Job ID = 9732083 sra ファイルのダウンロード中... Completed: 374862K bytes transferred in 13 seconds (229662K 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 16108326 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2675873/SRR5380649.sra Written 16108326 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: 00:06:58 16108326 reads; of these: 16108326 (100.00%) were paired; of these: 3573534 (22.18%) aligned concordantly 0 times 11325928 (70.31%) aligned concordantly exactly 1 time 1208864 (7.50%) aligned concordantly >1 times ---- 3573534 pairs aligned concordantly 0 times; of these: 574193 (16.07%) aligned discordantly 1 time ---- 2999341 pairs aligned 0 times concordantly or discordantly; of these: 5998682 mates make up the pairs; of these: 5385913 (89.78%) aligned 0 times 424682 (7.08%) aligned exactly 1 time 188087 (3.14%) aligned >1 times 83.28% overall alignment rate Time searching: 00:06:58 Overall time: 00:06:59 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 8 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] 2155035 / 12900196 = 0.1671 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 @ Sun, 03 Sep 2017 19:37:49: # Command line: callpeak -t SRX2675873.bam -f BAM -g 12100000 -n SRX2675873.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2675873.05 # format = BAM # ChIP-seq file = ['SRX2675873.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 @ Sun, 03 Sep 2017 19:37:49: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:37:49: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:37:49: # Command line: callpeak -t SRX2675873.bam -f BAM -g 12100000 -n SRX2675873.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2675873.20 # format = BAM # ChIP-seq file = ['SRX2675873.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 @ Sun, 03 Sep 2017 19:37:49: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:37:49: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:37:49: # Command line: callpeak -t SRX2675873.bam -f BAM -g 12100000 -n SRX2675873.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2675873.10 # format = BAM # ChIP-seq file = ['SRX2675873.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 @ Sun, 03 Sep 2017 19:37:49: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:37:49: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:37:53: 1000000 INFO @ Sun, 03 Sep 2017 19:37:53: 1000000 INFO @ Sun, 03 Sep 2017 19:37:53: 1000000 INFO @ Sun, 03 Sep 2017 19:37:58: 2000000 INFO @ Sun, 03 Sep 2017 19:37:58: 2000000 INFO @ Sun, 03 Sep 2017 19:37:59: 2000000 INFO @ Sun, 03 Sep 2017 19:38:03: 3000000 INFO @ Sun, 03 Sep 2017 19:38:03: 3000000 INFO @ Sun, 03 Sep 2017 19:38:04: 3000000 INFO @ Sun, 03 Sep 2017 19:38:08: 4000000 INFO @ Sun, 03 Sep 2017 19:38:08: 4000000 INFO @ Sun, 03 Sep 2017 19:38:09: 4000000 INFO @ Sun, 03 Sep 2017 19:38:13: 5000000 INFO @ Sun, 03 Sep 2017 19:38:13: 5000000 INFO @ Sun, 03 Sep 2017 19:38:14: 5000000 INFO @ Sun, 03 Sep 2017 19:38:18: 6000000 INFO @ Sun, 03 Sep 2017 19:38:18: 6000000 INFO @ Sun, 03 Sep 2017 19:38:19: 6000000 INFO @ Sun, 03 Sep 2017 19:38:22: 7000000 INFO @ Sun, 03 Sep 2017 19:38:23: 7000000 INFO @ Sun, 03 Sep 2017 19:38:24: 7000000 INFO @ Sun, 03 Sep 2017 19:38:27: 8000000 INFO @ Sun, 03 Sep 2017 19:38:28: 8000000 INFO @ Sun, 03 Sep 2017 19:38:30: 8000000 INFO @ Sun, 03 Sep 2017 19:38:32: 9000000 INFO @ Sun, 03 Sep 2017 19:38:33: 9000000 INFO @ Sun, 03 Sep 2017 19:38:35: 9000000 INFO @ Sun, 03 Sep 2017 19:38:37: 10000000 INFO @ Sun, 03 Sep 2017 19:38:38: 10000000 INFO @ Sun, 03 Sep 2017 19:38:40: 10000000 INFO @ Sun, 03 Sep 2017 19:38:41: 11000000 INFO @ Sun, 03 Sep 2017 19:38:43: 11000000 INFO @ Sun, 03 Sep 2017 19:38:45: 11000000 INFO @ Sun, 03 Sep 2017 19:38:46: 12000000 INFO @ Sun, 03 Sep 2017 19:38:48: 12000000 INFO @ Sun, 03 Sep 2017 19:38:50: 12000000 INFO @ Sun, 03 Sep 2017 19:38:51: 13000000 INFO @ Sun, 03 Sep 2017 19:38:53: 13000000 INFO @ Sun, 03 Sep 2017 19:38:55: 13000000 INFO @ Sun, 03 Sep 2017 19:38:56: 14000000 INFO @ Sun, 03 Sep 2017 19:38:58: 14000000 INFO @ Sun, 03 Sep 2017 19:39:00: 14000000 INFO @ Sun, 03 Sep 2017 19:39:00: 15000000 INFO @ Sun, 03 Sep 2017 19:39:03: 15000000 INFO @ Sun, 03 Sep 2017 19:39:05: 15000000 INFO @ Sun, 03 Sep 2017 19:39:05: 16000000 INFO @ Sun, 03 Sep 2017 19:39:08: 16000000 INFO @ Sun, 03 Sep 2017 19:39:10: 