Job ID = 10937544 sra ファイルのダウンロード中... Completed: 606534K bytes transferred in 82 seconds (60020K 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 6293000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3010337/SRR5833336.sra Written 6293000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3010337/SRR5833336.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: 00:09:02 6293000 reads; of these: 6293000 (100.00%) were paired; of these: 374466 (5.95%) aligned concordantly 0 times 4832467 (76.79%) aligned concordantly exactly 1 time 1086067 (17.26%) aligned concordantly >1 times ---- 374466 pairs aligned concordantly 0 times; of these: 56022 (14.96%) aligned discordantly 1 time ---- 318444 pairs aligned 0 times concordantly or discordantly; of these: 636888 mates make up the pairs; of these: 501936 (78.81%) aligned 0 times 85922 (13.49%) aligned exactly 1 time 49030 (7.70%) aligned >1 times 96.01% overall alignment rate Time searching: 00:09:02 Overall time: 00:09:02 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] 187189 / 5935250 = 0.0315 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 @ Fri, 10 Aug 2018 02:49:29: # Command line: callpeak -t SRX3010337.bam -f BAM -g 12100000 -n SRX3010337.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3010337.10 # format = BAM # ChIP-seq file = ['SRX3010337.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 @ Fri, 10 Aug 2018 02:49:29: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:49:29: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:49:29: # Command line: callpeak -t SRX3010337.bam -f BAM -g 12100000 -n SRX3010337.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3010337.05 # format = BAM # ChIP-seq file = ['SRX3010337.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 @ Fri, 10 Aug 2018 02:49:29: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:49:29: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:49:29: # Command line: callpeak -t SRX3010337.bam -f BAM -g 12100000 -n SRX3010337.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3010337.20 # format = BAM # ChIP-seq file = ['SRX3010337.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 @ Fri, 10 Aug 2018 02:49:29: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:49:29: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:49:40: 1000000 INFO @ Fri, 10 Aug 2018 02:49:40: 1000000 INFO @ Fri, 10 Aug 2018 02:49:42: 1000000 INFO @ Fri, 10 Aug 2018 02:49:51: 2000000 INFO @ Fri, 10 Aug 2018 02:49:51: 2000000 INFO @ Fri, 10 Aug 2018 02:49:55: 2000000 INFO @ Fri, 10 Aug 2018 02:50:02: 3000000 INFO @ Fri, 10 Aug 2018 02:50:02: 3000000 INFO @ Fri, 10 Aug 2018 02:50:08: 3000000 INFO @ Fri, 10 Aug 2018 02:50:13: 4000000 INFO @ Fri, 10 Aug 2018 02:50:13: 4000000 INFO @ Fri, 10 Aug 2018 02:50:21: 4000000 INFO @ Fri, 10 Aug 2018 02:50:24: 5000000 INFO @ Fri, 10 Aug 2018 02:50:24: 5000000 INFO @ Fri, 10 Aug 2018 02:50:34: 5000000 INFO @ Fri, 10 Aug 2018 02:50:35: 6000000 INFO @ Fri, 10 Aug 2018 02:50:35: 6000000 INFO @ Fri, 10 Aug 2018 02:50:46: 7000000 INFO @ Fri, 10 Aug 2018 02:50:46: 7000000 INFO @ Fri, 10 Aug 2018 02:50:47: 6000000 INFO @ Fri, 10 Aug 2018 02:50:57: 8000000 INFO @ Fri, 10 Aug 2018 02:50:57: 8000000 INFO @ Fri, 10 Aug 2018 02:51:01: 7000000 INFO @ Fri, 10 Aug 2018 02:51:09: 9000000 INFO @ Fri, 10 Aug 2018 02:51:09: 9000000 INFO @ Fri, 10 Aug 2018 02:51:15: 8000000 INFO @ Fri, 10 Aug 2018 02:51:20: 10000000 INFO @ Fri, 10 Aug 2018 02:51:20: 10000000 INFO @ Fri, 10 Aug 2018 02:51:29: 9000000 INFO @ Fri, 10 Aug 2018 02:51:32: 11000000 INFO @ Fri, 10 Aug 2018 02:51:32: 11000000 INFO @ Fri, 10 Aug 2018 02:51:39: #1 tag size is determined as 101 bps INFO @ Fri, 10 Aug 2018 02:51:39: #1 tag size = 101 INFO @ Fri, 10 Aug 2018 02:51:39: #1 total tags in treatment: 5731401 INFO @ Fri, 10 Aug 2018 02:51:39: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:51:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:51:39: #1 tag size is determined as 101 bps INFO @ Fri, 10 Aug 2018 02:51:39: #1 tag size = 101 INFO @ Fri, 10 Aug 2018 02:51:39: #1 total tags in treatment: 5731401 INFO @ Fri, 10 Aug 2018 02:51:39: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:51:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:51:40: #1 tags after filtering in treatment: 4402193 INFO @ Fri, 10 Aug 2018 02:51:40: #1 Redundant rate of treatment: 0.23 INFO @ Fri, 10 Aug 2018 02:51:40: #1 finished! INFO @ Fri, 10 Aug 2018 02:51:40: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:51:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:51:40: #1 tags after filtering in treatment: 4402193 INFO @ Fri, 10 Aug 2018 02:51:40: #1 Redundant rate of treatment: 0.23 INFO @ Fri, 10 Aug 2018 02:51:40: #1 finished! INFO @ Fri, 10 Aug 2018 02:51:40: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:51:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:51:40: #2 number of paired peaks: 34 WARNING @ Fri, 10 Aug 2018 02:51:40: Too few paired peaks (34) 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 @ Fri, 10 Aug 2018 02:51:40: Process for pairing-model is terminated! cat: SRX3010337.05_peaks.narrowPeak: そのようなファイルやディレクトリはありません INFO @ Fri, 10 Aug 2018 02:51:40: #2 number of paired peaks: 34 WARNING @ Fri, 10 Aug 2018 02:51:40: Too few paired peaks (34) 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 @ Fri, 10 Aug 2018 02:51:40: Process for pairing-model is terminated! cat: SRX3010337.10_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): 8 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3010337.05_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 `SRX3010337.05_*.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 `SRX3010337.05_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 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3010337.10_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 `SRX3010337.10_*.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 `SRX3010337.10_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 @ Fri, 10 Aug 2018 02:51:42: 10000000 INFO @ Fri, 10 Aug 2018 02:51:54: 11000000 INFO @ Fri, 10 Aug 2018 02:52:03: #1 tag size is determined as 101 bps INFO @ Fri, 10 Aug 2018 02:52:03: #1 tag size = 101 INFO @ Fri, 10 Aug 2018 02:52:03: #1 total tags in treatment: 5731401 INFO @ Fri, 10 Aug 2018 02:52:03: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:52:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:52:03: #1 tags after filtering in treatment: 4402193 INFO @ Fri, 10 Aug 2018 02:52:03: #1 Redundant rate of treatment: 0.23 INFO @ Fri, 10 Aug 2018 02:52:03: #1 finished! INFO @ Fri, 10 Aug 2018 02:52:03: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:52:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:52:03: #2 number of paired peaks: 34 WARNING @ Fri, 10 Aug 2018 02:52:03: Too few paired peaks (34) 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 @ Fri, 10 Aug 2018 02:52:03: Process for pairing-model is terminated! cat: SRX3010337.20_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 `SRX3010337.20_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 `SRX3010337.20_*.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 `SRX3010337.20_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。