Job ID = 10536510 sra ファイルのダウンロード中... Completed: 1144985K bytes transferred in 28 seconds (332831K 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 31954715 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3671204/SRR6696956.sra Written 31954715 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: 00:23:49 31954715 reads; of these: 31954715 (100.00%) were paired; of these: 3261028 (10.21%) aligned concordantly 0 times 25256700 (79.04%) aligned concordantly exactly 1 time 3436987 (10.76%) aligned concordantly >1 times ---- 3261028 pairs aligned concordantly 0 times; of these: 91051 (2.79%) aligned discordantly 1 time ---- 3169977 pairs aligned 0 times concordantly or discordantly; of these: 6339954 mates make up the pairs; of these: 6156411 (97.10%) aligned 0 times 124840 (1.97%) aligned exactly 1 time 58703 (0.93%) aligned >1 times 90.37% overall alignment rate Time searching: 00:23:49 Overall time: 00:23:49 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] 9995329 / 28750583 = 0.3477 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 10:32:36: # Command line: callpeak -t SRX3671204.bam -f BAM -g 12100000 -n SRX3671204.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3671204.10 # format = BAM # ChIP-seq file = ['SRX3671204.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 10:32:36: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:32:36: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:32:36: # Command line: callpeak -t SRX3671204.bam -f BAM -g 12100000 -n SRX3671204.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3671204.05 # format = BAM # ChIP-seq file = ['SRX3671204.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 10:32:36: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:32:36: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:32:36: # Command line: callpeak -t SRX3671204.bam -f BAM -g 12100000 -n SRX3671204.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3671204.20 # format = BAM # ChIP-seq file = ['SRX3671204.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 10:32:36: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:32:36: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:32:43: 1000000 INFO @ Thu, 05 Apr 2018 10:32:44: 1000000 INFO @ Thu, 05 Apr 2018 10:32:44: 1000000 INFO @ Thu, 05 Apr 2018 10:32:50: 2000000 INFO @ Thu, 05 Apr 2018 10:32:51: 2000000 INFO @ Thu, 05 Apr 2018 10:32:51: 2000000 INFO @ Thu, 05 Apr 2018 10:32:57: 3000000 INFO @ Thu, 05 Apr 2018 10:32:59: 3000000 INFO @ Thu, 05 Apr 2018 10:32:59: 3000000 INFO @ Thu, 05 Apr 2018 10:33:04: 4000000 INFO @ Thu, 05 Apr 2018 10:33:06: 4000000 INFO @ Thu, 05 Apr 2018 10:33:06: 4000000 INFO @ Thu, 05 Apr 2018 10:33:11: 5000000 INFO @ Thu, 05 Apr 2018 10:33:14: 5000000 INFO @ Thu, 05 Apr 2018 10:33:14: 5000000 INFO @ Thu, 05 Apr 2018 10:33:18: 6000000 INFO @ Thu, 05 Apr 2018 10:33:22: 6000000 INFO @ Thu, 05 Apr 2018 10:33:22: 6000000 INFO @ Thu, 05 Apr 2018 10:33:26: 7000000 INFO @ Thu, 05 Apr 2018 10:33:30: 7000000 INFO @ Thu, 05 Apr 2018 10:33:30: 7000000 INFO @ Thu, 05 Apr 2018 10:33:35: 8000000 INFO @ Thu, 05 Apr 2018 10:33:39: 8000000 INFO @ Thu, 05 Apr 2018 10:33:39: 8000000 INFO @ Thu, 05 Apr 2018 10:33:44: 9000000 INFO @ Thu, 05 Apr 2018 10:33:47: 9000000 INFO @ Thu, 05 Apr 2018 10:33:47: 9000000 INFO @ Thu, 05 Apr 2018 10:33:52: 10000000 INFO @ Thu, 05 Apr 2018 10:33:56: 10000000 INFO @ Thu, 05 Apr 2018 10:33:56: 10000000 INFO @ Thu, 05 Apr 