Job ID = 10536523 sra ファイルのダウンロード中... Completed: 1164043K bytes transferred in 27 seconds (343522K 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 32354102 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3671215/SRR6696967.sra Written 32354102 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: 00:21:33 32354102 reads; of these: 32354102 (100.00%) were paired; of these: 5679071 (17.55%) aligned concordantly 0 times 23085556 (71.35%) aligned concordantly exactly 1 time 3589475 (11.09%) aligned concordantly >1 times ---- 5679071 pairs aligned concordantly 0 times; of these: 165508 (2.91%) aligned discordantly 1 time ---- 5513563 pairs aligned 0 times concordantly or discordantly; of these: 11027126 mates make up the pairs; of these: 10820662 (98.13%) aligned 0 times 109196 (0.99%) aligned exactly 1 time 97268 (0.88%) aligned >1 times 83.28% overall alignment rate Time searching: 00:21:33 Overall time: 00:21:33 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] 8587475 / 26783759 = 0.3206 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 10:34:21: # Command line: callpeak -t SRX3671215.bam -f BAM -g 12100000 -n SRX3671215.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3671215.10 # format = BAM # ChIP-seq file = ['SRX3671215.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 10:34:21: # Command line: callpeak -t SRX3671215.bam -f BAM -g 12100000 -n SRX3671215.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3671215.20 # format = BAM # ChIP-seq file = ['SRX3671215.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 10:34:21: # Command line: callpeak -t SRX3671215.bam -f BAM -g 12100000 -n SRX3671215.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3671215.05 # format = BAM # ChIP-seq file = ['SRX3671215.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 10:34:21: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:34:21: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:34:21: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:34:21: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:34:21: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:34:21: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:34:27: 1000000 INFO @ Thu, 05 Apr 2018 10:34:27: 1000000 INFO @ Thu, 05 Apr 2018 10:34:27: 1000000 INFO @ Thu, 05 Apr 2018 10:34:33: 2000000 INFO @ Thu, 05 Apr 2018 10:34:33: 2000000 INFO @ Thu, 05 Apr 2018 10:34:33: 2000000 INFO @ Thu, 05 Apr 2018 10:34:38: 3000000 INFO @ Thu, 05 Apr 2018 10:34:39: 3000000 INFO @ Thu, 05 Apr 2018 10:34:39: 3000000 INFO @ Thu, 05 Apr 2018 10:34:44: 4000000 INFO @ Thu, 05 Apr 2018 10:34:46: 4000000 INFO @ Thu, 05 Apr 2018 10:34:46: 4000000 INFO @ Thu, 05 Apr 2018 10:34:50: 5000000 INFO @ Thu, 05 Apr 2018 10:34:52: 5000000 INFO @ Thu, 05 Apr 2018 10:34:52: 5000000 INFO @ Thu, 05 Apr 2018 10:34:56: 6000000 INFO @ Thu, 05 Apr 2018 10:34:58: 6000000 INFO @ Thu, 05 Apr 2018 10:34:58: 6000000 INFO @ Thu, 05 Apr 2018 10:35:02: 7000000 INFO @ Thu, 05 Apr 2018 10:35:04: 7000000 INFO @ Thu, 05 Apr 2018 10:35:04: 7000000 INFO @ Thu, 05 Apr 2018 10:35:08: 8000000 INFO @ Thu, 05 Apr 2018 10:35:10: 8000000 INFO @ Thu, 05 Apr 2018 10:35:10: 8000000 INFO @ Thu, 05 Apr 2018 10:35:13: 9000000 INFO @ Thu, 05 Apr 2018 10:35:17: 9000000 INFO @ Thu, 05 Apr 2018 10:35:17: 9000000 INFO @ Thu, 05 Apr 2018 10:35:19: 10000000 INFO @ Thu, 05 Apr 2018 10:35:23: 10000000 INFO @ Thu, 05 Apr 