Job ID = 9161802 sra ファイルのダウンロード中... Completed: 850105K bytes transferred in 9 seconds (720187K 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 23775628 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1054420/SRR2057641.sra Written 23775628 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: 00:13:08 23775628 reads; of these: 23775628 (100.00%) were paired; of these: 2060440 (8.67%) aligned concordantly 0 times 19001957 (79.92%) aligned concordantly exactly 1 time 2713231 (11.41%) aligned concordantly >1 times ---- 2060440 pairs aligned concordantly 0 times; of these: 526820 (25.57%) aligned discordantly 1 time ---- 1533620 pairs aligned 0 times concordantly or discordantly; of these: 3067240 mates make up the pairs; of these: 2418931 (78.86%) aligned 0 times 434813 (14.18%) aligned exactly 1 time 213496 (6.96%) aligned >1 times 94.91% overall alignment rate Time searching: 00:13:08 Overall time: 00:13:08 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] 2699626 / 22134111 = 0.1220 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 05:00:36: # Command line: callpeak -t SRX1054420.bam -f BAM -g 12100000 -n SRX1054420.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1054420.05 # format = BAM # ChIP-seq file = ['SRX1054420.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 05:00:36: # Command line: callpeak -t SRX1054420.bam -f BAM -g 12100000 -n SRX1054420.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1054420.20 # format = BAM # ChIP-seq file = ['SRX1054420.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 05:00:36: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:00:36: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:00:36: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:00:36: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:00:36: # Command line: callpeak -t SRX1054420.bam -f BAM -g 12100000 -n SRX1054420.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1054420.10 # format = BAM # ChIP-seq file = ['SRX1054420.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 05:00:36: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:00:36: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:00:41: 1000000 INFO @ Wed, 28 Jun 2017 05:00:41: 1000000 INFO @ Wed, 28 Jun 2017 05:00:41: 1000000 INFO @ Wed, 28 Jun 2017 05:00:46: 2000000 INFO @ Wed, 28 Jun 2017 05:00:46: 2000000 INFO @ Wed, 28 Jun 2017 05:00:46: 2000000 INFO @ Wed, 28 Jun 2017 05:00:51: 3000000 INFO @ Wed, 28 Jun 2017 05:00:51: 3000000 INFO @ Wed, 28 Jun 2017 05:00:52: 3000000 INFO @ Wed, 28 Jun 2017 05:00:56: 4000000 INFO @ Wed, 28 Jun 2017 05:00:56: 4000000 INFO @ Wed, 28 Jun 2017 05:00:57: 4000000 INFO @ Wed, 28 Jun 2017 05:01:01: 5000000 INFO @ Wed, 28 Jun 2017 05:01:02: 5000000 INFO @ Wed, 28 Jun 2017 05:01:03: 5000000 INFO @ Wed, 28 Jun 2017 05:01:07: 6000000 INFO @ Wed, 28 Jun 2017 05:01:08: 6000000 INFO @ Wed, 28 Jun 2017 05:01:08: 6000000 INFO @ Wed, 28 Jun 2017 05:01:13: 7000000 INFO @ Wed, 28 Jun 2017 05:01:14: 7000000 INFO @ Wed, 28 Jun 2017 05:01:14: 7000000 INFO @ Wed, 28 Jun 2017 05:01:19: 8000000 INFO @ Wed, 28 Jun 2017 05:01:20: 8000000 INFO @ Wed, 28 Jun 2017 05:01:20: 8000000 INFO @ Wed, 28 Jun 2017 05:01:24: 9000000 INFO @ Wed, 28 Jun 2017 05:01:26: 9000000 INFO @ Wed, 28 Jun 2017 05:01:26: 9000000 INFO @ Wed, 28 Jun 2017 05:01:30: 10000000 INFO @ Wed, 28 Jun 2017 05:01:32: 10000000 INFO @ Wed, 28 Jun 2017 05:01:33: 10000000 INFO @ Wed, 28 Jun 2017 05:01:36: 11000000 INFO @ Wed, 28 Jun 2017 05:01:38: 11000000 INFO @ Wed, 28 