Job ID = 10536337 sra ファイルのダウンロード中... Completed: 1080109K bytes transferred in 22 seconds (389228K 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 16573573 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3433204/SRR6333845.sra Written 16573573 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: 00:10:56 16573573 reads; of these: 16573573 (100.00%) were paired; of these: 2985075 (18.01%) aligned concordantly 0 times 12290956 (74.16%) aligned concordantly exactly 1 time 1297542 (7.83%) aligned concordantly >1 times ---- 2985075 pairs aligned concordantly 0 times; of these: 56789 (1.90%) aligned discordantly 1 time ---- 2928286 pairs aligned 0 times concordantly or discordantly; of these: 5856572 mates make up the pairs; of these: 5738028 (97.98%) aligned 0 times 91689 (1.57%) aligned exactly 1 time 26855 (0.46%) aligned >1 times 82.69% overall alignment rate Time searching: 00:10:56 Overall time: 00:10:56 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 12 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] 4967894 / 13623463 = 0.3647 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 08:58:03: # Command line: callpeak -t SRX3433204.bam -f BAM -g 12100000 -n SRX3433204.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3433204.20 # format = BAM # ChIP-seq file = ['SRX3433204.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 08:58:03: #1 read tag files... INFO @ Thu, 05 Apr 2018 08:58:03: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 08:58:03: # Command line: callpeak -t SRX3433204.bam -f BAM -g 12100000 -n SRX3433204.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3433204.05 # format = BAM # ChIP-seq file = ['SRX3433204.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 08:58:03: #1 read tag files... INFO @ Thu, 05 Apr 2018 08:58:03: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 08:58:03: # Command line: callpeak -t SRX3433204.bam -f BAM -g 12100000 -n SRX3433204.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3433204.10 # format = BAM # ChIP-seq file = ['SRX3433204.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 08:58:03: #1 read tag files... INFO @ Thu, 05 Apr 2018 08:58:03: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 08:58:10: 1000000 INFO @ Thu, 05 Apr 2018 08:58:10: 1000000 INFO @ Thu, 05 Apr 2018 08:58:10: 1000000 INFO @ Thu, 05 Apr 2018 08:58:17: 2000000 INFO @ Thu, 05 Apr 2018 08:58:17: 2000000 INFO @ Thu, 05 Apr 2018 08:58:17: 2000000 INFO @ Thu, 05 Apr 2018 08:58:24: 3000000 INFO @ Thu, 05 Apr 2018 08:58:24: 3000000 INFO @ Thu, 05 Apr 2018 08:58:24: 3000000 INFO @ Thu, 05 Apr 2018 08:58:31: 4000000 INFO @ Thu, 05 Apr 2018 08:58:31: 4000000 INFO @ Thu, 05 Apr 2018 08:58:31: 4000000 INFO @ Thu, 05 Apr 2018 08:58:38: 5000000 INFO @ Thu, 05 Apr 2018 08:58:38: 5000000 INFO @ Thu, 05 Apr 2018 08:58:38: 5000000 INFO @ Thu, 05 Apr 2018 08:58:45: 6000000 INFO @ Thu, 05 Apr 2018 08:58:45: 6000000 INFO @ Thu, 05 Apr 2018 08:58:45: 6000000 INFO @ Thu, 05 Apr 2018 08:58:51: 7000000 INFO @ Thu, 05 Apr 2018 08:58:51: 7000000 INFO @ Thu, 05 Apr 2018 08:58:51: 7000000 INFO @ Thu, 05 Apr 2018 08:58:57: 8000000 INFO @ Thu, 05 Apr 2018 08:58:57: 8000000 INFO @ Thu, 05 Apr 2018 08:58:58: 8000000 INFO @ Thu, 05 Apr 2018 08:59:02: 9000000 INFO @ Thu, 05 Apr 2018 08:59:03: 9000000 INFO @ Thu, 05 Apr 2018 08:59:04: 9000000 INFO @ Thu, 05 Apr 2018 08:59:08: 10000000 INFO @ Thu, 05 Apr 2018 08:59:09: 10000000 INFO @ Thu, 05 Apr 2018 08:59:10: 10000000 INFO @ Thu, 05 Apr 2018 08:59:14: 11000000 INFO @ Thu, 05 Apr 2018 08:59:15: 11000000 INFO @ Thu, 05 Apr 2018 08:59:16: 11000000 INFO @ Thu, 05 Apr 2018 08:59:20: 12000000 INFO @ Thu, 05 Apr 2018 08:59:21: 12000000 INFO @ Thu, 05 Apr 2018 08:59:22: 12000000 INFO @ Thu, 05 Apr 2018 08:59:27: 13000000 INFO @ Thu, 05 Apr 2018 08:59:27: 13000000 INFO @ Thu, 05 Apr 2018 08:59:28: 13000000 INFO @ Thu, 05 