Job ID = 10536502 sra ファイルのダウンロード中... Completed: 1154068K bytes transferred in 37 seconds (250930K 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 29366840 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3671197/SRR6696949.sra Written 29366840 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: 00:20:49 29366840 reads; of these: 29366840 (100.00%) were paired; of these: 4658892 (15.86%) aligned concordantly 0 times 21273973 (72.44%) aligned concordantly exactly 1 time 3433975 (11.69%) aligned concordantly >1 times ---- 4658892 pairs aligned concordantly 0 times; of these: 101981 (2.19%) aligned discordantly 1 time ---- 4556911 pairs aligned 0 times concordantly or discordantly; of these: 9113822 mates make up the pairs; of these: 8918522 (97.86%) aligned 0 times 116852 (1.28%) aligned exactly 1 time 78448 (0.86%) aligned >1 times 84.82% overall alignment rate Time searching: 00:20:49 Overall time: 00:20:49 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] 7002597 / 24770968 = 0.2827 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 10:25:43: # Command line: callpeak -t SRX3671197.bam -f BAM -g 12100000 -n SRX3671197.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3671197.20 # format = BAM # ChIP-seq file = ['SRX3671197.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 10:25:43: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:25:43: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:25:43: # Command line: callpeak -t SRX3671197.bam -f BAM -g 12100000 -n SRX3671197.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3671197.05 # format = BAM # ChIP-seq file = ['SRX3671197.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 10:25:43: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:25:43: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:25:43: # Command line: callpeak -t SRX3671197.bam -f BAM -g 12100000 -n SRX3671197.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3671197.10 # format = BAM # ChIP-seq file = ['SRX3671197.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 10:25:43: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:25:43: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:25:49: 1000000 INFO @ Thu, 05 Apr 2018 10:25:50: 1000000 INFO @ Thu, 05 Apr 2018 10:25:50: 1000000 INFO @ Thu, 05 Apr 2018 10:25:55: 2000000 INFO @ Thu, 05 Apr 2018 10:25:57: 2000000 INFO @ Thu, 05 Apr 2018 10:25:57: 2000000 INFO @ Thu, 05 Apr 2018 10:26:01: 3000000 INFO @ Thu, 05 Apr 2018 10:26:04: 3000000 INFO @ Thu, 05 Apr 2018 10:26:04: 3000000 INFO @ Thu, 05 Apr 2018 10:26:07: 4000000 INFO @ Thu, 05 Apr 2018 10:26:11: 4000000 INFO @ Thu, 05 Apr 2018 10:26:11: 4000000 INFO @ Thu, 05 Apr 2018 10:26:13: 5000000 INFO @ Thu, 05 Apr 2018 10:26:18: 5000000 INFO @ Thu, 05 Apr 2018 10:26:18: 5000000 INFO @ Thu, 05 Apr 2018 10:26:19: 6000000 INFO @ Thu, 05 Apr 2018 10:26:24: 6000000 INFO @ Thu, 05 Apr 2018 10:26:25: 7000000 INFO @ Thu, 05 Apr 2018 10:26:26: 6000000 INFO @ Thu, 05 Apr 2018 10:26:30: 7000000 INFO @ Thu, 05 Apr 2018 10:26:32: 8000000 INFO @ Thu, 05 Apr 2018 10:26:33: 7000000 INFO @ Thu, 05 Apr 2018 10:26:35: 8000000 INFO @ Thu, 05 Apr 2018 10:26:38: 9000000 INFO @ Thu, 05 Apr 2018 10:26:40: 8000000 INFO @ Thu, 05 Apr 2018 10:26:42: 9000000 INFO @ Thu, 05 Apr 2018 10:26:45: 10000000 INFO @ Thu, 05 Apr 2018 10:26:47: 9000000 