Job ID = 10536512 sra ファイルのダウンロード中... Completed: 1194368K bytes transferred in 29 seconds (328579K 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 31050668 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3671206/SRR6696958.sra Written 31050668 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: 00:23:24 31050668 reads; of these: 31050668 (100.00%) were paired; of these: 3337113 (10.75%) aligned concordantly 0 times 22280864 (71.76%) aligned concordantly exactly 1 time 5432691 (17.50%) aligned concordantly >1 times ---- 3337113 pairs aligned concordantly 0 times; of these: 343170 (10.28%) aligned discordantly 1 time ---- 2993943 pairs aligned 0 times concordantly or discordantly; of these: 5987886 mates make up the pairs; of these: 5552407 (92.73%) aligned 0 times 116898 (1.95%) aligned exactly 1 time 318581 (5.32%) aligned >1 times 91.06% overall alignment rate Time searching: 00:23:24 Overall time: 00:23:24 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] 8296480 / 27942900 = 0.2969 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 10:33:04: # Command line: callpeak -t SRX3671206.bam -f BAM -g 12100000 -n SRX3671206.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3671206.20 # format = BAM # ChIP-seq file = ['SRX3671206.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 10:33:04: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:33:04: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:33:04: # Command line: callpeak -t SRX3671206.bam -f BAM -g 12100000 -n SRX3671206.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3671206.10 # format = BAM # ChIP-seq file = ['SRX3671206.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 10:33:04: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:33:04: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:33:04: # Command line: callpeak -t SRX3671206.bam -f BAM -g 12100000 -n SRX3671206.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3671206.05 # format = BAM # ChIP-seq file = ['SRX3671206.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 10:33:04: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:33:04: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:33:10: 1000000 INFO @ Thu, 05 Apr 2018 10:33:10: 1000000 INFO @ Thu, 05 Apr 2018 10:33:10: 1000000 INFO @ Thu, 05 Apr 2018 10:33:16: 2000000 INFO @ Thu, 05 Apr 2018 10:33:16: 2000000 INFO @ Thu, 05 Apr 2018 10:33:16: 2000000 INFO @ Thu, 05 Apr 2018 10:33:22: 3000000 INFO @ Thu, 05 Apr 2018 10:33:22: 3000000 INFO @ Thu, 05 Apr 2018 10:33:22: 3000000 INFO @ Thu, 05 Apr 2018 10:33:27: 4000000 INFO @ Thu, 05 Apr 2018 10:33:28: 4000000 INFO @ Thu, 05 Apr 2018 10:33:28: 4000000 INFO @ Thu, 05 Apr 2018 10:33:33: 5000000 INFO @ Thu, 05 Apr 2018 10:33:34: 5000000 INFO @ Thu, 05 Apr 2018 10:33:34: 5000000 INFO @ Thu, 05 Apr 2018 10:33:39: 6000000 INFO @ Thu, 05 Apr 2018 10:33:40: 6000000 INFO @ Thu, 05 Apr 2018 10:33:40: 6000000 INFO @ Thu, 05 Apr 2018 10:33:45: 7000000 INFO @ Thu, 05 Apr 2018 10:33:46: 7000000 INFO @ Thu, 05 Apr 2018 10:33:46: 7000000 INFO @ Thu, 05 Apr 2018 10:33:50: 8000000 INFO @ Thu, 05 Apr 2018 10:33:52: 8000000 INFO @ Thu, 05 Apr 2018 10:33:52: 8000000 INFO @ Thu, 05 Apr 2018 10:33:56: 9000000 INFO @ Thu, 05 Apr 2018 10:33:58: 9000000 INFO @ Thu, 05 Apr 2018 10:33:58: 9000000 INFO @ Thu, 05 Apr 2018 10:34:02: 10000000 INFO @ Thu, 05 Apr 2018 10:34:03: 10000000 INFO @ Thu, 05 Apr 2018 10:34:03: 10000000 INFO @ Thu, 05 Apr 2018 10:34:08: 11000000 INFO @ Thu, 05 Apr 2018 