 2018 23:35:29: 7000000 INFO @ Thu, 03 May 2018 23:35:30: 7000000 INFO @ Thu, 03 May 2018 23:35:30: 7000000 INFO @ Thu, 03 May 2018 23:35:36: 8000000 INFO @ Thu, 03 May 2018 23:35:37: 8000000 INFO @ Thu, 03 May 2018 23:35:37: 8000000 INFO @ Thu, 03 May 2018 23:35:43: 9000000 INFO @ Thu, 03 May 2018 23:35:44: 9000000 INFO @ Thu, 03 May 2018 23:35:44: 9000000 INFO @ Thu, 03 May 2018 23:35:51: 10000000 INFO @ Thu, 03 May 2018 23:35:52: 10000000 INFO @ Thu, 03 May 2018 23:35:52: 10000000 INFO @ Thu, 03 May 2018 23:35:58: 11000000 INFO @ Thu, 03 May 2018 23:35:59: 11000000 INFO @ Thu, 03 May 2018 23:35:59: 11000000 INFO @ Thu, 03 May 2018 23:36:05: 12000000 INFO @ Thu, 03 May 2018 23:36:06: 12000000 INFO @ Thu, 03 May 2018 23:36:06: 12000000 INFO @ Thu, 03 May 2018 23:36:12: 13000000 INFO @ Thu, 03 May 2018 23:36:13: 13000000 INFO @ Thu, 03 May 2018 23:36:13: 13000000 INFO @ Thu, 03 May 2018 23:36:19: 14000000 INFO @ Thu, 03 May 2018 23:36:21: 14000000 INFO @ Thu, 03 May 2018 23:36:21: 14000000 INFO @ Thu, 03 May 2018 23:36:27: 15000000 INFO @ Thu, 03 May 2018 23:36:28: 15000000 INFO @ Thu, 03 May 2018 23:36:28: 15000000 INFO @ Thu, 03 May 2018 23:36:34: 16000000 INFO @ Thu, 03 May 2018 23:36:35: 16000000 INFO @ Thu, 03 May 2018 23:36:35: 16000000 INFO @ Thu, 03 May 2018 23:36:41: 17000000 INFO @ Thu, 03 May 2018 23:36:43: 17000000 INFO @ Thu, 03 May 2018 23:36:43: 17000000 INFO @ Thu, 03 May 2018 23:36:48: 18000000 INFO @ Thu, 03 May 2018 23:36:50: 18000000 INFO @ Thu, 03 May 2018 23:36:50: 18000000 INFO @ Thu, 03 May 2018 23:36:56: 19000000 INFO @ Thu, 03 May 2018 23:36:57: 19000000 INFO @ Thu, 03 May 2018 23:36:57: 19000000 INFO @ Thu, 03 May 2018 23:37:03: 20000000 INFO @ Thu, 03 May 2018 23:37:05: 20000000 INFO @ Thu, 03 May 2018 23:37:05: 20000000 INFO @ Thu, 03 May 2018 23:37:10: 21000000 INFO @ Thu, 03 May 2018 23:37:12: 21000000 INFO @ Thu, 03 May 2018 23:37:12: 21000000 INFO @ Thu, 03 May 2018 23:37:17: 22000000 INFO @ Thu, 03 May 2018 23:37:19: 22000000 INFO @ Thu, 03 May 2018 23:37:19: 22000000 INFO @ Thu, 03 May 2018 23:37:24: 23000000 INFO @ Thu, 03 May 2018 23:37:26: 23000000 INFO @ Thu, 03 May 2018 23:37:27: 23000000 INFO @ Thu, 03 May 2018 23:37:32: 24000000 INFO @ Thu, 03 May 2018 23:37:34: 24000000 INFO @ Thu, 03 May 2018 23:37:34: 24000000 INFO @ Thu, 03 May 2018 23:37:39: 25000000 INFO @ Thu, 03 May 2018 23:37:41: 25000000 INFO @ Thu, 03 May 2018 23:37:41: 25000000 INFO @ Thu, 03 May 2018 23:37:46: 26000000 INFO @ Thu, 03 May 2018 23:37:49: 26000000 INFO @ Thu, 03 May 2018 23:37:49: 26000000 INFO @ Thu, 03 May 2018 23:37:53: 27000000 INFO @ Thu, 03 May 2018 23:37:56: 27000000 INFO @ Thu, 03 May 2018 23:37:56: 27000000 INFO @ Thu, 03 May 2018 23:38:01: 28000000 INFO @ Thu, 03 May 2018 23:38:03: 28000000 INFO @ Thu, 03 May 2018 23:38:04: 28000000 INFO @ Thu, 03 May 2018 23:38:08: 29000000 INFO @ Thu, 03 May 2018 23:38:11: 29000000 INFO @ Thu, 03 May 2018 23:38:11: 29000000 INFO @ Thu, 03 May 2018 23:38:15: 30000000 INFO @ Thu, 03 May 2018 23:38:18: 30000000 INFO @ Thu, 03 May 2018 23:38:18: 30000000 INFO @ Thu, 03 May 2018 23:38:22: 31000000 INFO @ Thu, 03 May 2018 23:38:26: 31000000 INFO @ Thu, 03 May 2018 23:38:26: 31000000 INFO @ Thu, 03 May 2018 23:38:29: 32000000 INFO @ Thu, 03 May 2018 23:38:33: 32000000 INFO @ Thu, 03 May 2018 23:38:33: 32000000 INFO @ Thu, 03 May 2018 23:38:37: 33000000 INFO @ Thu, 03 May 2018 23:38:40: 33000000 INFO @ Thu, 03 May 2018 23:38:41: 33000000 INFO @ Thu, 03 