Jun 2017 05:01:39: 11000000 INFO @ Wed, 28 Jun 2017 05:01:42: 12000000 INFO @ Wed, 28 Jun 2017 05:01:43: 12000000 INFO @ Wed, 28 Jun 2017 05:01:46: 12000000 INFO @ Wed, 28 Jun 2017 05:01:48: 13000000 INFO @ Wed, 28 Jun 2017 05:01:49: 13000000 INFO @ Wed, 28 Jun 2017 05:01:53: 13000000 INFO @ Wed, 28 Jun 2017 05:01:53: 14000000 INFO @ Wed, 28 Jun 2017 05:01:55: 14000000 INFO @ Wed, 28 Jun 2017 05:01:59: 15000000 INFO @ Wed, 28 Jun 2017 05:01:59: 14000000 INFO @ Wed, 28 Jun 2017 05:02:01: 15000000 INFO @ Wed, 28 Jun 2017 05:02:05: 16000000 INFO @ Wed, 28 Jun 2017 05:02:06: 15000000 INFO @ Wed, 28 Jun 2017 05:02:07: 16000000 INFO @ Wed, 28 Jun 2017 05:02:10: 17000000 INFO @ Wed, 28 Jun 2017 05:02:12: 16000000 INFO @ Wed, 28 Jun 2017 05:02:13: 17000000 INFO @ Wed, 28 Jun 2017 05:02:16: 18000000 INFO @ Wed, 28 Jun 2017 05:02:18: 17000000 INFO @ Wed, 28 Jun 2017 05:02:18: 18000000 INFO @ Wed, 28 Jun 2017 05:02:21: 19000000 INFO @ Wed, 28 Jun 2017 05:02:24: 19000000 INFO @ Wed, 28 Jun 2017 05:02:25: 18000000 INFO @ Wed, 28 Jun 2017 05:02:27: 20000000 INFO @ Wed, 28 Jun 2017 05:02:30: 20000000 INFO @ Wed, 28 Jun 2017 05:02:31: 19000000 INFO @ Wed, 28 Jun 2017 05:02:33: 21000000 INFO @ Wed, 28 Jun 2017 05:02:36: 21000000 INFO @ Wed, 28 Jun 2017 05:02:37: 20000000 INFO @ Wed, 28 Jun 2017 05:02:39: 22000000 INFO @ Wed, 28 Jun 2017 05:02:42: 22000000 INFO @ Wed, 28 Jun 2017 05:02:44: 21000000 INFO @ Wed, 28 Jun 2017 05:02:44: 23000000 INFO @ Wed, 28 Jun 2017 05:02:48: 23000000 INFO @ Wed, 28 Jun 2017 05:02:50: 24000000 INFO @ Wed, 28 Jun 2017 05:02:51: 22000000 INFO @ Wed, 28 Jun 2017 05:02:54: 24000000 INFO @ Wed, 28 Jun 2017 05:02:56: 25000000 INFO @ Wed, 28 Jun 2017 05:02:57: 23000000 INFO @ Wed, 28 Jun 2017 05:03:00: 25000000 INFO @ Wed, 28 Jun 2017 05:03:02: 26000000 INFO @ Wed, 28 Jun 2017 05:03:04: 24000000 INFO @ Wed, 28 Jun 2017 05:03:06: 26000000 INFO @ Wed, 28 Jun 2017 05:03:08: 27000000 INFO @ Wed, 28 Jun 2017 05:03:10: 25000000 INFO @ Wed, 28 Jun 2017 05:03:12: 27000000 INFO @ Wed, 28 Jun 2017 05:03:13: 28000000 INFO @ Wed, 28 Jun 2017 05:03:17: 26000000 INFO @ Wed, 28 Jun 2017 05:03:18: 28000000 INFO @ Wed, 28 Jun 2017 05:03:19: 29000000 INFO @ Wed, 28 Jun 2017 05:03:24: 27000000 INFO @ Wed, 28 Jun 2017 05:03:24: 29000000 INFO @ Wed, 28 Jun 2017 05:03:25: 30000000 INFO @ Wed, 28 Jun 2017 05:03:30: 30000000 INFO @ Wed, 28 Jun 2017 05:03:30: 28000000 INFO @ Wed, 28 Jun 2017 05:03:31: 31000000 INFO @ Wed, 28 Jun 2017 05:03:36: 31000000 INFO @ Wed, 28 Jun 2017 05:03:37: 32000000 INFO @ Wed, 28 Jun 2017 05:03:37: 29000000 INFO @ Wed, 28 Jun 2017 05:03:42: 32000000 INFO @ Wed, 28 Jun 2017 05:03:43: 33000000 INFO @ Wed, 28 Jun 2017 05:03:44: 30000000 INFO @ Wed, 28 Jun 2017 05:03:49: 33000000 INFO @ Wed, 28 Jun 2017 05:03:49: 34000000 INFO @ Wed, 28 Jun 2017 05:03:51: 31000000 INFO @ Wed, 28 Jun 2017 05:03:55: 34000000 INFO @ Wed, 28 Jun 2017 05:03:56: 35000000 INFO @ Wed, 28 Jun 2017 05:03:59: 32000000 INFO @ Wed, 28 Jun 2017 05:04:02: 35000000 INFO @ Wed, 28 Jun 2017 05:04:02: 36000000 INFO @ Wed, 28 Jun 2017 05:04:06: 33000000 INFO @ Wed, 28 Jun 2017 05:04:08: 37000000 INFO @ Wed, 28 Jun 2017 05:04:08: 36000000 INFO @ Wed, 28 Jun 2017 05:04:13: 34000000 INFO @ Wed, 28 Jun 2017 05:04:15: 38000000 INFO @ Wed, 28 Jun 2017 05:04:15: 37000000 INFO @ Wed, 28 Jun 2017 05:04:20: 35000000 INFO @ Wed, 28 Jun 2017 05:04:21: 39000000 INFO @ Wed, 28 Jun 2017 05:04:22: 38000000 INFO @ Wed, 28 Jun 2017 05:04:26: #1 tag size is determined as 24 bps INFO @ Wed, 28 Jun 2017 