Job ID = 10608967 sra ファイルのダウンロード中... Completed: 3576467K bytes transferred in 440 seconds (66473K 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 29947119 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2741966/SRR5453800.sra Written 29947119 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: 00:36:19 29947119 reads; of these: 29947119 (100.00%) were paired; of these: 5139691 (17.16%) aligned concordantly 0 times 21452528 (71.63%) aligned concordantly exactly 1 time 3354900 (11.20%) aligned concordantly >1 times ---- 5139691 pairs aligned concordantly 0 times; of these: 1390143 (27.05%) aligned discordantly 1 time ---- 3749548 pairs aligned 0 times concordantly or discordantly; of these: 7499096 mates make up the pairs; of these: 5429308 (72.40%) aligned 0 times 1443436 (19.25%) aligned exactly 1 time 626352 (8.35%) aligned >1 times 90.94% overall alignment rate Time searching: 00:36:19 Overall time: 00:36:19 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 24 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] 8134260 / 26020765 = 0.3126 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 23:55:21: # Command line: callpeak -t SRX2741966.bam -f BAM -g 12100000 -n SRX2741966.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2741966.05 # format = BAM # ChIP-seq file = ['SRX2741966.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 23:55:21: #1 read tag files... INFO @ Thu, 03 May 2018 23:55:21: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:55:21: # Command line: callpeak -t SRX2741966.bam -f BAM -g 12100000 -n SRX2741966.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2741966.10 # format = BAM # ChIP-seq file = ['SRX2741966.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 23:55:21: #1 read tag files... INFO @ Thu, 03 May 2018 23:55:21: # Command line: callpeak -t SRX2741966.bam -f BAM -g 12100000 -n SRX2741966.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2741966.20 # format = BAM # ChIP-seq file = ['SRX2741966.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 23:55:21: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:55:21: #1 read tag files... INFO @ Thu, 03 May 2018 23:55:21: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:55:29: 1000000 INFO @ Thu, 03 May 2018 23:55:30: 1000000 INFO @ Thu, 03 May 2018 23:55:30: 1000000 INFO @ Thu, 03 May 2018 23:55:37: 2000000 INFO @ Thu, 03 May 2018 23:55:38: 2000000 INFO @ Thu, 03 May 2018 23:55:38: 2000000 INFO @ Thu, 03 May 2018 23:55:45: 3000000 INFO @ Thu, 03 May 2018 23:55:46: 3000000 INFO @ Thu, 03 May 2018 23:55:46: 3000000 INFO @ Thu, 03 May 2018 23:55:53: 4000000 INFO @ Thu, 03 May 2018 23:55:55: 4000000 INFO @ Thu, 03 May 2018 23:55:55: 4000000 INFO @ Thu, 03 May 2018 23:56:01: 5000000 INFO @ Thu, 03 May 2018 23:56:03: 5000000 INFO @ Thu, 03 May 2018 23:56:03: 5000000 INFO @ Thu, 03 May 2018 23:56:09: 6000000 INFO @ Thu, 03 May 2018 23:56:11: 6000000 INFO @ Thu, 03 May 2018 23:56:11: 6000000 INFO @ Thu, 03 May 2018 23:56:17: 7000000 INFO @ Thu, 03 May 2018 23:56:20: 7000000 INFO @ Thu, 03 May 2018 23:56:20: 7000000 INFO @ Thu, 03 May 2018 23:56:25: 8000000 INFO @ Thu, 03 May 2018 23:56:28: 8000000 INFO @ Thu, 03 May 2018 23:56:28: 8000000 INFO @ Thu, 03 May 2018 23:56:33: 9000000 INFO @ Thu, 03 May 2018 23:56:36: 9000000 INFO @ Thu, 03 May 2018 23:56:36: 9000000 INFO @ Thu, 03 May 2018 23:56:41: 10000000 INFO @ Thu, 03 May 2018 23:56:44: 10000000 INFO @ Thu, 03 May 2018 23:56:44: 10000000 INFO @ Thu, 03 May 2018 23:56:49: 11000000 INFO @ Thu, 03 May 2018 23:56:53: 11000000 INFO @ Thu, 03 May 2018 23:56:53: 11000000 INFO @ Thu, 03 May 2018 23:56:57: 12000000 INFO @ Thu, 03 May 2018 23:57:01: 12000000 INFO @ Thu, 03 May 2018 23:57:01: 12000000 INFO @ Thu, 03 May 2018 23:57:05: 13000000 INFO @ Thu, 03 May 2018 23:57:09: 13000000 INFO @ Thu, 03 May 2018 23:57:09: 13000000 INFO @ Thu, 03 May 2018 23:57:13: 14000000 INFO @ Thu, 03 May 2018 23:57:17: 14000000 INFO @ Thu, 03 May 2018 23:57:17: 14000000 INFO @ Thu, 03 May 2018 23:57:21: 15000000 INFO @ Thu, 03 May 2018 23:57:25: 15000000 INFO @ Thu, 03 May 2018 23:57:25: 15000000 INFO @ Thu, 03 May 2018 23:57:29: 16000000 INFO @ Thu, 03 May 2018 23:57:34: 16000000 INFO @ Thu, 03 May 2018 23:57:34: 16000000 INFO @ Thu, 03 May 2018 23:57:36: 17000000 INFO @ Thu, 03 May 2018 23:57:42: 17000000 INFO @ Thu, 03 May 2018 23:57:42: 17000000 INFO @ Thu, 03 May 2018 23:57:44: 18000000 INFO @ Thu, 03 May 2018 23:57:50: 18000000 INFO @ Thu, 03 May 2018 23:57:50: 18000000 INFO @ Thu, 03 May 2018 23:57:53: 19000000 INFO @ Thu, 03 May 2018 23:57:58: 19000000 INFO @ Thu, 03 May 2018 23:57:59: 19000000 INFO @ Thu, 03 May 2018 23:58:01: 20000000 INFO @ Thu, 03 May 2018 23:58:06: 20000000 INFO @ Thu, 03 May 2018 23:58:07: 20000000 INFO @ Thu, 03 May 2018 23:58:09: 21000000 INFO @ Thu, 03 May 2018 23:58:14: 21000000 INFO @ Thu, 03 May 2018 23:58:15: 21000000 INFO @ Thu, 03 May 2018 23:58:18: 22000000 INFO @ Thu, 03 May 2018 23:58:23: 22000000 INFO @ Thu, 03 May 2018 23:58:24: 22000000 INFO @ Thu, 03 May 2018 23:58:26: 23000000 INFO @ Thu, 03 May 2018 23:58:31: 23000000 INFO @ Thu, 03 May 2018 23:58:32: 23000000 INFO @ Thu, 03 May 2018 23:58:34: 24000000 INFO @ Thu, 03 May 2018 23:58:39: 24000000 INFO @ Thu, 03 May 2018 23:58:40: 24000000 INFO @ Thu, 03 May 2018 23:58:42: 25000000 INFO @ Thu, 03 May 2018 23:58:47: 25000000 INFO @ Thu, 03 May 2018 23:58:48: 25000000 INFO @ Thu, 03 May 2018 23:58:50: 26000000 INFO @ Thu, 03 May 2018 23:58:55: 26000000 INFO @ Thu, 03 May 2018 23:58:57: 26000000 INFO @ Thu, 03 May 2018 23:58:58: 27000000 INFO @ Thu, 03 May 2018 23:59:04: 27000000 INFO @ Thu, 03 May 2018 23:59:06: 27000000 INFO @ Thu, 03 May 2018 23:59:06: 28000000 INFO @ Thu, 03 May 2018 23:59:12: 28000000 INFO @ Thu, 03 May 2018 23:59:14: 29000000 INFO @ Thu, 03 May 2018 23:59:14: 28000000 INFO @ Thu, 03 May 2018 23:59:21: 29000000 INFO @ Thu, 03 May 2018 23:59:22: 30000000 INFO @ Thu, 03 May 2018 23:59:23: 29000000 INFO @ Thu, 03 May 2018 23:59:30: 30000000 INFO @ Thu, 03 May 2018 23:59:30: 31000000 INFO @ Thu, 03 May 2018 23:59:31: 30000000 INFO @ Thu, 03 May 2018 23:59:38: 32000000 INFO @ Thu, 03 May 2018 23:59:38: 31000000 INFO @ Thu, 03 May 2018 23:59:39: 31000000 INFO @ Thu, 03 May 2018 23:59:46: 33000000 INFO @ Thu, 03 May 2018 23:59:46: 32000000 INFO @ Thu, 03 May 2018 23:59:48: 32000000 INFO @ Thu, 03 May 2018 23:59:54: 34000000 INFO @ Thu, 03 May 2018 23:59:55: 33000000 INFO @ Thu, 03 May 2018 23:59:56: 33000000 INFO @ Fri, 04 May 2018 00:00:02: 35000000 INFO @ Fri, 04 May 2018 00:00:03: 34000000 INFO @ Fri, 04 May 2018 00:00:04: 34000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 04 May 2018 00:00:10: 36000000 INFO @ Fri, 04 May 2018 00:00:12: 35000000 INFO @ Fri, 04 May 2018 00:00:13: 35000000 INFO @ Fri, 04 May 2018 00:00:18: 37000000 INFO @ Fri, 04 May 2018 00:00:21: 36000000 INFO @ Fri, 04 May 2018 00:00:21: 36000000 INFO @ Fri, 04 May 2018 00:00:26: 38000000 BigWig に変換しました。 