INFO @ Thu, 05 Apr 2018 10:26:48: 10000000 INFO @ Thu, 05 Apr 2018 10:26:51: 11000000 INFO @ Thu, 05 Apr 2018 10:26:54: 10000000 INFO @ Thu, 05 Apr 2018 10:26:54: 11000000 INFO @ Thu, 05 Apr 2018 10:26:57: 12000000 INFO @ Thu, 05 Apr 2018 10:27:00: 12000000 INFO @ Thu, 05 Apr 2018 10:27:01: 11000000 INFO @ Thu, 05 Apr 2018 10:27:03: 13000000 INFO @ Thu, 05 Apr 2018 10:27:06: 13000000 INFO @ Thu, 05 Apr 2018 10:27:08: 12000000 INFO @ Thu, 05 Apr 2018 10:27:10: 14000000 INFO @ Thu, 05 Apr 2018 10:27:14: 14000000 INFO @ Thu, 05 Apr 2018 10:27:16: 13000000 INFO @ Thu, 05 Apr 2018 10:27:17: 15000000 INFO @ Thu, 05 Apr 2018 10:27:22: 15000000 INFO @ Thu, 05 Apr 2018 10:27:23: 16000000 INFO @ Thu, 05 Apr 2018 10:27:25: 14000000 INFO @ Thu, 05 Apr 2018 10:27:30: 17000000 INFO @ Thu, 05 Apr 2018 10:27:31: 16000000 INFO @ Thu, 05 Apr 2018 10:27:33: 15000000 INFO @ Thu, 05 Apr 2018 10:27:37: 18000000 INFO @ Thu, 05 Apr 2018 10:27:39: 17000000 INFO @ Thu, 05 Apr 2018 10:27:42: 16000000 INFO @ Thu, 05 Apr 2018 10:27:44: 19000000 INFO @ Thu, 05 Apr 2018 10:27:47: 18000000 INFO @ Thu, 05 Apr 2018 10:27:50: 17000000 INFO @ Thu, 05 Apr 2018 10:27:50: 20000000 INFO @ Thu, 05 Apr 2018 10:27:55: 19000000 INFO @ Thu, 05 Apr 2018 10:27:57: 21000000 INFO @ Thu, 05 Apr 2018 10:27:58: 18000000 INFO @ Thu, 05 Apr 2018 10:28:04: 20000000 INFO @ Thu, 05 Apr 2018 10:28:04: 22000000 INFO @ Thu, 05 Apr 2018 10:28:07: 19000000 INFO @ Thu, 05 Apr 2018 10:28:11: 23000000 INFO @ Thu, 05 Apr 2018 10:28:12: 21000000 INFO @ Thu, 05 Apr 2018 10:28:15: 20000000 INFO @ Thu, 05 Apr 2018 10:28:17: 24000000 INFO @ Thu, 05 Apr 2018 10:28:20: 22000000 INFO @ Thu, 05 Apr 2018 10:28:24: 21000000 INFO @ Thu, 05 Apr 2018 10:28:24: 25000000 INFO @ Thu, 05 Apr 2018 10:28:28: 23000000 INFO @ Thu, 05 Apr 2018 10:28:31: 26000000 INFO @ Thu, 05 Apr 2018 10:28:32: 22000000 INFO @ Thu, 05 Apr 2018 10:28:37: 24000000 INFO @ Thu, 05 Apr 2018 10:28:38: 27000000 INFO @ Thu, 05 Apr 2018 10:28:41: 23000000 INFO @ Thu, 05 Apr 2018 10:28:45: 28000000 INFO @ Thu, 05 Apr 2018 10:28:45: 25000000 INFO @ Thu, 05 Apr 2018 10:28:49: 24000000 INFO @ Thu, 05 Apr 2018 10:28:51: 29000000 INFO @ Thu, 05 Apr 2018 10:28:53: 26000000 INFO @ Thu, 05 Apr 2018 10:28:58: 25000000 INFO @ Thu, 05 Apr 2018 10:28:58: 30000000 INFO @ Thu, 05 Apr 2018 10:29:02: 27000000 INFO @ Thu, 05 Apr 2018 10:29:05: 31000000 INFO @ Thu, 05 Apr 2018 10:29:06: 26000000 INFO @ Thu, 05 Apr 2018 10:29:10: 28000000 INFO @ Thu, 05 Apr 2018 10:29:12: 32000000 INFO @ Thu, 05 Apr 2018 10:29:15: 27000000 INFO @ Thu, 05 Apr 2018 10:29:18: 29000000 INFO @ Thu, 05 Apr 2018 10:29:18: 33000000 INFO @ Thu, 05 Apr 2018 10:29:23: 28000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 05 Apr 2018 10:29:25: 34000000 INFO @ Thu, 05 Apr 2018 10:29:26: 30000000 INFO @ Thu, 05 Apr 2018 10:29:32: 29000000 INFO @ Thu, 05 Apr 2018 10:29:32: 35000000 INFO @ Thu, 05 Apr 2018 10:29:35: 31000000 INFO @ Thu, 05 Apr 2018 10:29:38: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:29:38: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:29:38: #1 total tags in treatment: 17723594 INFO @ Thu, 05 Apr 2018 10:29:38: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:29:38: #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 10:29:38: #1 tags after filtering in treatment: 6766656 INFO @ Thu, 05 