Job ID = 11245203 sra ファイルのダウンロード中... Completed: 414667K bytes transferred in 7 seconds (451351K bits/sec), in 1 file. Completed: 418145K bytes transferred in 7 seconds (453255K bits/sec), in 1 file. Completed: 142350K bytes transferred in 4 seconds (246349K 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... Read 1358870 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669656/SRR7818281.sra Written 1358870 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669656/SRR7818281.sra Read 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669656/SRR7818280.sra Written 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669656/SRR7818280.sra Read 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669656/SRR7818279.sra Written 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669656/SRR7818279.sra 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 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: 00:08:20 9358870 reads; of these: 9358870 (100.00%) were paired; of these: 1176252 (12.57%) aligned concordantly 0 times 7449190 (79.59%) aligned concordantly exactly 1 time 733428 (7.84%) aligned concordantly >1 times ---- 1176252 pairs aligned concordantly 0 times; of these: 94900 (8.07%) aligned discordantly 1 time ---- 1081352 pairs aligned 0 times concordantly or discordantly; of these: 2162704 mates make up the pairs; of these: 1878141 (86.84%) aligned 0 times 207094 (9.58%) aligned exactly 1 time 77469 (3.58%) aligned >1 times 89.97% overall alignment rate Time searching: 00:08:20 Overall time: 00:08:20 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 8 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] 89669 / 8256085 = 0.0109 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 @ Wed, 10 Oct 2018 00:04:29: # Command line: callpeak -t SRX4669656.bam -f BAM -g 12100000 -n SRX4669656.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4669656.10 # format = BAM # ChIP-seq file = ['SRX4669656.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 @ Wed, 10 Oct 2018 00:04:29: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:04:29: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:04:29: # Command line: callpeak -t SRX4669656.bam -f BAM -g 12100000 -n SRX4669656.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4669656.20 # format = BAM # ChIP-seq file = ['SRX4669656.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 @ Wed, 10 Oct 2018 00:04:29: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:04:29: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:04:29: # Command line: callpeak -t SRX4669656.bam -f BAM -g 12100000 -n SRX4669656.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4669656.05 # format = BAM # ChIP-seq file = ['SRX4669656.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 @ Wed, 10 Oct 2018 00:04:29: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:04:29: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:04:36: 1000000 INFO @ Wed, 10 Oct 2018 00:04:36: 1000000 INFO @ Wed, 10 Oct 2018 00:04:36: 1000000 INFO @ Wed, 10 Oct 2018 00:04:43: 2000000 INFO @ Wed, 10 Oct 2018 00:04:43: 2000000 INFO @ Wed, 10 Oct 2018 00:04:43: 2000000 INFO @ Wed, 10 Oct 2018 00:04:50: 3000000 INFO @ Wed, 10 Oct 2018 00:04:51: 3000000 INFO @ Wed, 10 Oct 2018 00:04:51: 3000000 INFO @ Wed, 10 Oct 2018 00:04:57: 4000000 INFO @ Wed, 10 Oct 2018 00:04:58: 4000000 INFO @ Wed, 10 Oct 2018 00:04:58: 4000000 INFO @ Wed, 10 Oct 2018 00:05:05: 5000000 INFO @ Wed, 10 Oct 2018 00:05:05: 5000000 INFO @ Wed, 10 Oct 2018 00:05:06: 5000000 INFO @ Wed, 10 Oct 2018 00:05:11: 6000000 INFO @ Wed, 10 Oct 2018 00:05:12: 6000000 INFO @ Wed, 10 Oct 2018 00:05:13: 6000000 INFO @ Wed, 10 Oct 2018 00:05:18: 7000000 INFO @ Wed, 10 Oct 2018 00:05:19: 7000000 INFO @ Wed, 10 Oct 2018 00:05:21: 7000000 INFO @ Wed, 10 Oct 2018 00:05:24: 8000000 INFO @ Wed, 10 Oct 2018 00:05:27: 8000000 INFO @ Wed, 10 Oct 2018 00:05:29: 8000000 INFO @ Wed, 10 Oct 2018 00:05:31: 9000000 INFO @ Wed, 10 Oct 2018 00:05:34: 9000000 INFO @ Wed, 10 Oct 2018 00:05:36: 9000000 INFO @ Wed, 10 Oct 2018 00:05:38: 10000000 INFO @ Wed, 10 Oct 2018 00:05:41: 10000000 INFO @ Wed, 10 Oct 2018 00:05:44: 10000000 INFO @ Wed, 10 Oct 