Job ID = 10608969 sra ファイルのダウンロード中... Completed: 2630287K bytes transferred in 301 seconds (71418K 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 20839355 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2741968/SRR5453802.sra Written 20839355 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: 00:23:17 20839355 reads; of these: 20839355 (100.00%) were paired; of these: 4089231 (19.62%) aligned concordantly 0 times 14204726 (68.16%) aligned concordantly exactly 1 time 2545398 (12.21%) aligned concordantly >1 times ---- 4089231 pairs aligned concordantly 0 times; of these: 814289 (19.91%) aligned discordantly 1 time ---- 3274942 pairs aligned 0 times concordantly or discordantly; of these: 6549884 mates make up the pairs; of these: 5443184 (83.10%) aligned 0 times 635724 (9.71%) aligned exactly 1 time 470976 (7.19%) aligned >1 times 86.94% overall alignment rate Time searching: 00:23:17 Overall time: 00:23:17 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 16 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] 5553165 / 17457483 = 0.3181 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 23:34:24: # Command line: callpeak -t SRX2741968.bam -f BAM -g 12100000 -n SRX2741968.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2741968.20 # format = BAM # ChIP-seq file = ['SRX2741968.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 23:34:24: #1 read tag files... INFO @ Thu, 03 May 2018 23:34:24: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:34:24: # Command line: callpeak -t SRX2741968.bam -f BAM -g 12100000 -n SRX2741968.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2741968.10 # format = BAM # ChIP-seq file = ['SRX2741968.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 23:34:24: #1 read tag files... INFO @ Thu, 03 May 2018 23:34:24: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:34:24: # Command line: callpeak -t SRX2741968.bam -f BAM -g 12100000 -n SRX2741968.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2741968.05 # format = BAM # ChIP-seq file = ['SRX2741968.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 23:34:24: #1 read tag files... INFO @ Thu, 03 May 2018 23:34:24: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:34:32: 1000000 INFO @ Thu, 03 May 2018 23:34:32: 1000000 INFO @ Thu, 03 May 2018 23:34:32: 1000000 INFO @ Thu, 03 May 2018 23:34:39: 2000000 INFO @ Thu, 03 May 2018 23:34:39: 2000000 INFO @ Thu, 03 May 2018 23:34:40: 2000000 INFO @ Thu, 03 May 2018 23:34:47: 3000000 INFO @ Thu, 03 May 2018 23:34:47: 3000000 INFO @ Thu, 03 May 2018 23:34:47: 3000000 INFO @ Thu, 03 May 2018 23:34:54: 4000000 INFO @ Thu, 03 May 2018 23:34:54: 4000000 INFO @ Thu, 03 May 2018 23:34:55: 4000000 INFO @ Thu, 03 May 2018 23:35:01: 5000000 INFO @ Thu, 03 May 2018 23:35:02: 5000000 INFO @ Thu, 03 May 2018 23:35:03: 5000000 INFO @ Thu, 03 May 2018 23:35:08: 6000000 INFO @ Thu, 03 May 2018 23:35:10: 6000000 INFO @ Thu, 03 May 2018 23:35:11: 6000000 INFO @ Thu, 03 May 2018 23:35:15: 7000000 INFO @ Thu, 03 May 2018 23:35:17: 7000000 INFO @ Thu, 03 May 2018 23:35:18: 7000000 INFO @ Thu, 03 May 2018 23:35:23: 8000000 INFO @ Thu, 03 May 2018 23:35:24: 8000000 INFO @ Thu, 03 May 2018 23:35:26: 8000000 INFO @ Thu, 03 May 2018 23:35:30: 9000000 INFO @ Thu, 03 May 2018 23:35:32: 9000000 INFO @ Thu, 03 May 2018 23:35:34: 9000000 INFO @ Thu, 03 May 2018 23:35:37: 10000000 INFO @ Thu, 03 May 2018 23:35:40: 10000000 INFO @ Thu, 03 May 2018 23:35:42: 10000000 INFO @ Thu, 03 May 2018 23:35:44: 11000000 INFO @ Thu, 03 May 2018 23:35:47: 11000000 INFO @ Thu, 03 May 2018 23:35:50: 11000000 INFO @ Thu, 03 May 2018 23:35:51: 12000000 INFO @ Thu, 03 May 2018 23:35:55: 12000000 INFO @ Thu, 03 May 2018 23:35:58: 12000000 INFO @ Thu, 03 May 2018 23:35:58: 13000000 INFO @ Thu, 03 May 2018 23:36:02: 13000000 INFO @ Thu, 03 May 2018 23:36:05: 14000000 INFO @ Thu, 03 May 2018 23:36:06: 13000000 INFO @ Thu, 03 May 2018 23:36:10: 14000000 INFO @ Thu, 03 May 2018 23:36:12: 15000000 INFO @ Thu, 03 May 2018 23:36:14: 14000000 INFO @ Thu, 03 May 2018 23:36:18: 15000000 INFO @ Thu, 03 May 2018 23:36:19: 16000000 INFO @ Thu, 03 May 2018 23:36:22: 15000000 INFO @ Thu, 03 May 2018 23:36:26: 16000000 INFO @ Thu, 03 May 2018 23:36:26: 17000000 INFO @ Thu, 03 May 2018 23:36:30: 16000000 INFO @ Thu, 03 May 2018 23:36:33: 18000000 INFO @ Thu, 03 May 2018 23:36:33: 17000000 INFO @ Thu, 