Apr 2018 10:29:38: #1 Redundant rate of treatment: 0.62 INFO @ Thu, 05 Apr 2018 10:29:38: #1 finished! INFO @ Thu, 05 Apr 2018 10:29:38: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:29:38: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:29:38: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:29:38: 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 10:29:38: Process for pairing-model is terminated! cat: SRX3671197.10_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 `SRX3671197.10_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 `SRX3671197.10_*.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 `SRX3671197.10_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 10:29:39: 30000000 INFO @ Thu, 05 Apr 2018 10:29:42: 32000000 BigWig に変換しました。 INFO @ Thu, 05 Apr 2018 10:29:47: 31000000 INFO @ Thu, 05 Apr 2018 10:29:49: 33000000 INFO @ Thu, 05 Apr 2018 10:29:54: 32000000 INFO @ Thu, 05 Apr 2018 10:29:56: 34000000 INFO @ Thu, 05 Apr 2018 10:30:02: 33000000 INFO @ Thu, 05 Apr 2018 10:30:03: 35000000 INFO @ Thu, 05 Apr 2018 10:30:09: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:30:09: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:30:09: #1 total tags in treatment: 17723594 INFO @ Thu, 05 Apr 2018 10:30:09: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:30:09: #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 10:30:09: 34000000 INFO @ Thu, 05 Apr 2018 10:30:09: #1 tags after filtering in treatment: 6766656 INFO @ Thu, 05 Apr 2018 10:30:09: #1 Redundant rate of treatment: 0.62 INFO @ Thu, 05 Apr 2018 10:30:09: #1 finished! INFO @ Thu, 05 Apr 2018 10:30:09: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:30:09: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:30:10: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:30:10: 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 10:30:10: Process for pairing-model is terminated! cat: SRX3671197.05_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 `SRX3671197.05_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 `SRX3671197.05_*.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 `SRX3671197.05_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 10:30:15: 35000000 INFO @ Thu, 05 Apr 2018 10:30:20: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:30:20: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:30:20: #1 total tags in treatment: 17723594 INFO @ Thu, 05 Apr 2018 10:30:20: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:30:20: #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 10:30:21: #1 tags after filtering in treatment: 6766656 INFO @ Thu, 05 Apr 2018 10:30:21: #1 Redundant rate of treatment: 0.62 INFO @ Thu, 05 Apr 2018 10:30:21: #1 finished! INFO @ Thu, 05 Apr 2018 10:30:21: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:30:21: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:30:21: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:30:21: 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 10:30:21: Process for pairing-model is terminated! cat: SRX3671197.20_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 `SRX3671197.20_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 `SRX3671197.20_*.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 `SRX3671197.20_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