Job ID = 10536528 sra ファイルのダウンロード中... Completed: 1079949K bytes transferred in 22 seconds (388372K 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 29018451 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3671220/SRR6696972.sra Written 29018451 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: 00:18:48 29018451 reads; of these: 29018451 (100.00%) were paired; of these: 6019173 (20.74%) aligned concordantly 0 times 19493859 (67.18%) aligned concordantly exactly 1 time 3505419 (12.08%) aligned concordantly >1 times ---- 6019173 pairs aligned concordantly 0 times; of these: 26483 (0.44%) aligned discordantly 1 time ---- 5992690 pairs aligned 0 times concordantly or discordantly; of these: 11985380 mates make up the pairs; of these: 11784014 (98.32%) aligned 0 times 156769 (1.31%) aligned exactly 1 time 44597 (0.37%) aligned >1 times 79.70% overall alignment rate Time searching: 00:18:48 Overall time: 00:18:48 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 20 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] 12899958 / 23005508 = 0.5607 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 10:43:10: # Command line: callpeak -t SRX3671220.bam -f BAM -g 12100000 -n SRX3671220.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3671220.05 # format = BAM # ChIP-seq file = ['SRX3671220.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 10:43:10: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:43:10: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:43:10: # Command line: callpeak -t SRX3671220.bam -f BAM -g 12100000 -n SRX3671220.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3671220.20 # format = BAM # ChIP-seq file = ['SRX3671220.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 10:43:10: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:43:10: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:43:10: # Command line: callpeak -t SRX3671220.bam -f BAM -g 12100000 -n SRX3671220.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3671220.10 # format = BAM # ChIP-seq file = ['SRX3671220.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 10:43:10: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:43:10: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:43:16: 1000000 INFO @ Thu, 05 Apr 2018 10:43:16: 1000000 INFO @ Thu, 05 Apr 2018 10:43:16: 1000000 INFO @ Thu, 05 Apr 2018 10:43:21: 2000000 INFO @ Thu, 05 Apr 2018 10:43:21: 2000000 INFO @ Thu, 05 Apr 2018 10:43:21: 2000000 INFO @ Thu, 05 Apr 2018 10:43:27: 3000000 INFO @ Thu, 05 Apr 2018 10:43:27: 3000000 INFO @ Thu, 05 Apr 2018 10:43:27: 3000000 INFO @ Thu, 05 Apr 2018 10:43:32: 4000000 INFO @ Thu, 05 Apr 2018 10:43:33: 4000000 INFO @ Thu, 05 Apr 2018 10:43:33: 4000000 INFO @ Thu, 05 Apr 2018 10:43:37: 5000000 INFO @ Thu, 05 Apr 2018 10:43:38: 5000000 INFO @ Thu, 05 Apr 2018 10:43:38: 5000000 INFO @ Thu, 05 Apr 2018 10:43:43: 6000000 INFO @ Thu, 05 Apr 2018 10:43:44: 6000000 INFO @ Thu, 05 Apr 2018 10:43:44: 6000000 INFO @ Thu, 05 Apr 2018 10:43:48: 7000000 INFO @ Thu, 05 Apr 2018 10:43:49: 7000000 INFO @ Thu, 05 Apr 2018 10:43:49: 7000000 INFO @ Thu, 05 Apr 2018 10:43:54: 8000000 INFO @ Thu, 05 Apr 2018 10:43:55: 8000000 INFO @ Thu, 05 Apr 2018 10:43:55: 8000000 INFO @ Thu, 05 Apr 2018 10:44:00: 9000000 INFO @ Thu, 05 Apr 2018 10:44:02: 9000000 INFO @ Thu, 05 Apr 2018 10:44:03: 9000000 INFO @ Thu, 05 Apr 2018 10:44:06: 10000000 INFO @ Thu, 05 Apr 2018 10:44:10: 10000000 INFO @ Thu, 05 Apr 2018 10:44:10: 10000000 INFO @ Thu, 05 Apr 2018 10:44:13: 11000000 INFO @ Thu, 05 Apr 2018 10:44:16: 11000000 INFO @ Thu, 05 Apr 2018 10:44:16: 11000000 INFO @ Thu, 05 Apr 2018 10:44:18: 12000000 INFO @ Thu, 05 Apr 2018 10:44:23: 12000000 INFO @ Thu, 05 Apr 2018 10:44:23: 12000000 INFO @ Thu, 05 Apr 2018 10:44:25: 13000000 INFO @ Thu, 05 Apr 2018 10:44:30: 13000000 INFO @ Thu, 05 Apr 2018 10:44:30: 13000000 INFO @ Thu, 05 Apr 2018 10:44:32: 14000000 INFO @ Thu, 05 Apr 2018 10:44:35: 14000000 INFO @ Thu, 05 Apr 2018 10:44:36: 14000000 INFO @ Thu, 05 Apr 2018 10:44:39: 15000000 INFO @ Thu, 05 Apr 2018 10:44:44: 15000000 INFO @ Thu, 05 Apr 2018 10:44:45: 15000000 INFO @ Thu, 05 Apr 2018 10:44:47: 16000000 INFO @ Thu, 05 Apr 2018 10:44:49: 16000000 INFO @ Thu, 05 Apr 2018 10:44:51: 16000000 INFO @ Thu, 05 Apr 2018 10:44:52: 17000000 INFO @ Thu, 05 Apr 2018 10:44:54: 17000000 INFO @ Thu, 05 Apr 2018 10:44:56: 17000000 INFO @ Thu, 05 Apr 2018 10:44:58: 18000000 INFO @ Thu, 05 Apr 2018 10:45:00: 18000000 INFO @ Thu, 05 Apr 2018 10:45:02: 18000000 INFO @ Thu, 05 Apr 2018 10:45:04: 19000000 INFO @ Thu, 05 Apr 2018 10:45:05: 19000000 INFO @ Thu, 05 Apr 2018 10:45:07: 19000000 INFO @ Thu, 05 Apr 2018 10:45:09: 20000000 INFO @ Thu, 05 Apr 2018 10:45:10: 20000000 INFO @ Thu, 05 Apr 2018 10:45:12: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:45:12: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:45:12: #1 total tags in treatment: 10103233 INFO @ Thu, 05 Apr 2018 10:45:12: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:45:12: #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 10:45:12: #1 tags after filtering in treatment: 5137384 INFO @ Thu, 05 Apr 2018 10:45:12: #1 Redundant rate of treatment: 0.49 INFO @ Thu, 05 Apr 2018 10:45:12: #1 finished! INFO @ Thu, 05 Apr 2018 10:45:12: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:45:12: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:45:13: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:45:13: 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 10:45:13: Process for pairing-model is terminated! INFO @ Thu, 05 Apr 2018 10:45:13: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:45:13: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:45:13: #1 total tags in treatment: 10103233 INFO @ Thu, 05 Apr 2018 10:45:13: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:45:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) cat: SRX3671220.20_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 `SRX3671220.20_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 `SRX3671220.20_*.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 `SRX3671220.20_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 10:45:13: 20000000 INFO @ Thu, 05 Apr 2018 10:45:13: #1 tags after filtering in treatment: 5137384 INFO @ Thu, 05 Apr 2018 10:45:13: #1 Redundant rate of treatment: 0.49 INFO @ Thu, 05 Apr 2018 10:45:13: #1 finished! INFO @ Thu, 05 Apr 2018 10:45:13: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:45:13: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:45:13: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:45:13: 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 10:45:13: Process for pairing-model is terminated! cat: SRX3671220.05_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 `SRX3671220.05_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 `SRX3671220.05_*.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 `SRX3671220.05_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 10:45:15: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:45:15: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:45:15: #1 total tags in treatment: 10103233 INFO @ Thu, 05 Apr 2018 10:45:15: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:45:15: #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 10:45:15: #1 tags after filtering in treatment: 5137384 INFO @ Thu, 05 Apr 2018 10:45:15: #1 Redundant rate of treatment: 0.49 INFO @ Thu, 05 Apr 2018 10:45:15: #1 finished! INFO @ Thu, 05 Apr 2018 10:45:15: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:45:15: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:45:16: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:45:16: 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 10:45:16: Process for pairing-model is terminated! cat: SRX3671220.10_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 `SRX3671220.10_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 `SRX3671220.10_*.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 `SRX3671220.10_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。