Job ID = 11632821 sra ファイルのダウンロード中... Completed: 72070K bytes transferred in 4 seconds (133070K 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 1122698 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1173778/ERR1094292.sra Written 1122698 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1173778/ERR1094292.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: 00:01:00 1122698 reads; of these: 1122698 (100.00%) were paired; of these: 93737 (8.35%) aligned concordantly 0 times 925274 (82.42%) aligned concordantly exactly 1 time 103687 (9.24%) aligned concordantly >1 times ---- 93737 pairs aligned concordantly 0 times; of these: 41921 (44.72%) aligned discordantly 1 time ---- 51816 pairs aligned 0 times concordantly or discordantly; of these: 103632 mates make up the pairs; of these: 86278 (83.25%) aligned 0 times 5857 (5.65%) aligned exactly 1 time 11497 (11.09%) aligned >1 times 96.16% overall alignment rate Time searching: 00:01:00 Overall time: 00:01:00 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_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] 8215 / 1068182 = 0.0077 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, 15 Feb 2019 08:08:19: # Command line: callpeak -t ERX1173778.bam -f BAM -g 12100000 -n ERX1173778.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX1173778.20 # format = BAM # ChIP-seq file = ['ERX1173778.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, 15 Feb 2019 08:08:19: #1 read tag files... INFO @ Fri, 15 Feb 2019 08:08:19: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 08:08:19: # Command line: callpeak -t ERX1173778.bam -f BAM -g 12100000 -n ERX1173778.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX1173778.10 # format = BAM # ChIP-seq file = ['ERX1173778.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, 15 Feb 2019 08:08:19: #1 read tag files... INFO @ Fri, 15 Feb 2019 08:08:19: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 08:08:19: # Command line: callpeak -t ERX1173778.bam -f BAM -g 12100000 -n ERX1173778.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX1173778.05 # format = BAM # ChIP-seq file = ['ERX1173778.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, 15 Feb 2019 08:08:19: #1 read tag files... INFO @ Fri, 15 Feb 2019 08:08:19: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 08:08:25: 1000000 INFO @ Fri, 15 Feb 2019 08:08:26: 1000000 INFO @ Fri, 15 Feb 2019 08:08:26: 1000000 INFO @ Fri, 15 Feb 2019 08:08:32: 2000000 INFO @ Fri, 15 Feb 2019 08:08:32: 2000000 INFO @ Fri, 15 Feb 2019 08:08:32: 2000000 INFO @ Fri, 15 Feb 2019 08:08:33: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 08:08:33: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 08:08:33: #1 total tags in treatment: 1020968 INFO @ Fri, 15 Feb 2019 08:08:33: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 08:08:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 08:08:33: #1 tags after filtering in treatment: 977925 INFO @ Fri, 15 Feb 2019 08:08:33: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 15 Feb 2019 08:08:33: #1 finished! INFO @ Fri, 15 Feb 2019 08:08:33: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 08:08:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 08:08:33: #2 number of paired peaks: 34 WARNING @ Fri, 15 Feb 2019 08:08:33: 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, 15 Feb 2019 08:08:33: Process for pairing-model is terminated! cat: ERX1173778.10_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): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `ERX1173778.10_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 `ERX1173778.10_*.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 `ERX1173778.10_peaks.narrowPeak': そのようなファイルやディレクトリはありません INFO @ Fri, 15 Feb 2019 08:08:33: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 08:08:33: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 08:08:33: #1 total tags in treatment: 1020968 INFO @ Fri, 15 Feb 2019 08:08:33: #1 user defined the maximum tags... CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 08:08:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 08:08:33: #1 tags after filtering in treatment: 977925 INFO @ Fri, 15 Feb 2019 08:08:33: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 15 Feb 2019 08:08:33: #1 finished! INFO @ Fri, 15 Feb 2019 08:08:33: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 08:08:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 08:08:33: #2 number of paired peaks: 34 WARNING @ Fri, 15 Feb 2019 08:08:33: 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, 15 Feb 2019 08:08:33: Process for pairing-model is terminated! INFO @ Fri, 15 Feb 2019 08:08:33: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 08:08:33: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 08:08:33: #1 total tags in treatment: 1020968 INFO @ Fri, 15 Feb 2019 08:08:33: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 08:08:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) cat: ERX1173778.20_peaks.narrowPeak: そのようなファイルやディレクトリはありません INFO @ Fri, 15 Feb 2019 08:08:33: #1 tags after filtering in treatment: 977925 INFO @ Fri, 15 Feb 2019 08:08:33: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 15 Feb 2019 08:08:33: #1 finished! INFO @ Fri, 15 Feb 2019 08:08:33: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 08:08:33: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (0 chroms): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `ERX1173778.20_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 `ERX1173778.20_*.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 `ERX1173778.20_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 @ Fri, 15 Feb 2019 08:08:33: #2 number of paired peaks: 34 WARNING @ Fri, 15 Feb 2019 08:08:33: 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, 15 Feb 2019 08:08:33: Process for pairing-model is terminated! cat: ERX1173778.05_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): 4 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `ERX1173778.05_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 `ERX1173778.05_*.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 `ERX1173778.05_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。