2018 00:05:44: 11000000 INFO @ Wed, 10 Oct 2018 00:05:48: 11000000 INFO @ Wed, 10 Oct 2018 00:05:51: 12000000 INFO @ Wed, 10 Oct 2018 00:05:52: 11000000 INFO @ Wed, 10 Oct 2018 00:05:55: 12000000 INFO @ Wed, 10 Oct 2018 00:05:57: 13000000 INFO @ Wed, 10 Oct 2018 00:05:59: 12000000 INFO @ Wed, 10 Oct 2018 00:06:02: 13000000 INFO @ Wed, 10 Oct 2018 00:06:04: 14000000 INFO @ Wed, 10 Oct 2018 00:06:07: 13000000 INFO @ Wed, 10 Oct 2018 00:06:09: 14000000 INFO @ Wed, 10 Oct 2018 00:06:11: 15000000 INFO @ Wed, 10 Oct 2018 00:06:14: 14000000 INFO @ Wed, 10 Oct 2018 00:06:16: 15000000 INFO @ Wed, 10 Oct 2018 00:06:17: 16000000 INFO @ Wed, 10 Oct 2018 00:06:22: 15000000 INFO @ Wed, 10 Oct 2018 00:06:22: #1 tag size is determined as 75 bps INFO @ Wed, 10 Oct 2018 00:06:22: #1 tag size = 75 INFO @ Wed, 10 Oct 2018 00:06:22: #1 total tags in treatment: 8093479 INFO @ Wed, 10 Oct 2018 00:06:22: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:06:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 10 Oct 2018 00:06:22: #1 tags after filtering in treatment: 6325220 INFO @ Wed, 10 Oct 2018 00:06:22: #1 Redundant rate of treatment: 0.22 INFO @ Wed, 10 Oct 2018 00:06:22: #1 finished! INFO @ Wed, 10 Oct 2018 00:06:22: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:06:22: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:06:22: #2 number of paired peaks: 0 WARNING @ Wed, 10 Oct 2018 00:06:22: 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 @ Wed, 10 Oct 2018 00:06:22: Process for pairing-model is terminated! cat: SRX4669656.10_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 `SRX4669656.10_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 `SRX4669656.10_*.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 `SRX4669656.10_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 @ Wed, 10 Oct 2018 00:06:23: 16000000 INFO @ Wed, 10 Oct 2018 00:06:28: #1 tag size is determined as 75 bps INFO @ Wed, 10 Oct 2018 00:06:28: #1 tag size = 75 INFO @ Wed, 10 Oct 2018 00:06:28: #1 total tags in treatment: 8093479 INFO @ Wed, 10 Oct 2018 00:06:28: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:06:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 10 Oct 2018 00:06:28: #1 tags after filtering in treatment: 6325220 INFO @ Wed, 10 Oct 2018 00:06:28: #1 Redundant rate of treatment: 0.22 INFO @ Wed, 10 Oct 2018 00:06:28: #1 finished! INFO @ Wed, 10 Oct 2018 00:06:28: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:06:28: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:06:28: #2 number of paired peaks: 0 WARNING @ Wed, 10 Oct 2018 00:06:28: 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 @ Wed, 10 Oct 2018 00:06:28: Process for pairing-model is terminated! cat: SRX4669656.20_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 `SRX4669656.20_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 `SRX4669656.20_*.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 `SRX4669656.20_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 @ Wed, 10 Oct 2018 00:06:29: 16000000 INFO @ Wed, 10 Oct 2018 00:06:33: #1 tag size is determined as 75 bps INFO @ Wed, 10 Oct 2018 00:06:33: #1 tag size = 75 INFO @ Wed, 10 Oct 2018 00:06:33: #1 total tags in treatment: 8093479 INFO @ Wed, 10 Oct 2018 00:06:33: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:06:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 10 Oct 2018 00:06:33: #1 tags after filtering in treatment: 6325220 INFO @ Wed, 10 Oct 2018 00:06:33: #1 Redundant rate of treatment: 0.22 INFO @ Wed, 10 Oct 2018 00:06:33: #1 finished! INFO @ Wed, 10 Oct 2018 00:06:33: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:06:33: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:06:34: #2 number of paired peaks: 0 WARNING @ Wed, 10 Oct 2018 00:06:34: 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 @ Wed, 10 Oct 2018 00:06:34: Process for pairing-model is terminated! cat: SRX4669656.05_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 `SRX4669656.05_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 `SRX4669656.05_*.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 `SRX4669656.05_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。