Job ID = 10536372 sra ファイルのダウンロード中... Completed: 1265723K bytes transferred in 18 seconds (559723K 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 32672887 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3433233/SRR6333874.sra Written 32672887 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: 00:37:02 32672887 reads; of these: 32672887 (100.00%) were paired; of these: 2649072 (8.11%) aligned concordantly 0 times 25308369 (77.46%) aligned concordantly exactly 1 time 4715446 (14.43%) aligned concordantly >1 times ---- 2649072 pairs aligned concordantly 0 times; of these: 51231 (1.93%) aligned discordantly 1 time ---- 2597841 pairs aligned 0 times concordantly or discordantly; of these: 5195682 mates make up the pairs; of these: 4737078 (91.17%) aligned 0 times 299013 (5.76%) aligned exactly 1 time 159591 (3.07%) aligned >1 times 92.75% overall alignment rate Time searching: 00:37:02 Overall time: 00:37:02 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 28 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] 8958237 / 30041112 = 0.2982 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 09:54:45: # Command line: callpeak -t SRX3433233.bam -f BAM -g 12100000 -n SRX3433233.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3433233.05 # format = BAM # ChIP-seq file = ['SRX3433233.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 09:54:45: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:54:45: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:54:45: # Command line: callpeak -t SRX3433233.bam -f BAM -g 12100000 -n SRX3433233.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3433233.20 # format = BAM # ChIP-seq file = ['SRX3433233.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 09:54:45: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:54:45: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:54:45: # Command line: callpeak -t SRX3433233.bam -f BAM -g 12100000 -n SRX3433233.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3433233.10 # format = BAM # ChIP-seq file = ['SRX3433233.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 09:54:45: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:54:45: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:54:50: 1000000 INFO @ Thu, 05 Apr 2018 09:54:50: 1000000 INFO @ Thu, 05 Apr 2018 09:54:50: 1000000 INFO @ Thu, 05 Apr 2018 09:54:56: 2000000 INFO @ Thu, 05 Apr 2018 09:54:56: 2000000 INFO @ Thu, 05 Apr 2018 09:54:57: 2000000 INFO @ Thu, 05 Apr 2018 09:55:01: 3000000 INFO @ Thu, 05 Apr 2018 09:55:02: 3000000 INFO @ Thu, 05 Apr 2018 09:55:03: 3000000 INFO @ Thu, 05 Apr 2018 09:55:07: 4000000 INFO @ Thu, 05 Apr 2018 09:55:08: 4000000 INFO @ Thu, 05 Apr 2018 09:55:10: 4000000 INFO @ Thu, 05 Apr 2018 09:55:12: 5000000 INFO @ Thu, 05 Apr 2018 09:55:14: 5000000 INFO @ Thu, 05 Apr 2018 09:55:16: 5000000 INFO @ Thu, 05 Apr 2018 09:55:17: 6000000 INFO @ Thu, 05 Apr 2018 09:55:21: 6000000 INFO @ Thu, 05 Apr 2018 09:55:23: 7000000 INFO @ Thu, 05 Apr 2018 09:55:23: 6000000 INFO @ Thu, 05 Apr 2018 09:55:27: 7000000 INFO @ Thu, 05 Apr 2018 09:55:28: 8000000 INFO @ Thu, 05 Apr 2018 09:55:29: 7000000 INFO @ Thu, 05 Apr 2018 09:55:33: 8000000 INFO @ Thu, 05 Apr 2018 09:55:33: 9000000 INFO @ Thu, 05 Apr 2018 09:55:36: 8000000 INFO @ Thu, 05 Apr 2018 09:55:39: 10000000 INFO @ Thu, 05 Apr 2018 09:55:39: 9000000 INFO @ Thu, 05 Apr 2018 09:55:43: 9000000 INFO @ Thu, 05 Apr 2018 09:55:44: 11000000 INFO @ Thu, 05 Apr 2018 09:55:45: 10000000 INFO @ Thu, 05 Apr 2018 09:55:49: 10000000 INFO @ Thu, 05 Apr 2018 09:55:50: 12000000 INFO @ Thu, 05 Apr 2018 09:55:51: 11000000 INFO @ Thu, 05 Apr 2018 09:55:55: 13000000 INFO @ Thu, 05 Apr 2018 09:55:56: 11000000 INFO @ Thu, 05 Apr 2018 09:55:58: 12000000 INFO @ Thu, 05 Apr 2018 09:56:00: 14000000 INFO @ Thu, 05 Apr 2018 09:56:02: 12000000 INFO @ Thu, 05 Apr 2018 09:56:04: 13000000 INFO @ Thu, 05 Apr 2018 09:56:06: 15000000 INFO @ Thu, 05 Apr 2018 09:56:09: 13000000 INFO @ Thu, 05 Apr 2018 09:56:10: 14000000 INFO @ Thu, 05 Apr 2018 09:56:11: 16000000 INFO @ Thu, 05 Apr 2018 09:56:16: 14000000 INFO @ Thu, 05 Apr 2018 09:56:16: 17000000 INFO @ Thu, 05 Apr 2018 09:56:16: 15000000 INFO @ Thu, 05 Apr 2018 09:56:22: 18000000 INFO @ Thu, 05 Apr 2018 09:56:22: 15000000 INFO @ Thu, 05 Apr 2018 09:56:23: 16000000 INFO @ Thu, 05 Apr 2018 09:56:27: 19000000 INFO @ Thu, 05 Apr 2018 09:56:29: 16000000 INFO @ Thu, 05 Apr 2018 09:56:29: 17000000 INFO @ Thu, 05 Apr 2018 09:56:32: 20000000 INFO @ Thu, 05 Apr 2018 09:56:35: 18000000 INFO @ Thu, 05 Apr 2018 09:56:35: 17000000 INFO @ Thu, 05 Apr 2018 09:56:38: 21000000 INFO @ Thu, 05 Apr 2018 09:56:41: 19000000 INFO @ Thu, 05 Apr 2018 09:56:42: 18000000 INFO @ Thu, 05 Apr 2018 09:56:43: 22000000 INFO @ Thu, 05 Apr 2018 09:56:47: 20000000 INFO @ Thu, 05 Apr 2018 09:56:48: 19000000 INFO @ Thu, 05 Apr 2018 09:56:48: 23000000 INFO @ Thu, 05 Apr 2018 09:56:53: 21000000 INFO @ Thu, 05 Apr 2018 09:56:54: 24000000 INFO @ Thu, 05 Apr 2018 09:56:55: 20000000 INFO @ Thu, 05 Apr 2018 09:56:59: 25000000 INFO @ Thu, 05 Apr 2018 09:56:59: 22000000 INFO @ Thu, 05 Apr 2018 09:57:01: 21000000 INFO @ Thu, 05 Apr 2018 09:57:05: 26000000 INFO @ Thu, 05 Apr 2018 09:57:06: 23000000 INFO @ Thu, 05 Apr 2018 09:57:08: 22000000 INFO @ Thu, 05 Apr 2018 09:57:10: 27000000 INFO @ Thu, 05 Apr 2018 09:57:12: 24000000 INFO @ Thu, 05 Apr 2018 09:57:14: 23000000 INFO @ Thu, 05 Apr 2018 09:57:15: 28000000 INFO @ Thu, 05 Apr 2018 09:57:18: 25000000 INFO @ Thu, 05 Apr 2018 09:57:20: 29000000 INFO @ Thu, 05 Apr 2018 09:57:21: 24000000 INFO @ Thu, 05 Apr 2018 09:57:24: 26000000 INFO @ Thu, 05 Apr 2018 09:57:26: 30000000 INFO @ Thu, 05 Apr 2018 09:57:27: 25000000 INFO @ Thu, 05 Apr 2018 09:57:30: 27000000 INFO @ Thu, 05 Apr 2018 09:57:31: 31000000 INFO @ Thu, 05 Apr 2018 09:57:34: 26000000 INFO @ Thu, 05 Apr 2018 09:57:36: 28000000 INFO @ Thu, 05 Apr 2018 09:57:37: 32000000 INFO @ Thu, 05 Apr 2018 09:57:40: 27000000 INFO @ Thu, 05 Apr 2018 09:57:42: 33000000 INFO @ Thu, 05 Apr 2018 09:57:42: 29000000 INFO @ Thu, 05 Apr 2018 09:57:47: 28000000 INFO @ Thu, 05 Apr 2018 09:57:47: 34000000 INFO @ Thu, 05 Apr 2018 09:57:49: 30000000 INFO @ Thu, 05 Apr 2018 09:57:53: 35000000 INFO @ Thu, 05 Apr 2018 09:57:53: 29000000 INFO @ Thu, 05 Apr 2018 09:57:55: 31000000 INFO @ Thu, 05 Apr 2018 09:57:58: 36000000 INFO @ Thu, 05 Apr 2018 09:58:00: 30000000 INFO @ Thu, 05 Apr 2018 09:58:01: 32000000 INFO @ Thu, 05 Apr 2018 09:58:03: 37000000 INFO @ Thu, 05 Apr 2018 09:58:06: 31000000 INFO @ Thu, 05 Apr 2018 09:58:07: 33000000 INFO @ Thu, 05 Apr 2018 09:58:09: 38000000 INFO @ Thu, 05 Apr 2018 09:58:13: 32000000 INFO @ Thu, 05 Apr 2018 09:58:13: 34000000 INFO @ Thu, 05 Apr 2018 09:58:14: 39000000 INFO @ Thu, 05 Apr 2018 09:58:20: 33000000 INFO @ Thu, 05 Apr 2018 09:58:20: 40000000 INFO @ Thu, 05 Apr 2018 09:58:20: 35000000 INFO @ Thu, 05 Apr 2018 09:58:25: 41000000 INFO @ Thu, 05 Apr 2018 09:58:26: 36000000 INFO @ Thu, 05 Apr 2018 09:58:26: 34000000 INFO @ Thu, 05 Apr 2018 09:58:30: 42000000 INFO @ Thu, 05 Apr 2018 09:58:32: 37000000 INFO @ Thu, 05 Apr 2018 09:58:33: 35000000 INFO @ Thu, 05 Apr 2018 09:58:34: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:58:34: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:58:34: #1 total tags in treatment: 21070541 INFO @ Thu, 05 Apr 2018 