Job ID = 10536370 sra ファイルのダウンロード中... Completed: 1396634K bytes transferred in 22 seconds (502880K 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 33132349 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3433231/SRR6333872.sra Written 33132349 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: 00:32:12 33132349 reads; of these: 33132349 (100.00%) were paired; of these: 3704017 (11.18%) aligned concordantly 0 times 22863551 (69.01%) aligned concordantly exactly 1 time 6564781 (19.81%) aligned concordantly >1 times ---- 3704017 pairs aligned concordantly 0 times; of these: 33741 (0.91%) aligned discordantly 1 time ---- 3670276 pairs aligned 0 times concordantly or discordantly; of these: 7340552 mates make up the pairs; of these: 6901490 (94.02%) aligned 0 times 266964 (3.64%) aligned exactly 1 time 172098 (2.34%) aligned >1 times 89.58% overall alignment rate Time searching: 00:32:12 Overall time: 00:32:12 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] 9964981 / 29445651 = 0.3384 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 09:51:46: # Command line: callpeak -t SRX3433231.bam -f BAM -g 12100000 -n SRX3433231.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3433231.20 # format = BAM # ChIP-seq file = ['SRX3433231.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 09:51:46: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:51:46: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:51:46: # Command line: callpeak -t SRX3433231.bam -f BAM -g 12100000 -n SRX3433231.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3433231.05 # format = BAM # ChIP-seq file = ['SRX3433231.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 09:51:46: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:51:46: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:51:46: # Command line: callpeak -t SRX3433231.bam -f BAM -g 12100000 -n SRX3433231.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3433231.10 # format = BAM # ChIP-seq file = ['SRX3433231.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 09:51:46: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:51:46: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:51:52: 1000000 INFO @ Thu, 05 Apr 2018 09:51:52: 1000000 INFO @ Thu, 05 Apr 2018 09:51:52: 1000000 INFO @ Thu, 05 Apr 2018 09:51:58: 2000000 INFO @ Thu, 05 Apr 2018 09:51:58: 2000000 INFO @ Thu, 05 Apr 2018 09:51:58: 2000000 INFO @ Thu, 05 Apr 2018 09:52:04: 3000000 INFO @ Thu, 05 Apr 2018 09:52:05: 3000000 INFO @ Thu, 05 Apr 2018 09:52:05: 3000000 INFO @ Thu, 05 Apr 2018 09:52:10: 4000000 INFO @ Thu, 05 Apr 2018 09:52:11: 4000000 INFO @ Thu, 05 Apr 2018 09:52:11: 4000000 INFO @ Thu, 05 Apr 2018 09:52:16: 5000000 INFO @ Thu, 05 Apr 2018 09:52:17: 5000000 INFO @ Thu, 05 Apr 2018 09:52:18: 5000000 INFO @ Thu, 05 Apr 2018 09:52:22: 6000000 INFO @ Thu, 05 Apr 2018 09:52:24: 6000000 INFO @ Thu, 05 Apr 2018 09:52:24: 6000000 INFO @ Thu, 05 Apr 2018 09:52:29: 7000000 INFO @ Thu, 05 Apr 2018 09:52:30: 7000000 INFO @ Thu, 05 Apr 2018 09:52:30: 7000000 INFO @ Thu, 05 Apr 2018 09:52:35: 8000000 INFO @ Thu, 05 Apr 2018 09:52:36: 8000000 INFO @ Thu, 05 Apr 2018 09:52:37: 8000000 INFO @ Thu, 05 Apr 2018 09:52:41: 9000000 INFO @ Thu, 05 Apr 2018 09:52:43: 9000000 INFO @ Thu, 05 Apr 2018 09:52:43: 9000000 INFO @ Thu, 05 Apr 2018 09:52:48: 10000000 INFO @ Thu, 05 Apr 2018 09:52:49: 10000000 INFO @ Thu, 05 Apr 2018 09:52:50: 10000000 INFO @ Thu, 05 Apr 2018 09:52:54: 11000000 INFO @ Thu, 05 Apr 2018 09:52:56: 11000000 INFO @ Thu, 05 Apr 2018 09:52:56: 11000000 INFO @ Thu, 05 Apr 2018 09:53:00: 12000000 INFO @ Thu, 05 Apr 2018 09:53:02: 12000000 INFO @ Thu, 05 Apr 2018 09:53:03: 12000000 INFO @ Thu, 05 Apr 2018 09:53:06: 13000000 INFO @ Thu, 05 Apr 2018 09:53:09: 13000000 INFO @ Thu, 05 Apr 2018 09:53:10: 13000000 INFO @ Thu, 05 Apr 2018 09:53:12: 14000000 INFO @ Thu, 05 Apr 2018 09:53:16: 14000000 INFO @ Thu, 05 Apr 2018 09:53:17: 14000000 INFO @ Thu, 05 Apr 2018 09:53:19: 15000000 INFO @ Thu, 05 Apr 2018 09:53:23: 15000000 INFO @ Thu, 05 Apr 2018 09:53:24: 15000000 INFO @ Thu, 05 Apr 2018 09:53:25: 16000000 INFO @ Thu, 05 Apr 2018 09:53:30: 16000000 INFO @ Thu, 05 Apr 2018 09:53:31: 16000000 INFO @ Thu, 05 Apr 2018 09:53:31: 17000000 INFO @ Thu, 05 Apr 2018 09:53:37: 17000000 INFO @ Thu, 05 Apr 2018 09:53:37: 18000000 INFO @ Thu, 05 Apr 2018 09:53:38: 17000000 INFO @ Thu, 05 Apr 2018 09:53:43: 18000000 INFO @ Thu, 05 Apr 2018 09:53:43: 19000000 INFO @ Thu, 05 Apr 2018 09:53:45: 18000000 INFO @ Thu, 05 Apr 2018 09:53:50: 20000000 INFO @ Thu, 05 Apr 2018 09:53:50: 19000000 INFO @ Thu, 05 Apr 2018 09:53:51: 19000000 INFO @ Thu, 05 Apr 2018 09:53:56: 21000000 INFO @ Thu, 05 Apr 2018 09:53:57: 20000000 INFO @ Thu, 05 Apr 2018 09:53:58: 20000000 INFO @ Thu, 05 Apr 2018 09:54:02: 22000000 INFO @ Thu, 05 Apr 2018 09:54:03: 21000000 INFO @ Thu, 05 Apr 2018 09:54:04: 21000000 INFO @ Thu, 05 Apr 2018 09:54:09: 23000000 INFO @ Thu, 05 Apr 2018 09:54:10: 22000000 INFO @ Thu, 05 Apr 2018 09:54:11: 22000000 INFO @ Thu, 05 Apr 2018 09:54:15: 24000000 INFO @ Thu, 05 Apr 2018 09:54:16: 23000000 INFO @ Thu, 05 Apr 2018 09:54:18: 23000000 INFO @ Thu, 05 Apr 2018 09:54:21: 25000000 INFO @ Thu, 05 Apr 2018 09:54:23: 24000000 INFO @ Thu, 05 Apr 2018 09:54:24: 24000000 INFO @ Thu, 05 Apr 2018 09:54:27: 26000000 INFO @ Thu, 05 Apr 2018 09:54:29: 25000000 INFO @ Thu, 05 Apr 2018 09:54:31: 25000000 INFO @ Thu, 05 Apr 2018 09:54:34: 27000000 INFO @ Thu, 05 Apr 2018 09:54:35: 26000000 INFO @ Thu, 05 Apr 2018 09:54:37: 26000000 INFO @ Thu, 05 Apr 2018 09:54:40: 28000000 INFO @ Thu, 05 Apr 2018 09:54:42: 27000000 INFO @ Thu, 05 Apr 2018 09:54:44: 27000000 INFO @ Thu, 05 Apr 2018 09:54:46: 29000000 INFO @ Thu, 05 Apr 2018 09:54:48: 28000000 INFO @ Thu, 05 Apr 2018 09:54:50: 28000000 INFO @ Thu, 05 Apr 2018 09:54:52: 30000000 INFO @ Thu, 05 Apr 2018 09:54:55: 29000000 INFO @ Thu, 05 Apr 2018 09:54:57: 29000000 INFO @ Thu, 05 Apr 2018 09:54:59: 31000000 INFO @ Thu, 05 Apr 2018 09:55:01: 30000000 INFO @ Thu, 05 Apr 2018 09:55:03: 30000000 INFO @ Thu, 05 Apr 2018 09:55:05: 32000000 INFO @ Thu, 05 Apr 2018 09:55:08: 31000000 INFO @ Thu, 05 Apr 2018 09:55:10: 31000000 INFO @ Thu, 05 Apr 2018 09:55:11: 33000000 INFO @ Thu, 05 Apr 2018 09:55:14: 32000000 INFO @ Thu, 05 Apr 2018 09:55:16: 32000000 INFO @ Thu, 05 Apr 2018 09:55:18: 34000000 INFO @ Thu, 05 Apr 2018 09:55:21: 33000000 INFO @ Thu, 05 Apr 2018 09:55:23: 33000000 INFO @ Thu, 05 Apr 2018 09:55:24: 35000000 INFO @ Thu, 05 Apr 2018 09:55:27: 34000000 INFO @ Thu, 05 Apr 2018 09:55:30: 34000000 INFO @ Thu, 05 Apr 2018 09:55:30: 36000000 INFO @ Thu, 05 Apr 2018 09:55:34: 35000000 INFO @ Thu, 05 Apr 2018 09:55:36: 35000000 INFO @ Thu, 05 Apr 2018 09:55:37: 37000000 INFO @ Thu, 05 Apr 2018 09:55:40: 36000000 INFO @ Thu, 05 Apr 2018 09:55:43: 36000000 INFO @ Thu, 05 Apr 2018 09:55:43: 38000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 05 Apr 2018 09:55:47: 37000000 INFO @ Thu, 05 Apr 2018 09:55:49: 39000000 INFO @ Thu, 05 Apr 2018 09:55:49: 37000000 