Apr 2018 08:59:33: 14000000 INFO @ Thu, 05 Apr 2018 08:59:33: 14000000 INFO @ Thu, 05 Apr 2018 08:59:34: 14000000 INFO @ Thu, 05 Apr 2018 08:59:39: 15000000 INFO @ Thu, 05 Apr 2018 08:59:39: 15000000 INFO @ Thu, 05 Apr 2018 08:59:40: 15000000 INFO @ Thu, 05 Apr 2018 08:59:45: 16000000 INFO @ Thu, 05 Apr 2018 08:59:45: 16000000 INFO @ Thu, 05 Apr 2018 08:59:47: 16000000 INFO @ Thu, 05 Apr 2018 08:59:51: 17000000 INFO @ Thu, 05 Apr 2018 08:59:51: 17000000 INFO @ Thu, 05 Apr 2018 08:59:53: 17000000 INFO @ Thu, 05 Apr 2018 08:59:53: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 08:59:53: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 08:59:53: #1 total tags in treatment: 8643117 INFO @ Thu, 05 Apr 2018 08:59:53: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 08:59:53: #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 08:59:54: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 08:59:54: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 08:59:54: #1 total tags in treatment: 8643117 INFO @ Thu, 05 Apr 2018 08:59:54: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 08:59:54: #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 08:59:54: #1 tags after filtering in treatment: 6079829 INFO @ Thu, 05 Apr 2018 08:59:54: #1 Redundant rate of treatment: 0.30 INFO @ Thu, 05 Apr 2018 08:59:54: #1 finished! INFO @ Thu, 05 Apr 2018 08:59:54: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 08:59:54: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 08:59:54: #1 tags after filtering in treatment: 6079829 INFO @ Thu, 05 Apr 2018 08:59:54: #1 Redundant rate of treatment: 0.30 INFO @ Thu, 05 Apr 2018 08:59:54: #1 finished! INFO @ Thu, 05 Apr 2018 08:59:54: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 08:59:54: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 08:59:54: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 08:59:54: 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 08:59:54: Process for pairing-model is terminated! cat: SRX3433204.05_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 `SRX3433204.05_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 `SRX3433204.05_*.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 `SRX3433204.05_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 08:59:54: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 08:59:54: 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 08:59:54: Process for pairing-model is terminated! cat: SRX3433204.10_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 `SRX3433204.10_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 `SRX3433204.10_*.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 `SRX3433204.10_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 @ Thu, 05 Apr 2018 08:59:56: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 08:59:56: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 08:59:56: #1 total tags in treatment: 8643117 INFO @ Thu, 05 Apr 2018 08:59:56: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 08:59:56: #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 08:59:56: #1 tags after filtering in treatment: 6079829 INFO @ Thu, 05 Apr 2018 08:59:56: #1 Redundant rate of treatment: 0.30 INFO @ Thu, 05 Apr 2018 08:59:56: #1 finished! INFO @ Thu, 05 Apr 2018 08:59:56: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 08:59:56: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 08:59:56: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 08:59:56: 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 08:59:56: Process for pairing-model is terminated! cat: SRX3433204.20_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 `SRX3433204.20_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 `SRX3433204.20_*.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 `SRX3433204.20_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。