09:58:34: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:58:34: #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 09:58:35: #1 tags after filtering in treatment: 10303691 INFO @ Thu, 05 Apr 2018 09:58:35: #1 Redundant rate of treatment: 0.51 INFO @ Thu, 05 Apr 2018 09:58:35: #1 finished! INFO @ Thu, 05 Apr 2018 09:58:35: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:58:35: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:58:35: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:58:35: 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 09:58:35: Process for pairing-model is terminated! cat: SRX3433233.05_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3433233.05_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 `SRX3433233.05_*.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 `SRX3433233.05_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, 05 Apr 2018 09:58:38: 38000000 INFO @ Thu, 05 Apr 2018 09:58:39: 36000000 INFO @ Thu, 05 Apr 2018 09:58:44: 39000000 INFO @ Thu, 05 Apr 2018 09:58:45: 37000000 INFO @ Thu, 05 Apr 2018 09:58:50: 40000000 INFO @ Thu, 05 Apr 2018 09:58:52: 38000000 INFO @ Thu, 05 Apr 2018 09:58:56: 41000000 INFO @ Thu, 05 Apr 2018 09:58:58: 39000000 INFO @ Thu, 05 Apr 2018 09:59:02: 42000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 05 Apr 2018 09:59:04: 40000000 INFO @ Thu, 05 Apr 2018 09:59:06: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:59:06: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:59:06: #1 total tags in treatment: 21070541 INFO @ Thu, 05 Apr 2018 09:59:06: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:59:06: #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 09:59:07: #1 tags after filtering in treatment: 10303691 INFO @ Thu, 05 Apr 2018 09:59:07: #1 Redundant rate of treatment: 0.51 INFO @ Thu, 05 Apr 2018 09:59:07: #1 finished! INFO @ Thu, 05 Apr 2018 09:59:07: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:59:07: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:59:07: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:59:07: 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 09:59:07: Process for pairing-model is terminated! cat: SRX3433233.20_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 `SRX3433233.20_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 `SRX3433233.20_*.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 `SRX3433233.20_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 09:59:10: 41000000 INFO @ Thu, 05 Apr 2018 09:59:15: 42000000 INFO @ Thu, 05 Apr 2018 09:59:19: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:59:19: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:59:19: #1 total tags in treatment: 21070541 INFO @ Thu, 05 Apr 2018 09:59:19: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:59:19: #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 09:59:20: #1 tags after filtering in treatment: 10303691 INFO @ Thu, 05 Apr 2018 09:59:20: #1 Redundant rate of treatment: 0.51 INFO @ Thu, 05 Apr 2018 09:59:20: #1 finished! INFO @ Thu, 05 Apr 2018 09:59:20: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:59:20: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:59:21: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:59:21: 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 09:59:21: Process for pairing-model is terminated! cat: SRX3433233.10_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 `SRX3433233.10_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 `SRX3433233.10_*.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 `SRX3433233.10_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 BigWig に変換しました。