INFO @ Fri, 04 May 2018 00:00:27: #1 tag size is determined as 100 bps INFO @ Fri, 04 May 2018 00:00:27: #1 tag size = 100 INFO @ Fri, 04 May 2018 00:00:27: #1 total tags in treatment: 16944693 INFO @ Fri, 04 May 2018 00:00:27: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 00:00:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 00:00:28: #1 tags after filtering in treatment: 10882804 INFO @ Fri, 04 May 2018 00:00:28: #1 Redundant rate of treatment: 0.36 INFO @ Fri, 04 May 2018 00:00:28: #1 finished! INFO @ Fri, 04 May 2018 00:00:28: #2 Build Peak Model... INFO @ Fri, 04 May 2018 00:00:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 00:00:28: #2 number of paired peaks: 0 WARNING @ Fri, 04 May 2018 00:00:28: 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 @ Fri, 04 May 2018 00:00:28: Process for pairing-model is terminated! cat: SRX2741966.10_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2741966.10_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 `SRX2741966.10_*.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 `SRX2741966.10_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 @ Fri, 04 May 2018 00:00:29: 37000000 INFO @ Fri, 04 May 2018 00:00:30: 37000000 INFO @ Fri, 04 May 2018 00:00:38: 38000000 INFO @ Fri, 04 May 2018 00:00:39: 38000000 INFO @ Fri, 04 May 2018 00:00:40: #1 tag size is determined as 100 bps INFO @ Fri, 04 May 2018 00:00:40: #1 tag size = 100 INFO @ Fri, 04 May 2018 00:00:40: #1 total tags in treatment: 16944693 INFO @ Fri, 04 May 2018 00:00:40: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 00:00:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 00:00:40: #1 tags after filtering in treatment: 10882804 INFO @ Fri, 04 May 2018 00:00:40: #1 Redundant rate of treatment: 0.36 INFO @ Fri, 04 May 2018 00:00:40: #1 finished! INFO @ Fri, 04 May 2018 00:00:40: #2 Build Peak Model... INFO @ Fri, 04 May 2018 00:00:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 00:00:40: #1 tag size is determined as 100 bps INFO @ Fri, 04 May 2018 00:00:40: #1 tag size = 100 INFO @ Fri, 04 May 2018 00:00:40: #1 total tags in treatment: 16944693 INFO @ Fri, 04 May 2018 00:00:40: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 00:00:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 00:00:41: #2 number of paired peaks: 0 WARNING @ Fri, 04 May 2018 00:00:41: 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 @ Fri, 04 May 2018 00:00:41: Process for pairing-model is terminated! cat: SRX2741966.20_peaks.narrowPeak: そのようなファイルやディレクトリはありません INFO @ Fri, 04 May 2018 00:00:41: #1 tags after filtering in treatment: 10882804 INFO @ Fri, 04 May 2018 00:00:41: #1 Redundant rate of treatment: 0.36 INFO @ Fri, 04 May 2018 00:00:41: #1 finished! INFO @ Fri, 04 May 2018 00:00:41: #2 Build Peak Model... INFO @ Fri, 04 May 2018 00:00:41: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2741966.20_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 `SRX2741966.20_*.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 `SRX2741966.20_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 @ Fri, 04 May 2018 00:00:42: #2 number of paired peaks: 0 WARNING @ Fri, 04 May 2018 00:00:42: 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 @ Fri, 04 May 2018 00:00:42: Process for pairing-model is terminated! cat: SRX2741966.05_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 `SRX2741966.05_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 `SRX2741966.05_*.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 `SRX2741966.05_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