Job ID = 10536365 sra ファイルのダウンロード中... Completed: 1019547K bytes transferred in 81 seconds (101952K 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 28127992 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3433227/SRR6333868.sra Written 28127992 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: 00:20:22 28127992 reads; of these: 28127992 (100.00%) were paired; of these: 4996072 (17.76%) aligned concordantly 0 times 21201978 (75.38%) aligned concordantly exactly 1 time 1929942 (6.86%) aligned concordantly >1 times ---- 4996072 pairs aligned concordantly 0 times; of these: 584391 (11.70%) aligned discordantly 1 time ---- 4411681 pairs aligned 0 times concordantly or discordantly; of these: 8823362 mates make up the pairs; of these: 7307349 (82.82%) aligned 0 times 1290370 (14.62%) aligned exactly 1 time 225643 (2.56%) aligned >1 times 87.01% overall alignment rate Time searching: 00:20:22 Overall time: 00:20:22 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] 5575185 / 23199495 = 0.2403 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 09:34:55: # Command line: callpeak -t SRX3433227.bam -f BAM -g 12100000 -n SRX3433227.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3433227.10 # format = BAM # ChIP-seq file = ['SRX3433227.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 09:34:55: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:34:55: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:34:55: # Command line: callpeak -t SRX3433227.bam -f BAM -g 12100000 -n SRX3433227.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3433227.05 # format = BAM # ChIP-seq file = ['SRX3433227.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 09:34:55: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:34:55: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:34:55: # Command line: callpeak -t SRX3433227.bam -f BAM -g 12100000 -n SRX3433227.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3433227.20 # format = BAM # ChIP-seq file = ['SRX3433227.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 09:34:55: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:34:55: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:35:01: 1000000 INFO @ Thu, 05 Apr 2018 09:35:02: 1000000 INFO @ Thu, 05 Apr 2018 09:35:02: 1000000 INFO @ Thu, 05 Apr 2018 09:35:07: 2000000 INFO @ Thu, 05 Apr 2018 09:35:08: 2000000 INFO @ Thu, 05 Apr 2018 09:35:08: 2000000 INFO @ Thu, 05 Apr 2018 09:35:13: 3000000 INFO @ Thu, 05 Apr 2018 09:35:15: 3000000 INFO @ Thu, 05 Apr 2018 09:35:15: 3000000 INFO @ Thu, 05 Apr 2018 09:35:19: 4000000 INFO @ Thu, 05 Apr 2018 09:35:22: 4000000 INFO @ Thu, 05 Apr 2018 09:35:22: 4000000 INFO @ Thu, 05 Apr 2018 09:35:25: 5000000 INFO @ Thu, 05 Apr 2018 09:35:28: 5000000 INFO @ Thu, 05 Apr 2018 09:35:28: 5000000 INFO @ Thu, 05 Apr 2018 09:35:31: 6000000 INFO @ Thu, 05 Apr 2018 09:35:35: 6000000 INFO @ Thu, 05 Apr 2018 09:35:35: 6000000 INFO @ Thu, 05 Apr 2018 09:35:37: 7000000 INFO @ Thu, 05 Apr 2018 09:35:41: 7000000 INFO @ Thu, 05 Apr 2018 09:35:41: 7000000 INFO @ Thu, 05 Apr 2018 09:35:43: 8000000 INFO @ Thu, 05 Apr 2018 09:35:48: 8000000 INFO @ Thu, 05 Apr 2018 09:35:48: 8000000 INFO @ Thu, 05 Apr 2018 09:35:49: 9000000 INFO @ Thu, 05 Apr 2018 09:35:54: 9000000 INFO @ Thu, 05 Apr 2018 09:35:54: 9000000 INFO @ Thu, 05 Apr 2018 09:35:55: 10000000 INFO @ Thu, 05 Apr 2018 09:36:00: 11000000 INFO @ Thu, 05 Apr 2018 09:36:01: 10000000 