Job ID = 10536526 sra ファイルのダウンロード中... Completed: 1407170K bytes transferred in 38 seconds (298662K 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 39780914 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3671218/SRR6696970.sra Written 39780914 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: 00:21:53 39780914 reads; of these: 39780914 (100.00%) were paired; of these: 15528464 (39.03%) aligned concordantly 0 times 20987103 (52.76%) aligned concordantly exactly 1 time 3265347 (8.21%) aligned concordantly >1 times ---- 15528464 pairs aligned concordantly 0 times; of these: 263035 (1.69%) aligned discordantly 1 time ---- 15265429 pairs aligned 0 times concordantly or discordantly; of these: 30530858 mates make up the pairs; of these: 30259874 (99.11%) aligned 0 times 125746 (0.41%) aligned exactly 1 time 145238 (0.48%) aligned >1 times 61.97% overall alignment rate Time searching: 00:21:53 Overall time: 00:21:53 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] 7056857 / 24436079 = 0.2888 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 10:38:01: # Command line: callpeak -t SRX3671218.bam -f BAM -g 12100000 -n SRX3671218.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3671218.10 # format = BAM # ChIP-seq file = ['SRX3671218.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 10:38:01: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:38:01: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:38:01: # Command line: callpeak -t SRX3671218.bam -f BAM -g 12100000 -n SRX3671218.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3671218.20 # format = BAM # ChIP-seq file = ['SRX3671218.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 10:38:01: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:38:01: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:38:01: # Command line: callpeak -t SRX3671218.bam -f BAM -g 12100000 -n SRX3671218.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3671218.05 # format = BAM # ChIP-seq file = ['SRX3671218.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 10:38:01: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:38:01: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:38:06: 1000000 INFO @ Thu, 05 Apr 2018 10:38:07: 1000000 INFO @ Thu, 05 Apr 2018 10:38:07: 1000000 INFO @ Thu, 05 Apr 2018 10:38:12: 2000000 INFO @ Thu, 05 Apr 2018 10:38:12: 2000000 INFO @ Thu, 05 Apr 2018 10:38:12: 2000000 INFO @ Thu, 05 Apr 2018 10:38:17: 3000000 INFO @ Thu, 05 Apr 2018 10:38:17: 3000000 INFO @ Thu, 05 Apr 2018 10:38:17: 3000000 INFO @ Thu, 05 Apr 2018 10:38:22: 4000000 INFO @ Thu, 05 Apr 2018 10:38:23: 4000000 INFO @ Thu, 05 Apr 2018 10:38:23: 4000000 INFO @ Thu, 05 Apr 2018 10:38:28: 5000000 INFO @ Thu, 05 Apr 2018 10:38:28: 5000000 INFO @ Thu, 05 Apr 2018 10:38:28: 5000000 INFO @ Thu, 05 Apr 2018 10:38:33: 6000000 INFO @ Thu, 05 Apr 2018 10:38:33: 6000000 INFO @ Thu, 05 Apr 2018 10:38:33: 6000000 INFO @ Thu, 05 Apr 2018 10:38:38: 7000000 INFO @ Thu, 05 Apr 2018 10:38:39: 7000000 INFO @ Thu, 05 Apr 2018 10:38:39: 7000000 INFO @ Thu, 05 Apr 2018 10:38:44: 8000000 INFO @ Thu, 05 Apr 2018 10:38:44: 8000000 INFO @ Thu, 05 Apr 2018 10:38:44: 8000000 INFO @ Thu, 05 Apr 2018 10:38:49: 9000000 INFO @ Thu, 05 Apr 2018 10:38:49: 9000000 INFO @ Thu, 05 Apr 2018 10:38:50: 9000000 INFO @ Thu, 05 Apr 2018 10:38:55: 