2018 10:35:23: 10000000 INFO @ Thu, 05 Apr 2018 10:35:25: 11000000 INFO @ Thu, 05 Apr 2018 10:35:29: 11000000 INFO @ Thu, 05 Apr 2018 10:35:29: 11000000 INFO @ Thu, 05 Apr 2018 10:35:31: 12000000 INFO @ Thu, 05 Apr 2018 10:35:35: 12000000 INFO @ Thu, 05 Apr 2018 10:35:35: 12000000 INFO @ Thu, 05 Apr 2018 10:35:37: 13000000 INFO @ Thu, 05 Apr 2018 10:35:41: 13000000 INFO @ Thu, 05 Apr 2018 10:35:41: 13000000 INFO @ Thu, 05 Apr 2018 10:35:42: 14000000 INFO @ Thu, 05 Apr 2018 10:35:48: 14000000 INFO @ Thu, 05 Apr 2018 10:35:48: 14000000 INFO @ Thu, 05 Apr 2018 10:35:48: 15000000 INFO @ Thu, 05 Apr 2018 10:35:54: 15000000 INFO @ Thu, 05 Apr 2018 10:35:54: 15000000 INFO @ Thu, 05 Apr 2018 10:35:54: 16000000 INFO @ Thu, 05 Apr 2018 10:36:00: 17000000 INFO @ Thu, 05 Apr 2018 10:36:00: 16000000 INFO @ Thu, 05 Apr 2018 10:36:00: 16000000 INFO @ Thu, 05 Apr 2018 10:36:06: 18000000 INFO @ Thu, 05 Apr 2018 10:36:06: 17000000 INFO @ Thu, 05 Apr 2018 10:36:06: 17000000 INFO @ Thu, 05 Apr 2018 10:36:12: 19000000 INFO @ Thu, 05 Apr 2018 10:36:13: 18000000 INFO @ Thu, 05 Apr 2018 10:36:13: 18000000 INFO @ Thu, 05 Apr 2018 10:36:17: 20000000 INFO @ Thu, 05 Apr 2018 10:36:19: 19000000 INFO @ Thu, 05 Apr 2018 10:36:19: 19000000 INFO @ Thu, 05 Apr 2018 10:36:23: 21000000 INFO @ Thu, 05 Apr 2018 10:36:25: 20000000 INFO @ Thu, 05 Apr 2018 10:36:25: 20000000 INFO @ Thu, 05 Apr 2018 10:36:29: 22000000 INFO @ Thu, 05 Apr 2018 10:36:31: 21000000 INFO @ Thu, 05 Apr 2018 10:36:31: 21000000 INFO @ Thu, 05 Apr 2018 10:36:35: 23000000 INFO @ Thu, 05 Apr 2018 10:36:37: 22000000 INFO @ Thu, 05 Apr 2018 10:36:37: 22000000 INFO @ Thu, 05 Apr 2018 10:36:40: 24000000 INFO @ Thu, 05 Apr 2018 10:36:44: 23000000 INFO @ Thu, 05 Apr 2018 10:36:44: 23000000 INFO @ Thu, 05 Apr 2018 10:36:46: 25000000 INFO @ Thu, 05 Apr 2018 10:36:50: 24000000 INFO @ Thu, 05 Apr 2018 10:36:50: 24000000 INFO @ Thu, 05 Apr 2018 10:36:52: 26000000 INFO @ Thu, 05 Apr 2018 10:36:56: 25000000 INFO @ Thu, 05 Apr 2018 10:36:56: 25000000 INFO @ Thu, 05 Apr 2018 10:36:58: 27000000 INFO @ Thu, 05 Apr 2018 10:37:02: 26000000 INFO @ Thu, 05 Apr 2018 10:37:02: 26000000 INFO @ Thu, 05 Apr 2018 10:37:04: 28000000 INFO @ Thu, 05 Apr 2018 10:37:08: 27000000 INFO @ Thu, 05 Apr 2018 10:37:08: 27000000 INFO @ Thu, 05 Apr 2018 10:37:10: 29000000 INFO @ Thu, 05 Apr 2018 10:37:15: 28000000 INFO @ Thu, 05 Apr 2018 10:37:15: 28000000 INFO @ Thu, 05 Apr 2018 10:37:16: 30000000 INFO @ Thu, 05 Apr 2018 10:37:21: 29000000 INFO @ Thu, 05 Apr 2018 10:37:21: 29000000 INFO @ Thu, 05 Apr 2018 10:37:21: 31000000 INFO @ Thu, 05 Apr 2018 10:37:27: 30000000 INFO @ Thu, 05 Apr 2018 10:37:27: 30000000 INFO @ Thu, 05 Apr 2018 10:37:27: 32000000 INFO @ Thu, 05 Apr 2018 10:37:33: 33000000 INFO @ Thu, 05 Apr 2018 10:37:33: 31000000 INFO @ Thu, 05 Apr 2018 10:37:33: 31000000 INFO @ Thu, 05 Apr 2018 10:37:39: 34000000 INFO @ Thu, 05 Apr 2018 10:37:39: 32000000 INFO @ Thu, 05 Apr 2018 10:37:39: 32000000 INFO @ Thu, 05 Apr 2018 10:37:45: 35000000 INFO @ Thu, 05 Apr 2018 10:37:46: 33000000 INFO @ Thu, 05 Apr 2018 10:37:46: 33000000 INFO @ Thu, 05 Apr 2018 10:37:50: 36000000 INFO @ Thu, 05 Apr 2018 10:37:52: 34000000 INFO @ Thu, 05 Apr 2018 10:37:52: 34000000 INFO @ Thu, 05 Apr 2018 10:37:55: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:37:55: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:37:55: #1 total tags in treatment: 18136264 