INFO @ Thu, 05 Apr 2018 09:36:01: 10000000 INFO @ Thu, 05 Apr 2018 09:36:06: 12000000 INFO @ Thu, 05 Apr 2018 09:36:07: 11000000 INFO @ Thu, 05 Apr 2018 09:36:07: 11000000 INFO @ Thu, 05 Apr 2018 09:36:12: 13000000 INFO @ Thu, 05 Apr 2018 09:36:14: 12000000 INFO @ Thu, 05 Apr 2018 09:36:14: 12000000 INFO @ Thu, 05 Apr 2018 09:36:18: 14000000 INFO @ Thu, 05 Apr 2018 09:36:20: 13000000 INFO @ Thu, 05 Apr 2018 09:36:20: 13000000 INFO @ Thu, 05 Apr 2018 09:36:24: 15000000 INFO @ Thu, 05 Apr 2018 09:36:27: 14000000 INFO @ Thu, 05 Apr 2018 09:36:27: 14000000 INFO @ Thu, 05 Apr 2018 09:36:30: 16000000 INFO @ Thu, 05 Apr 2018 09:36:33: 15000000 INFO @ Thu, 05 Apr 2018 09:36:33: 15000000 INFO @ Thu, 05 Apr 2018 09:36:36: 17000000 INFO @ Thu, 05 Apr 2018 09:36:40: 16000000 INFO @ Thu, 05 Apr 2018 09:36:40: 16000000 INFO @ Thu, 05 Apr 2018 09:36:41: 18000000 INFO @ Thu, 05 Apr 2018 09:36:47: 17000000 INFO @ Thu, 05 Apr 2018 09:36:47: 17000000 INFO @ Thu, 05 Apr 2018 09:36:47: 19000000 INFO @ Thu, 05 Apr 2018 09:36:53: 20000000 INFO @ Thu, 05 Apr 2018 09:36:53: 18000000 INFO @ Thu, 05 Apr 2018 09:36:53: 18000000 INFO @ Thu, 05 Apr 2018 09:36:59: 21000000 INFO @ Thu, 05 Apr 2018 09:37:00: 19000000 INFO @ Thu, 05 Apr 2018 09:37:00: 19000000 INFO @ Thu, 05 Apr 2018 09:37:05: 22000000 INFO @ Thu, 05 Apr 2018 09:37:06: 20000000 INFO @ Thu, 05 Apr 2018 09:37:06: 20000000 INFO @ Thu, 05 Apr 2018 09:37:11: 23000000 INFO @ Thu, 05 Apr 2018 09:37:13: 21000000 INFO @ Thu, 05 Apr 2018 09:37:13: 21000000 INFO @ Thu, 05 Apr 2018 09:37:16: 24000000 INFO @ Thu, 05 Apr 2018 09:37:19: 22000000 INFO @ Thu, 05 Apr 2018 09:37:19: 22000000 INFO @ Thu, 05 Apr 2018 09:37:22: 25000000 INFO @ Thu, 05 Apr 2018 09:37:26: 23000000 INFO @ Thu, 05 Apr 2018 09:37:26: 23000000 INFO @ Thu, 05 Apr 2018 09:37:28: 26000000 INFO @ Thu, 05 Apr 2018 09:37:33: 24000000 INFO @ Thu, 05 Apr 2018 09:37:33: 24000000 INFO @ Thu, 05 Apr 2018 09:37:34: 27000000 INFO @ Thu, 05 Apr 2018 09:37:39: 25000000 INFO @ Thu, 05 Apr 2018 09:37:39: 25000000 INFO @ Thu, 05 Apr 2018 09:37:40: 28000000 INFO @ Thu, 05 Apr 2018 09:37:45: 26000000 INFO @ Thu, 05 Apr 2018 09:37:46: 26000000 INFO @ Thu, 05 Apr 2018 09:37:46: 29000000 INFO @ Thu, 05 Apr 2018 09:37:52: 27000000 INFO @ Thu, 05 Apr 2018 09:37:52: 27000000 INFO @ Thu, 05 Apr 2018 09:37:52: 30000000 INFO @ Thu, 05 Apr 2018 09:37:58: 28000000 INFO @ Thu, 05 Apr 2018 09:37:58: 28000000 INFO @ Thu, 05 Apr 2018 09:37:59: 31000000 INFO @ Thu, 05 Apr 2018 09:38:04: 29000000 INFO @ Thu, 05 Apr 2018 09:38:05: 29000000 INFO @ Thu, 05 Apr 2018 09:38:05: 32000000 INFO @ Thu, 05 Apr 2018 09:38:10: 30000000 INFO @ Thu, 05 Apr 2018 09:38:11: 30000000 INFO @ Thu, 05 Apr 2018 09:38:12: 33000000 INFO @ Thu, 05 Apr 2018 09:38:16: 31000000 INFO @ Thu, 05 Apr 2018 09:38:18: 31000000 INFO @ Thu, 05 Apr 2018 09:38:18: 34000000 INFO @ Thu, 05 Apr 2018 09:38:22: 32000000 INFO @ Thu, 05 Apr 2018 09:38:24: 32000000 INFO @ Thu, 05 Apr 2018 09:38:25: 35000000 INFO @ Thu, 05 Apr 2018 09:38:28: 33000000 INFO @ Thu, 05 Apr 2018 09:38:31: 33000000 INFO @ Thu, 05 Apr 2018 09:38:31: 36000000 INFO @ Thu, 05 Apr 2018 09:38:34: 34000000 INFO @ Thu, 05 Apr 2018 09:38:37: 37000000 INFO @ Thu, 05 Apr 2018 09:38:37: 34000000 INFO @ Thu, 05 Apr 2018 09:38:40: 35000000 INFO @ Thu, 05 Apr 2018 09:38:43: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:38:43: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:38:43: #1 total tags in treatment: 17572746 INFO @ Thu, 05 Apr 2018 09:38:43: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:38:43: #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 09:38:43: #1 tags after filtering in treatment: 10308021 INFO @ Thu, 05 Apr 2018 09:38:43: #1 Redundant rate of treatment: 0.41 INFO @ Thu, 05 Apr 2018 09:38:43: #1 finished! INFO @ Thu, 05 Apr 2018 09:38:43: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:38:43: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:38:44: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:38:44: 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 09:38:44: Process for pairing-model is terminated! cat: SRX3433227.10_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 `SRX3433227.10_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 `SRX3433227.10_*.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 `SRX3433227.10_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 09:38:45: 35000000 INFO @ Thu, 05 Apr 2018 09:38:48: 36000000 INFO @ Thu, 05 Apr 2018 09:38:52: 36000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 05 Apr 2018 09:38:56: 37000000 INFO @ Thu, 05 Apr 2018 09:38:58: 37000000 INFO @ Thu, 05 Apr 2018 09:39:03: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:39:03: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:39:03: #1 total tags in treatment: 17572746 INFO @ Thu, 05 Apr 2018 09:39:03: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:39:03: #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 09:39:03: #1 tags after filtering in treatment: 10308021 INFO @ Thu, 05 Apr 2018 09:39:03: #1 Redundant rate of treatment: 0.41 INFO @ Thu, 05 Apr 2018 09:39:03: #1 finished! INFO @ Thu, 05 Apr 2018 09:39:03: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:39:03: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:39:04: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:39:04: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:39:04: #1 total tags in treatment: 17572746 INFO @ Thu, 05 Apr 2018 09:39:04: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:39:04: #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 09:39:04: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:39:04: 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 09:39:04: Process for pairing-model is terminated! cat: SRX3433227.05_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 `SRX3433227.05_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 `SRX3433227.05_*.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 `SRX3433227.05_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 09:39:04: #1 tags after filtering in treatment: 10308021 INFO @ Thu, 05 Apr 2018 09:39:04: #1 Redundant rate of treatment: 0.41 INFO @ Thu, 05 Apr 2018 09:39:04: #1 finished! INFO @ Thu, 05 Apr 2018 09:39:04: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:39:04: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:39:05: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:39:05: 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 09:39:05: Process for pairing-model is terminated! cat: SRX3433227.20_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 `SRX3433227.20_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 `SRX3433227.20_*.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 `SRX3433227.20_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 BigWig に変換しました。