17000000 INFO @ Sun, 03 Sep 2017 19:39:10: 16000000 INFO @ Sun, 03 Sep 2017 19:39:13: 17000000 INFO @ Sun, 03 Sep 2017 19:39:15: 18000000 INFO @ Sun, 03 Sep 2017 19:39:15: 17000000 INFO @ Sun, 03 Sep 2017 19:39:18: 18000000 INFO @ Sun, 03 Sep 2017 19:39:19: 19000000 INFO @ Sun, 03 Sep 2017 19:39:20: 18000000 INFO @ Sun, 03 Sep 2017 19:39:23: 19000000 INFO @ Sun, 03 Sep 2017 19:39:24: 20000000 INFO @ Sun, 03 Sep 2017 19:39:25: 19000000 INFO @ Sun, 03 Sep 2017 19:39:28: 20000000 INFO @ Sun, 03 Sep 2017 19:39:29: 21000000 INFO @ Sun, 03 Sep 2017 19:39:31: 20000000 INFO @ Sun, 03 Sep 2017 19:39:33: 21000000 INFO @ Sun, 03 Sep 2017 19:39:34: 22000000 INFO @ Sun, 03 Sep 2017 19:39:36: 21000000 INFO @ Sun, 03 Sep 2017 19:39:36: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:39:36: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:39:36: #1 total tags in treatment: 10385545 INFO @ Sun, 03 Sep 2017 19:39:36: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:39:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 19:39:36: #1 tags after filtering in treatment: 4714463 INFO @ Sun, 03 Sep 2017 19:39:36: #1 Redundant rate of treatment: 0.55 INFO @ Sun, 03 Sep 2017 19:39:36: #1 finished! INFO @ Sun, 03 Sep 2017 19:39:36: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:39:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:39:37: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:39:37: 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 @ Sun, 03 Sep 2017 19:39:37: Process for pairing-model is terminated! cat: SRX2675873.05_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): 8 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675873.05_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 `SRX2675873.05_*.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 `SRX2675873.05_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 @ Sun, 03 Sep 2017 19:39:37: 22000000 INFO @ Sun, 03 Sep 2017 19:39:40: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:39:40: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:39:40: #1 total tags in treatment: 10385545 INFO @ Sun, 03 Sep 2017 19:39:40: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:39:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 19:39:40: #1 tags after filtering in treatment: 4714463 INFO @ Sun, 03 Sep 2017 19:39:40: #1 Redundant rate of treatment: 0.55 INFO @ Sun, 03 Sep 2017 19:39:40: #1 finished! INFO @ Sun, 03 Sep 2017 19:39:40: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:39:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:39:41: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:39:41: 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 @ Sun, 03 Sep 2017 19:39:41: Process for pairing-model is terminated! cat: SRX2675873.10_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): 9 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675873.10_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 `SRX2675873.10_*.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 `SRX2675873.10_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 @ Sun, 03 Sep 2017 19:39:41: 22000000 INFO @ Sun, 03 Sep 2017 19:39:43: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:39:43: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:39:43: #1 total tags in treatment: 10385545 INFO @ Sun, 03 Sep 2017 19:39:43: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:39:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 19:39:44: #1 tags after filtering in treatment: 4714463 INFO @ Sun, 03 Sep 2017 19:39:44: #1 Redundant rate of treatment: 0.55 INFO @ Sun, 03 Sep 2017 19:39:44: #1 finished! INFO @ Sun, 03 Sep 2017 19:39:44: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:39:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:39:44: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:39:44: 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 @ Sun, 03 Sep 2017 19:39:44: Process for pairing-model is terminated! cat: SRX2675873.20_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): 11 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675873.20_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 `SRX2675873.20_*.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 `SRX2675873.20_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。