03 May 2018 23:36:38: 17000000 INFO @ Thu, 03 May 2018 23:36:40: 19000000 INFO @ Thu, 03 May 2018 23:36:41: 18000000 INFO @ Thu, 03 May 2018 23:36:46: 18000000 INFO @ Thu, 03 May 2018 23:36:47: 20000000 INFO @ Thu, 03 May 2018 23:36:49: 19000000 INFO @ Thu, 03 May 2018 23:36:54: 19000000 INFO @ Thu, 03 May 2018 23:36:54: 21000000 INFO @ Thu, 03 May 2018 23:36:56: 20000000 INFO @ Thu, 03 May 2018 23:37:01: 22000000 INFO @ Thu, 03 May 2018 23:37:02: 20000000 INFO @ Thu, 03 May 2018 23:37:04: 21000000 INFO @ Thu, 03 May 2018 23:37:08: 23000000 INFO @ Thu, 03 May 2018 23:37:09: 21000000 INFO @ Thu, 03 May 2018 23:37:11: 22000000 INFO @ Thu, 03 May 2018 23:37:15: 24000000 INFO @ Thu, 03 May 2018 23:37:17: 22000000 INFO @ Thu, 03 May 2018 23:37:19: 23000000 INFO @ Thu, 03 May 2018 23:37:22: 25000000 INFO @ Thu, 03 May 2018 23:37:23: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 23:37:23: #1 tag size = 100 INFO @ Thu, 03 May 2018 23:37:23: #1 total tags in treatment: 11417017 INFO @ Thu, 03 May 2018 23:37:23: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:37:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 23:37:23: #1 tags after filtering in treatment: 8083701 INFO @ Thu, 03 May 2018 23:37:23: #1 Redundant rate of treatment: 0.29 INFO @ Thu, 03 May 2018 23:37:23: #1 finished! INFO @ Thu, 03 May 2018 23:37:23: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:37:23: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:37:24: #2 number of paired peaks: 0 WARNING @ Thu, 03 May 2018 23:37:24: 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, 03 May 2018 23:37:24: Process for pairing-model is terminated! cat: SRX2741968.10_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 `SRX2741968.10_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 `SRX2741968.10_*.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 `SRX2741968.10_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, 03 May 2018 23:37:25: 23000000 INFO @ Thu, 03 May 2018 23:37:27: 24000000 INFO @ Thu, 03 May 2018 23:37:33: 24000000 INFO @ Thu, 03 May 2018 23:37:34: 25000000 INFO @ Thu, 03 May 2018 23:37:35: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 23:37:35: #1 tag size = 100 INFO @ Thu, 03 May 2018 23:37:35: #1 total tags in treatment: 11417017 INFO @ Thu, 03 May 2018 23:37:35: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:37:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 23:37:35: #1 tags after filtering in treatment: 8083701 INFO @ Thu, 03 May 2018 23:37:35: #1 Redundant rate of treatment: 0.29 INFO @ Thu, 03 May 2018 23:37:35: #1 finished! INFO @ Thu, 03 May 2018 23:37:35: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:37:35: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:37:36: #2 number of paired peaks: 0 WARNING @ Thu, 03 May 2018 23:37:36: 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, 03 May 2018 23:37:36: Process for pairing-model is terminated! cat: SRX2741968.05_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 `SRX2741968.05_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 `SRX2741968.05_*.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 `SRX2741968.05_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, 03 May 2018 23:37:40: 25000000 INFO @ Thu, 03 May 2018 23:37:41: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 23:37:41: #1 tag size = 100 INFO @ Thu, 03 May 2018 23:37:41: #1 total tags in treatment: 11417017 INFO @ Thu, 03 May 2018 23:37:41: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:37:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 23:37:41: #1 tags after filtering in treatment: 8083701 INFO @ Thu, 03 May 2018 23:37:41: #1 Redundant rate of treatment: 0.29 INFO @ Thu, 03 May 2018 23:37:41: #1 finished! INFO @ Thu, 03 May 2018 23:37:41: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:37:41: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:37:42: #2 number of paired peaks: 0 WARNING @ Thu, 03 May 2018 23:37:42: 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 @ Thu, 03 May 2018 23:37:42: Process for pairing-model is terminated! cat: SRX2741968.20_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 `SRX2741968.20_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 `SRX2741968.20_*.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 `SRX2741968.20_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。