10:34:09: 11000000 INFO @ Thu, 05 Apr 2018 10:34:09: 11000000 INFO @ Thu, 05 Apr 2018 10:34:14: 12000000 INFO @ Thu, 05 Apr 2018 10:34:15: 12000000 INFO @ Thu, 05 Apr 2018 10:34:15: 12000000 INFO @ Thu, 05 Apr 2018 10:34:19: 13000000 INFO @ Thu, 05 Apr 2018 10:34:21: 13000000 INFO @ Thu, 05 Apr 2018 10:34:21: 13000000 INFO @ Thu, 05 Apr 2018 10:34:25: 14000000 INFO @ Thu, 05 Apr 2018 10:34:27: 14000000 INFO @ Thu, 05 Apr 2018 10:34:27: 14000000 INFO @ Thu, 05 Apr 2018 10:34:31: 15000000 INFO @ Thu, 05 Apr 2018 10:34:33: 15000000 INFO @ Thu, 05 Apr 2018 10:34:33: 15000000 INFO @ Thu, 05 Apr 2018 10:34:37: 16000000 INFO @ Thu, 05 Apr 2018 10:34:39: 16000000 INFO @ Thu, 05 Apr 2018 10:34:39: 16000000 INFO @ Thu, 05 Apr 2018 10:34:42: 17000000 INFO @ Thu, 05 Apr 2018 10:34:45: 17000000 INFO @ Thu, 05 Apr 2018 10:34:45: 17000000 INFO @ Thu, 05 Apr 2018 10:34:48: 18000000 INFO @ Thu, 05 Apr 2018 10:34:51: 18000000 INFO @ Thu, 05 Apr 2018 10:34:51: 18000000 INFO @ Thu, 05 Apr 2018 10:34:54: 19000000 INFO @ Thu, 05 Apr 2018 10:34:57: 19000000 INFO @ Thu, 05 Apr 2018 10:34:57: 19000000 INFO @ Thu, 05 Apr 2018 10:35:00: 20000000 INFO @ Thu, 05 Apr 2018 10:35:03: 20000000 INFO @ Thu, 05 Apr 2018 10:35:03: 20000000 INFO @ Thu, 05 Apr 2018 10:35:05: 21000000 INFO @ Thu, 05 Apr 2018 10:35:09: 21000000 INFO @ Thu, 05 Apr 2018 10:35:09: 21000000 INFO @ Thu, 05 Apr 2018 10:35:11: 22000000 INFO @ Thu, 05 Apr 2018 10:35:15: 22000000 INFO @ Thu, 05 Apr 2018 10:35:15: 22000000 INFO @ Thu, 05 Apr 2018 10:35:17: 23000000 INFO @ Thu, 05 Apr 2018 10:35:21: 23000000 INFO @ Thu, 05 Apr 2018 10:35:21: 23000000 INFO @ Thu, 05 Apr 2018 10:35:23: 24000000 INFO @ Thu, 05 Apr 2018 10:35:26: 24000000 INFO @ Thu, 05 Apr 2018 10:35:26: 24000000 INFO @ Thu, 05 Apr 2018 10:35:28: 25000000 INFO @ Thu, 05 Apr 2018 10:35:32: 25000000 INFO @ Thu, 05 Apr 2018 10:35:32: 25000000 INFO @ Thu, 05 Apr 2018 10:35:34: 26000000 INFO @ Thu, 05 Apr 2018 10:35:38: 26000000 INFO @ Thu, 05 Apr 2018 10:35:38: 26000000 INFO @ Thu, 05 Apr 2018 10:35:39: 27000000 INFO @ Thu, 05 Apr 2018 10:35:44: 27000000 INFO @ Thu, 05 Apr 2018 10:35:44: 27000000 INFO @ Thu, 05 Apr 2018 10:35:45: 28000000 INFO @ Thu, 05 Apr 2018 10:35:50: 28000000 INFO @ Thu, 05 Apr 2018 10:35:50: 28000000 INFO @ Thu, 05 Apr 2018 10:35:51: 29000000 INFO @ Thu, 05 Apr 2018 10:35:56: 29000000 INFO @ Thu, 05 Apr 2018 10:35:56: 29000000 INFO @ Thu, 05 Apr 2018 10:35:56: 30000000 INFO @ Thu, 05 Apr 2018 10:36:02: 30000000 INFO @ Thu, 05 Apr 2018 10:36:02: 30000000 INFO @ Thu, 05 Apr 2018 10:36:02: 31000000 INFO @ Thu, 05 Apr 2018 10:36:08: 32000000 INFO @ Thu, 05 Apr 2018 10:36:08: 31000000 INFO @ Thu, 05 Apr 2018 10:36:08: 31000000 INFO @ Thu, 05 Apr 2018 10:36:13: 33000000 INFO @ Thu, 05 Apr 2018 10:36:14: 32000000 INFO @ Thu, 05 Apr 2018 10:36:14: 32000000 INFO @ Thu, 05 Apr 2018 10:36:19: 34000000 INFO @ Thu, 05 Apr 2018 10:36:20: 33000000 INFO @ Thu, 05 Apr 2018 10:36:20: 33000000 INFO @ Thu, 05 Apr 2018 10:36:25: 35000000 INFO @ Thu, 05 Apr 2018 10:36:26: 34000000 INFO @ Thu, 05 Apr 2018 10:36:26: 34000000 INFO @ Thu, 05 Apr 2018 10:36:31: 36000000 INFO @ Thu, 05 Apr 2018 10:36:31: 35000000 INFO @ Thu, 05 Apr 2018 10:36:31: 35000000 INFO @ Thu, 05 Apr 2018 10:36:36: 37000000 INFO @ Thu, 05 Apr 2018 10:36:37: 36000000 INFO @ Thu, 05 Apr 2018 10:36:37: 36000000 INFO @ Thu, 05 Apr 2018 10:36:42: 38000000 INFO @ Thu, 05 Apr 2018 10:36:43: 37000000 INFO @ Thu, 05 Apr 2018 10:36:43: 37000000 INFO @ Thu, 05 Apr 2018 