INFO @ Thu, 05 Apr 2018 10:37:55: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:37:55: #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 10:37:55: #1 tags after filtering in treatment: 6831161 INFO @ Thu, 05 Apr 2018 10:37:55: #1 Redundant rate of treatment: 0.62 INFO @ Thu, 05 Apr 2018 10:37:55: #1 finished! INFO @ Thu, 05 Apr 2018 10:37:55: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:37:55: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:37:55: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:37:55: 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 10:37:55: Process for pairing-model is terminated! cat: SRX3671215.20_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 `SRX3671215.20_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 `SRX3671215.20_*.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 `SRX3671215.20_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 10:37:58: 35000000 INFO @ Thu, 05 Apr 2018 10:37:58: 35000000 INFO @ Thu, 05 Apr 2018 10:38:04: 36000000 INFO @ Thu, 05 Apr 2018 10:38:04: 36000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 05 Apr 2018 10:38:09: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:38:09: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:38:09: #1 total tags in treatment: 18136264 INFO @ Thu, 05 Apr 2018 10:38:09: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:38:09: #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 10:38:09: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:38:09: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:38:09: #1 total tags in treatment: 18136264 INFO @ Thu, 05 Apr 2018 10:38:09: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:38:09: #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 10:38:09: #1 tags after filtering in treatment: 6831161 INFO @ Thu, 05 Apr 2018 10:38:09: #1 Redundant rate of treatment: 0.62 INFO @ Thu, 05 Apr 2018 10:38:09: #1 finished! INFO @ Thu, 05 Apr 2018 10:38:09: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:38:09: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:38:09: #1 tags after filtering in treatment: 6831161 INFO @ Thu, 05 Apr 2018 10:38:09: #1 Redundant rate of treatment: 0.62 INFO @ Thu, 05 Apr 2018 10:38:09: #1 finished! INFO @ Thu, 05 Apr 2018 10:38:09: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:38:09: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:38:10: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:38:10: 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 10:38:10: Process for pairing-model is terminated! INFO @ Thu, 05 Apr 2018 10:38:10: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:38:10: 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 10:38:10: Process for pairing-model is terminated! cat: SRX3671215.10_peaks.narrowPeak: そのようなファイルやディレクトリはありません cat: SRX3671215.05_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) pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3671215.10_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 `SRX3671215.10_*.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 `SRX3671215.10_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 rm: cannot remove `SRX3671215.05_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 `SRX3671215.05_*.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 `SRX3671215.05_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。