05:04:26: #1 tag size = 24 INFO @ Wed, 28 Jun 2017 05:04:26: #1 total tags in treatment: 19022826 INFO @ Wed, 28 Jun 2017 05:04:26: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:04:26: #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 05:04:26: #1 tags after filtering in treatment: 8006355 INFO @ Wed, 28 Jun 2017 05:04:26: #1 Redundant rate of treatment: 0.58 INFO @ Wed, 28 Jun 2017 05:04:26: #1 finished! INFO @ Wed, 28 Jun 2017 05:04:26: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:04:26: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:04:27: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:04:27: 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 05:04:27: Process for pairing-model is terminated! cat: SRX1054420.05_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 `SRX1054420.05_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 `SRX1054420.05_*.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 `SRX1054420.05_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 05:04:28: 36000000 INFO @ Wed, 28 Jun 2017 05:04:28: 39000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 28 Jun 2017 05:04:33: #1 tag size is determined as 24 bps INFO @ Wed, 28 Jun 2017 05:04:33: #1 tag size = 24 INFO @ Wed, 28 Jun 2017 05:04:33: #1 total tags in treatment: 19022826 INFO @ Wed, 28 Jun 2017 05:04:33: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:04:33: #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 05:04:34: #1 tags after filtering in treatment: 8006355 INFO @ Wed, 28 Jun 2017 05:04:34: #1 Redundant rate of treatment: 0.58 INFO @ Wed, 28 Jun 2017 05:04:34: #1 finished! INFO @ Wed, 28 Jun 2017 05:04:34: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:04:34: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:04:34: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:04:34: 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 05:04:34: Process for pairing-model is terminated! cat: SRX1054420.10_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 `SRX1054420.10_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 `SRX1054420.10_*.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 `SRX1054420.10_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 05:04:35: 37000000 INFO @ Wed, 28 Jun 2017 05:04:41: 38000000 INFO @ Wed, 28 Jun 2017 05:04:48: 39000000 BigWig に変換しました。 INFO @ Wed, 28 Jun 2017 05:04:53: #1 tag size is determined as 24 bps INFO @ Wed, 28 Jun 2017 05:04:53: #1 tag size = 24 INFO @ Wed, 28 Jun 2017 05:04:53: #1 total tags in treatment: 19022826 INFO @ Wed, 28 Jun 2017 05:04:53: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:04:53: #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 05:04:54: #1 tags after filtering in treatment: 8006355 INFO @ Wed, 28 Jun 2017 05:04:54: #1 Redundant rate of treatment: 0.58 INFO @ Wed, 28 Jun 2017 05:04:54: #1 finished! INFO @ Wed, 28 Jun 2017 05:04:54: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:04:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:04:54: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:04:54: 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 05:04:54: Process for pairing-model is terminated! cat: SRX1054420.20_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 needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX1054420.20_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 `SRX1054420.20_*.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 `SRX1054420.20_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