10:36:48: 39000000 INFO @ Thu, 05 Apr 2018 10:36:49: 38000000 INFO @ Thu, 05 Apr 2018 10:36:49: 38000000 INFO @ Thu, 05 Apr 2018 10:36:53: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:36:53: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:36:53: #1 total tags in treatment: 19514113 INFO @ Thu, 05 Apr 2018 10:36:53: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:36:53: #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 10:36:54: #1 tags after filtering in treatment: 7186433 INFO @ Thu, 05 Apr 2018 10:36:54: #1 Redundant rate of treatment: 0.63 INFO @ Thu, 05 Apr 2018 10:36:54: #1 finished! INFO @ Thu, 05 Apr 2018 10:36:54: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:36:54: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:36:54: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:36:54: 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 10:36:54: Process for pairing-model is terminated! cat: SRX3671206.20_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 `SRX3671206.20_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 `SRX3671206.20_*.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 `SRX3671206.20_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 10:36:55: 39000000 INFO @ Thu, 05 Apr 2018 10:36:55: 39000000 INFO @ Thu, 05 Apr 2018 10:37:01: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:37:01: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:37:01: #1 total tags in treatment: 19514113 INFO @ Thu, 05 Apr 2018 10:37:01: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:37:01: #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 10:37:01: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:37:01: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:37:01: #1 total tags in treatment: 19514113 INFO @ Thu, 05 Apr 2018 10:37:01: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:37:01: #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 10:37:01: #1 tags after filtering in treatment: 7186433 INFO @ Thu, 05 Apr 2018 10:37:01: #1 Redundant rate of treatment: 0.63 INFO @ Thu, 05 Apr 2018 10:37:01: #1 finished! INFO @ Thu, 05 Apr 2018 10:37:01: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:37:01: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:37:01: #1 tags after filtering in treatment: 7186433 INFO @ Thu, 05 Apr 2018 10:37:01: #1 Redundant rate of treatment: 0.63 INFO @ Thu, 05 Apr 2018 10:37:01: #1 finished! INFO @ Thu, 05 Apr 2018 10:37:01: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:37:01: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:37:02: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:37:02: 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 10:37:02: Process for pairing-model is terminated! cat: SRX3671206.10_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 `SRX3671206.10_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 `SRX3671206.10_*.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 `SRX3671206.10_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 10:37:02: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:37:02: 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 10:37:02: Process for pairing-model is terminated! cat: SRX3671206.05_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 `SRX3671206.05_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 `SRX3671206.05_*.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 `SRX3671206.05_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。