10000000 INFO @ Thu, 05 Apr 2018 10:38:55: 10000000 INFO @ Thu, 05 Apr 2018 10:38:55: 10000000 INFO @ Thu, 05 Apr 2018 10:39:00: 11000000 INFO @ Thu, 05 Apr 2018 10:39:00: 11000000 INFO @ Thu, 05 Apr 2018 10:39:01: 11000000 INFO @ Thu, 05 Apr 2018 10:39:05: 12000000 INFO @ Thu, 05 Apr 2018 10:39:06: 12000000 INFO @ Thu, 05 Apr 2018 10:39:07: 12000000 INFO @ Thu, 05 Apr 2018 10:39:11: 13000000 INFO @ Thu, 05 Apr 2018 10:39:11: 13000000 INFO @ Thu, 05 Apr 2018 10:39:12: 13000000 INFO @ Thu, 05 Apr 2018 10:39:16: 14000000 INFO @ Thu, 05 Apr 2018 10:39:17: 14000000 INFO @ Thu, 05 Apr 2018 10:39:18: 14000000 INFO @ Thu, 05 Apr 2018 10:39:21: 15000000 INFO @ Thu, 05 Apr 2018 10:39:23: 15000000 INFO @ Thu, 05 Apr 2018 10:39:24: 15000000 INFO @ Thu, 05 Apr 2018 10:39:26: 16000000 INFO @ Thu, 05 Apr 2018 10:39:28: 16000000 INFO @ Thu, 05 Apr 2018 10:39:30: 16000000 INFO @ Thu, 05 Apr 2018 10:39:31: 17000000 INFO @ Thu, 05 Apr 2018 10:39:34: 17000000 INFO @ Thu, 05 Apr 2018 10:39:35: 17000000 INFO @ Thu, 05 Apr 2018 10:39:37: 18000000 INFO @ Thu, 05 Apr 2018 10:39:40: 18000000 INFO @ Thu, 05 Apr 2018 10:39:41: 18000000 INFO @ Thu, 05 Apr 2018 10:39:42: 19000000 INFO @ Thu, 05 Apr 2018 10:39:45: 19000000 INFO @ Thu, 05 Apr 2018 10:39:47: 19000000 INFO @ Thu, 05 Apr 2018 10:39:47: 20000000 INFO @ Thu, 05 Apr 2018 10:39:51: 20000000 INFO @ Thu, 05 Apr 2018 10:39:52: 21000000 INFO @ Thu, 05 Apr 2018 10:39:53: 20000000 INFO @ Thu, 05 Apr 2018 10:39:56: 21000000 INFO @ Thu, 05 Apr 2018 10:39:57: 22000000 INFO @ Thu, 05 Apr 2018 10:39:58: 21000000 INFO @ Thu, 05 Apr 2018 10:40:02: 22000000 INFO @ Thu, 05 Apr 2018 10:40:02: 23000000 INFO @ Thu, 05 Apr 2018 10:40:04: 22000000 INFO @ Thu, 05 Apr 2018 10:40:08: 24000000 INFO @ Thu, 05 Apr 2018 10:40:08: 23000000 INFO @ Thu, 05 Apr 2018 10:40:10: 23000000 INFO @ Thu, 05 Apr 2018 10:40:13: 24000000 INFO @ Thu, 05 Apr 2018 10:40:13: 25000000 INFO @ Thu, 05 Apr 2018 10:40:16: 24000000 INFO @ Thu, 05 Apr 2018 10:40:18: 25000000 INFO @ Thu, 05 Apr 2018 10:40:19: 26000000 INFO @ Thu, 05 Apr 2018 10:40:21: 25000000 INFO @ Thu, 05 Apr 2018 10:40:23: 26000000 INFO @ Thu, 05 Apr 2018 10:40:24: 27000000 INFO @ Thu, 05 Apr 2018 10:40:27: 26000000 INFO @ Thu, 05 Apr 2018 10:40:28: 27000000 INFO @ Thu, 05 Apr 2018 10:40:29: 28000000 INFO @ Thu, 05 Apr 2018 10:40:33: 27000000 INFO @ Thu, 05 Apr 2018 10:40:33: 28000000 INFO @ Thu, 05 Apr 2018 10:40:35: 29000000 INFO @ Thu, 05 Apr 2018 10:40:38: 28000000 INFO @ Thu, 05 Apr 2018 10:40:38: 29000000 INFO @ Thu, 05 Apr 2018 10:40:40: 30000000 INFO @ Thu, 05 Apr 2018 10:40:43: 30000000 INFO @ Thu, 05 Apr 2018 10:40:44: 29000000 INFO @ Thu, 05 Apr 2018 10:40:46: 31000000 INFO @ Thu, 05 Apr 2018 10:40:49: 31000000 INFO @ Thu, 05 Apr 2018 10:40:49: 30000000 INFO @ Thu, 05 Apr 2018 10:40:51: 32000000 INFO @ Thu, 05 Apr 2018 10:40:54: 32000000 INFO @ Thu, 05 Apr 2018 10:40:55: 31000000 INFO @ Thu, 05 Apr 2018 10:40:57: 33000000 INFO @ Thu, 05 Apr 2018 10:40:59: 33000000 INFO @ Thu, 05 Apr 2018 10:41:00: 32000000 INFO @ Thu, 05 Apr 2018 10:41:02: 34000000 INFO @ Thu, 05 Apr 2018 10:41:04: 34000000 INFO @ Thu, 05 Apr 2018 10:41:06: 33000000 INFO @ Thu, 05 Apr 2018 10:41:07: 35000000 INFO @ Thu, 05 Apr 2018 10:41:09: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:41:09: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:41:09: #1 total tags in treatment: 17269006 INFO @ Thu, 05 Apr 2018 10:41:09: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:41:09: #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 10:41:09: #1 tags after filtering in treatment: 6599327 INFO @ Thu, 05 Apr 2018 10:41:09: #1 Redundant rate of treatment: 0.62 INFO @ Thu, 05 Apr 2018 10:41:09: #1 finished! INFO @ Thu, 05 Apr 2018 10:41:09: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:41:09: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:41:10: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:41:10: 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 10:41:10: Process for pairing-model is terminated! cat: SRX3671218.05_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 `SRX3671218.05_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 `SRX3671218.05_*.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 `SRX3671218.05_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 10:41:10: 35000000 INFO @ Thu, 05 Apr 2018 10:41:11: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:41:11: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:41:11: #1 total tags in treatment: 17269006 INFO @ Thu, 05 Apr 2018 10:41:11: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:41:11: #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 10:41:11: #1 tags after filtering in treatment: 6599327 INFO @ Thu, 05 Apr 2018 10:41:11: #1 Redundant rate of treatment: 0.62 INFO @ Thu, 05 Apr 2018 10:41:11: #1 finished! INFO @ Thu, 05 Apr 2018 10:41:11: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:41:11: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:41:12: 34000000 INFO @ Thu, 05 Apr 2018 10:41:12: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:41:12: 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 10:41:12: Process for pairing-model is terminated! cat: SRX3671218.20_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 `SRX3671218.20_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 `SRX3671218.20_*.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 `SRX3671218.20_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 10:41:17: 35000000 INFO @ Thu, 05 Apr 2018 10:41:18: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:41:18: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:41:18: #1 total tags in treatment: 17269006 INFO @ Thu, 05 Apr 2018 10:41:18: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:41:18: #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 10:41:18: #1 tags after filtering in treatment: 6599327 INFO @ Thu, 05 Apr 2018 10:41:18: #1 Redundant rate of treatment: 0.62 INFO @ Thu, 05 Apr 2018 10:41:18: #1 finished! INFO @ Thu, 05 Apr 2018 10:41:18: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:41:18: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:41:19: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:41:19: 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 10:41:19: Process for pairing-model is terminated! cat: SRX3671218.10_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): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3671218.10_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 `SRX3671218.10_*.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 `SRX3671218.10_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。