INFO @ Thu, 05 Apr 2018 09:55:52: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:55:52: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:55:52: #1 total tags in treatment: 19468562 INFO @ Thu, 05 Apr 2018 09:55:52: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:55:52: #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 09:55:52: #1 tags after filtering in treatment: 9671144 INFO @ Thu, 05 Apr 2018 09:55:52: #1 Redundant rate of treatment: 0.50 INFO @ Thu, 05 Apr 2018 09:55:52: #1 finished! INFO @ Thu, 05 Apr 2018 09:55:52: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:55:52: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:55:53: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:55:53: 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 09:55:53: Process for pairing-model is terminated! cat: SRX3433231.20_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 `SRX3433231.20_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 `SRX3433231.20_*.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 `SRX3433231.20_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 09:55:53: 38000000 INFO @ Thu, 05 Apr 2018 09:55:56: 38000000 INFO @ Thu, 05 Apr 2018 09:56:00: 39000000 INFO @ Thu, 05 Apr 2018 09:56:02: 39000000 INFO @ Thu, 05 Apr 2018 09:56:03: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:56:03: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:56:03: #1 total tags in treatment: 19468562 INFO @ Thu, 05 Apr 2018 09:56:03: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:56:03: #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 09:56:03: #1 tags after filtering in treatment: 9671144 INFO @ Thu, 05 Apr 2018 09:56:03: #1 Redundant rate of treatment: 0.50 INFO @ Thu, 05 Apr 2018 09:56:03: #1 finished! INFO @ Thu, 05 Apr 2018 09:56:03: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:56:03: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:56:04: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:56:04: 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 09:56:04: Process for pairing-model is terminated! cat: SRX3433231.05_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 `SRX3433231.05_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 `SRX3433231.05_*.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 `SRX3433231.05_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 BigWig に変換しました。 INFO @ Thu, 05 Apr 2018 09:56:05: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:56:05: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:56:05: #1 total tags in treatment: 19468562 INFO @ Thu, 05 Apr 2018 09:56:05: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:56:05: #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 09:56:05: #1 tags after filtering in treatment: 9671144 INFO @ Thu, 05 Apr 2018 09:56:05: #1 Redundant rate of treatment: 0.50 INFO @ Thu, 05 Apr 2018 09:56:05: #1 finished! INFO @ Thu, 05 Apr 2018 09:56:05: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:56:05: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:56:06: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:56:06: 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 09:56:06: Process for pairing-model is terminated! cat: SRX3433231.10_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 `SRX3433231.10_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 `SRX3433231.10_*.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 `SRX3433231.10_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