2018 10:34:01: 11000000 INFO @ Thu, 05 Apr 2018 10:34:04: 11000000 INFO @ Thu, 05 Apr 2018 10:34:04: 11000000 INFO @ Thu, 05 Apr 2018 10:34:10: 12000000 INFO @ Thu, 05 Apr 2018 10:34:13: 12000000 INFO @ Thu, 05 Apr 2018 10:34:13: 12000000 INFO @ Thu, 05 Apr 2018 10:34:18: 13000000 INFO @ Thu, 05 Apr 2018 10:34:21: 13000000 INFO @ Thu, 05 Apr 2018 10:34:21: 13000000 INFO @ Thu, 05 Apr 2018 10:34:27: 14000000 INFO @ Thu, 05 Apr 2018 10:34:29: 14000000 INFO @ Thu, 05 Apr 2018 10:34:29: 14000000 INFO @ Thu, 05 Apr 2018 10:34:35: 15000000 INFO @ Thu, 05 Apr 2018 10:34:38: 15000000 INFO @ Thu, 05 Apr 2018 10:34:38: 15000000 INFO @ Thu, 05 Apr 2018 10:34:44: 16000000 INFO @ Thu, 05 Apr 2018 10:34:46: 16000000 INFO @ Thu, 05 Apr 2018 10:34:46: 16000000 INFO @ Thu, 05 Apr 2018 10:34:53: 17000000 INFO @ Thu, 05 Apr 2018 10:34:55: 17000000 INFO @ Thu, 05 Apr 2018 10:34:55: 17000000 INFO @ Thu, 05 Apr 2018 10:35:02: 18000000 INFO @ Thu, 05 Apr 2018 10:35:03: 18000000 INFO @ Thu, 05 Apr 2018 10:35:03: 18000000 INFO @ Thu, 05 Apr 2018 10:35:10: 19000000 INFO @ Thu, 05 Apr 2018 10:35:12: 19000000 INFO @ Thu, 05 Apr 2018 10:35:12: 19000000 INFO @ Thu, 05 Apr 2018 10:35:19: 20000000 INFO @ Thu, 05 Apr 2018 10:35:20: 20000000 INFO @ Thu, 05 Apr 2018 10:35:20: 20000000 INFO @ Thu, 05 Apr 2018 10:35:28: 21000000 INFO @ Thu, 05 Apr 2018 10:35:29: 21000000 INFO @ Thu, 05 Apr 2018 10:35:29: 21000000 INFO @ Thu, 05 Apr 2018 10:35:36: 22000000 INFO @ Thu, 05 Apr 2018 10:35:37: 22000000 INFO @ Thu, 05 Apr 2018 10:35:37: 22000000 INFO @ Thu, 05 Apr 2018 10:35:45: 23000000 INFO @ Thu, 05 Apr 2018 10:35:45: 23000000 INFO @ Thu, 05 Apr 2018 10:35:45: 23000000 INFO @ Thu, 05 Apr 2018 10:35:53: 24000000 INFO @ Thu, 05 Apr 2018 10:35:54: 24000000 INFO @ Thu, 05 Apr 2018 10:35:54: 24000000 INFO @ Thu, 05 Apr 2018 10:36:02: 25000000 INFO @ Thu, 05 Apr 2018 10:36:02: 25000000 INFO @ Thu, 05 Apr 2018 10:36:02: 25000000 INFO @ Thu, 05 Apr 2018 10:36:10: 26000000 INFO @ Thu, 05 Apr 2018 10:36:10: 26000000 INFO @ Thu, 05 Apr 2018 10:36:10: 26000000 INFO @ Thu, 05 Apr 2018 10:36:19: 27000000 INFO @ Thu, 05 Apr 2018 10:36:19: 27000000 INFO @ Thu, 05 Apr 2018 10:36:19: 27000000 INFO @ Thu, 05 Apr 2018 10:36:27: 28000000 INFO @ Thu, 05 Apr 2018 10:36:28: 28000000 INFO @ Thu, 05 Apr 2018 10:36:28: 28000000 INFO @ Thu, 05 Apr 2018 10:36:36: 29000000 INFO @ Thu, 05 Apr 2018 10:36:36: 29000000 INFO @ Thu, 05 Apr 2018 10:36:36: 29000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 05 Apr 2018 10:36:44: 30000000 INFO @ Thu, 05 Apr 2018 10:36:45: 30000000 INFO @ Thu, 05 Apr 2018 10:36:45: 30000000 INFO @ Thu, 05 Apr 2018 10:36:53: 31000000 INFO @ Thu, 05 Apr 2018 10:36:53: 31000000 INFO @ Thu, 05 Apr 2018 10:36:53: 31000000 BigWig に変換しました。 INFO @ Thu, 05 Apr 2018 10:37:01: 32000000 INFO @ Thu, 05 Apr 2018 10:37:01: 32000000 INFO @ Thu, 05 Apr 2018 10:37:01: 32000000 INFO @ Thu, 05 Apr 2018 10:37:09: 33000000 INFO @ Thu, 05 Apr 2018 10:37:10: 33000000 INFO @ Thu, 05 Apr 2018 10:37:10: 33000000 INFO @ Thu, 05 Apr 2018 10:37:18: 34000000 INFO @ Thu, 05 Apr 2018 10:37:19: 34000000 INFO @ Thu, 05 Apr 2018 10:37:19: 34000000 INFO @ Thu, 05 Apr 2018 10:37:25: 35000000 INFO @ Thu, 05 Apr 2018 10:37:25: 35000000 INFO @ Thu, 05 Apr 2018 10:37:26: 35000000 INFO @ Thu, 05 Apr 2018 10:37:31: 36000000 INFO @ Thu, 05 Apr 2018 10:37:31: 36000000 INFO @ Thu, 05 Apr 2018 10:37:32: 36000000 INFO @ Thu, 05 Apr 2018 10:37:37: 37000000 INFO @ Thu, 05 Apr 2018 10:37:37: 37000000 INFO @ Thu, 05 Apr 2018 10:37:37: 37000000 INFO @ Thu, 05 Apr 2018 10:37:42: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:37:42: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:37:42: #1 total tags in treatment: 18720608 INFO @ Thu, 05 Apr 2018 10:37:42: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:37:42: #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 10:37:42: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:37:42: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:37:42: #1 total tags in treatment: 18720608 INFO @ Thu, 05 Apr 2018 10:37:42: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:37:42: #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 10:37:42: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:37:42: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:37:42: #1 total tags in treatment: 18720608 INFO @ Thu, 05 Apr 2018 10:37:42: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:37:42: #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 10:37:42: #1 tags after filtering in treatment: 6843005 INFO @ Thu, 05 Apr 2018 10:37:42: #1 Redundant rate of treatment: 0.63 INFO @ Thu, 05 Apr 2018 10:37:42: #1 finished! INFO @ Thu, 05 Apr 2018 10:37:42: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:37:42: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:37:43: #1 tags after filtering in treatment: 6843005 INFO @ Thu, 05 Apr 2018 10:37:43: #1 Redundant rate of treatment: 0.63 INFO @ Thu, 05 Apr 2018 10:37:43: #1 finished! INFO @ Thu, 05 Apr 2018 10:37:43: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:37:43: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:37:43: #1 tags after filtering in treatment: 6843005 INFO @ Thu, 05 Apr 2018 10:37:43: #1 Redundant rate of treatment: 0.63 INFO @ Thu, 05 Apr 2018 10:37:43: #1 finished! INFO @ Thu, 05 Apr 2018 10:37:43: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:37:43: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:37:43: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:37:43: 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 10:37:43: Process for pairing-model is terminated! cat: SRX3671204.20_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 `SRX3671204.20_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 `SRX3671204.20_*.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 `SRX3671204.20_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 10:37:43: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:37:43: 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 10:37:43: Process for pairing-model is terminated! INFO @ Thu, 05 Apr 2018 10:37:43: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:37:43: 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 10:37:43: Process for pairing-model is terminated! cat: SRX3671204.05_peaks.narrowPeak: そのようなファイルやディレクトリはありません cat: SRX3671204.10_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 `SRX3671204.05_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 `SRX3671204.05_*.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 `SRX3671204.05_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 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3671204.10_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 `SRX3671204.10_*.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 `SRX3671204.10_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