Job ID = 11192838 sra ファイルのダウンロード中... Completed: 598474K bytes transferred in 10 seconds (485152K 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 15691084 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1972006/SRR3946121.sra Written 15691084 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1972006/SRR3946121.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 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: 00:09:56 15691084 reads; of these: 15691084 (100.00%) were paired; of these: 8655682 (55.16%) aligned concordantly 0 times 5952449 (37.94%) aligned concordantly exactly 1 time 1082953 (6.90%) aligned concordantly >1 times ---- 8655682 pairs aligned concordantly 0 times; of these: 57225 (0.66%) aligned discordantly 1 time ---- 8598457 pairs aligned 0 times concordantly or discordantly; of these: 17196914 mates make up the pairs; of these: 9806077 (57.02%) aligned 0 times 6059125 (35.23%) aligned exactly 1 time 1331712 (7.74%) aligned >1 times 68.75% overall alignment rate Time searching: 00:09:56 Overall time: 00:09:56 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] 4926047 / 7059785 = 0.6978 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 @ Sat, 15 Sep 2018 10:14:08: # Command line: callpeak -t SRX1972006.bam -f BAM -g 12100000 -n SRX1972006.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1972006.05 # format = BAM # ChIP-seq file = ['SRX1972006.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 @ Sat, 15 Sep 2018 10:14:08: # Command line: callpeak -t SRX1972006.bam -f BAM -g 12100000 -n SRX1972006.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1972006.10 # format = BAM # ChIP-seq file = ['SRX1972006.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 @ Sat, 15 Sep 2018 10:14:08: # Command line: callpeak -t SRX1972006.bam -f BAM -g 12100000 -n SRX1972006.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1972006.20 # format = BAM # ChIP-seq file = ['SRX1972006.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 @ Sat, 15 Sep 2018 10:14:08: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:14:08: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:14:08: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:14:08: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:14:08: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:14:08: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:14:14: 1000000 INFO @ Sat, 15 Sep 2018 10:14:14: 1000000 INFO @ Sat, 15 Sep 2018 10:14:14: 1000000 INFO @ Sat, 15 Sep 2018 10:14:20: 2000000 INFO @ Sat, 15 Sep 2018 10:14:20: 2000000 INFO @ Sat, 15 Sep 2018 10:14:20: 2000000 INFO @ Sat, 15 Sep 2018 10:14:25: 3000000 INFO @ Sat, 15 Sep 2018 10:14:27: 3000000 INFO @ Sat, 15 Sep 2018 10:14:27: 3000000 INFO @ Sat, 15 Sep 2018 10:14:30: 4000000 INFO @ Sat, 15 Sep 2018 10:14:34: 4000000 INFO @ Sat, 15 Sep 2018 10:14:34: 4000000 INFO @ Sat, 15 Sep 2018 10:14:36: 5000000 INFO @ Sat, 15 Sep 2018 10:14:40: 5000000 INFO @ Sat, 15 Sep 2018 10:14:40: 5000000 INFO @ Sat, 15 Sep 2018 10:14:41: 6000000 INFO @ Sat, 15 Sep 2018 10:14:46: 6000000 INFO @ Sat, 15 Sep 2018 10:14:46: 6000000 INFO @ Sat, 15 Sep 2018 10:14:47: 7000000 INFO @ Sat, 15 Sep 2018 10:14:52: 7000000 INFO @ Sat, 15 Sep 2018 10:14:52: 7000000 INFO @ Sat, 15 Sep 2018 10:14:52: 8000000 INFO @ Sat, 15 Sep 2018 10:14:57: 8000000 INFO @ Sat, 15 Sep 2018 10:14:57: 8000000 INFO @ Sat, 15 Sep 2018 10:14:58: 9000000 INFO @ Sat, 15 Sep 2018 10:15:03: 10000000 INFO @ Sat, 15 Sep 2018 10:15:03: 9000000 INFO @ Sat, 15 Sep 2018 10:15:03: 9000000 INFO @ Sat, 15 Sep 2018 10:15:08: 11000000 INFO @ Sat, 15 Sep 2018 10:15:10: 10000000 INFO @ Sat, 15 Sep 2018 10:15:10: 10000000 INFO @ Sat, 15 Sep 2018 10:15:12: #1 tag size is determined as 40 bps INFO @ Sat, 15 Sep 2018 10:15:12: #1 tag size = 40 INFO @ Sat, 15 Sep 2018 10:15:12: #1 total tags in treatment: 2123069 INFO @ Sat, 15 Sep 2018 10:15:12: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:15:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:15:12: #1 tags after filtering in treatment: 1765720 INFO @ Sat, 15 Sep 2018 10:15:12: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 15 Sep 2018 10:15:12: #1 finished! INFO @ Sat, 15 Sep 2018 10:15:12: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:15:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:15:12: #2 number of paired peaks: 33 WARNING @ Sat, 15 Sep 2018 10:15:12: Too few paired peaks (33) 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 @ Sat, 15 Sep 2018 10:15:12: Process for pairing-model is terminated! cat: SRX1972006.05_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 `SRX1972006.05_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 `SRX1972006.05_*.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 `SRX1972006.05_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 @ Sat, 15 Sep 2018 10:15:16: 11000000 INFO @ Sat, 15 Sep 2018 10:15:16: 11000000 INFO @ Sat, 15 Sep 2018 10:15:20: #1 tag size is determined as 40 bps INFO @ Sat, 15 Sep 2018 10:15:20: #1 tag size = 40 INFO @ Sat, 15 Sep 2018 10:15:20: #1 total tags in treatment: 2123069 INFO @ Sat, 15 Sep 2018 10:15:20: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:15:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:15:20: #1 tags after filtering in treatment: 1765720 INFO @ Sat, 15 Sep 2018 10:15:20: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 15 Sep 2018 10:15:20: #1 finished! INFO @ Sat, 15 Sep 2018 10:15:20: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:15:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:15:20: #2 number of paired peaks: 33 WARNING @ Sat, 15 Sep 2018 10:15:20: Too few paired peaks (33) 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 @ Sat, 15 Sep 2018 10:15:20: Process for pairing-model is terminated! cat: SRX1972006.10_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 `SRX1972006.10_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 `SRX1972006.10_*.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 `SRX1972006.10_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 @ Sat, 15 Sep 2018 10:15:20: #1 tag size is determined as 40 bps INFO @ Sat, 15 Sep 2018 10:15:20: #1 tag size = 40 INFO @ Sat, 15 Sep 2018 10:15:20: #1 total tags in treatment: 2123069 INFO @ Sat, 15 Sep 2018 10:15:20: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:15:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:15:21: #1 tags after filtering in treatment: 1765720 INFO @ Sat, 15 Sep 2018 10:15:21: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 15 Sep 2018 10:15:21: #1 finished! INFO @ Sat, 15 Sep 2018 10:15:21: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:15:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:15:21: #2 number of paired peaks: 33 WARNING @ Sat, 15 Sep 2018 10:15:21: Too few paired peaks (33) 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 @ Sat, 15 Sep 2018 10:15:21: Process for pairing-model is terminated! cat: SRX1972006.20_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 `SRX1972006.20_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 `SRX1972006.20_*.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 `SRX1972006.20_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。