May 2018 23:38:44: 34000000 INFO @ Thu, 03 May 2018 23:38:46: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 23:38:46: #1 tag size = 100 INFO @ Thu, 03 May 2018 23:38:46: #1 total tags in treatment: 15695591 INFO @ Thu, 03 May 2018 23:38:46: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:38:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 23:38:46: #1 tags after filtering in treatment: 10469319 INFO @ Thu, 03 May 2018 23:38:46: #1 Redundant rate of treatment: 0.33 INFO @ Thu, 03 May 2018 23:38:46: #1 finished! INFO @ Thu, 03 May 2018 23:38:46: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:38:46: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:38:47: #2 number of paired peaks: 0 WARNING @ Thu, 03 May 2018 23:38:47: 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, 03 May 2018 23:38:47: Process for pairing-model is terminated! cat: SRX2741967.20_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 `SRX2741967.20_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 `SRX2741967.20_*.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 `SRX2741967.20_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, 03 May 2018 23:38:48: 34000000 INFO @ Thu, 03 May 2018 23:38:48: 34000000 INFO @ Thu, 03 May 2018 23:38:50: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 23:38:50: #1 tag size = 100 INFO @ Thu, 03 May 2018 23:38:50: #1 total tags in treatment: 15695591 INFO @ Thu, 03 May 2018 23:38:50: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:38:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 23:38:50: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 23:38:50: #1 tag size = 100 INFO @ Thu, 03 May 2018 23:38:50: #1 total tags in treatment: 15695591 INFO @ Thu, 03 May 2018 23:38:50: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:38:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 23:38:50: #1 tags after filtering in treatment: 10469319 INFO @ Thu, 03 May 2018 23:38:50: #1 Redundant rate of treatment: 0.33 INFO @ Thu, 03 May 2018 23:38:50: #1 finished! INFO @ Thu, 03 May 2018 23:38:50: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:38:50: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:38:51: #1 tags after filtering in treatment: 10469319 INFO @ Thu, 03 May 2018 23:38:51: #1 Redundant rate of treatment: 0.33 INFO @ Thu, 03 May 2018 23:38:51: #1 finished! INFO @ Thu, 03 May 2018 23:38:51: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:38:51: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:38:51: #2 number of paired peaks: 0 WARNING @ Thu, 03 May 2018 23:38:51: 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, 03 May 2018 23:38:51: Process for pairing-model is terminated! cat: SRX2741967.05_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 `SRX2741967.05_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 `SRX2741967.05_*.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 `SRX2741967.05_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 @ Thu, 03 May 2018 23:38:51: #2 number of paired peaks: 0 WARNING @ Thu, 03 May 2018 23:38:51: 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, 03 May 2018 23:38:51: Process for pairing-model is terminated! cat: SRX2741967.10_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 `SRX2741967.10_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 `SRX2741967.10_*.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 `SRX2741967.10_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。