Job ID = 11633321 sra ファイルのダウンロード中... Completed: 268441K bytes transferred in 6 seconds (364352K 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 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1236100/ERR1162693.sra Written 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1236100/ERR1162693.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: 00:03:12 4000000 reads; of these: 4000000 (100.00%) were paired; of these: 177310 (4.43%) aligned concordantly 0 times 3312377 (82.81%) aligned concordantly exactly 1 time 510313 (12.76%) aligned concordantly >1 times ---- 177310 pairs aligned concordantly 0 times; of these: 49234 (27.77%) aligned discordantly 1 time ---- 128076 pairs aligned 0 times concordantly or discordantly; of these: 256152 mates make up the pairs; of these: 206112 (80.46%) aligned 0 times 28882 (11.28%) aligned exactly 1 time 21158 (8.26%) aligned >1 times 97.42% overall alignment rate Time searching: 00:03:12 Overall time: 00:03:12 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] 23950 / 3828524 = 0.0063 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 08:46:31: # Command line: callpeak -t ERX1236100.bam -f BAM -g 12100000 -n ERX1236100.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX1236100.05 # format = BAM # ChIP-seq file = ['ERX1236100.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 08:46:31: #1 read tag files... INFO @ Fri, 15 Feb 2019 08:46:31: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 08:46:31: # Command line: callpeak -t ERX1236100.bam -f BAM -g 12100000 -n ERX1236100.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX1236100.20 # format = BAM # ChIP-seq file = ['ERX1236100.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 08:46:31: #1 read tag files... INFO @ Fri, 15 Feb 2019 08:46:31: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 08:46:31: # Command line: callpeak -t ERX1236100.bam -f BAM -g 12100000 -n ERX1236100.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX1236100.10 # format = BAM # ChIP-seq file = ['ERX1236100.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 08:46:31: #1 read tag files... INFO @ Fri, 15 Feb 2019 08:46:31: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 08:46:37: 1000000 INFO @ Fri, 15 Feb 2019 08:46:38: 1000000 INFO @ Fri, 15 Feb 2019 08:46:38: 1000000 INFO @ Fri, 15 Feb 2019 08:46:43: 2000000 INFO @ Fri, 15 Feb 2019 08:46:44: 2000000 INFO @ Fri, 15 Feb 2019 08:46:44: 2000000 INFO @ Fri, 15 Feb 2019 08:46:50: 3000000 INFO @ Fri, 15 Feb 2019 08:46:51: 3000000 INFO @ Fri, 15 Feb 2019 08:46:51: 3000000 INFO @ Fri, 15 Feb 2019 08:46:56: 4000000 INFO @ Fri, 15 Feb 2019 08:46:59: 4000000 INFO @ Fri, 15 Feb 2019 08:46:59: 4000000 INFO @ Fri, 15 Feb 2019 08:47:02: 5000000 INFO @ Fri, 15 Feb 2019 08:47:06: 5000000 INFO @ Fri, 15 Feb 2019 08:47:06: 5000000 INFO @ Fri, 15 Feb 2019 08:47:08: 6000000 INFO @ Fri, 15 Feb 2019 08:47:14: 6000000 INFO @ Fri, 15 Feb 2019 08:47:14: 6000000 INFO @ Fri, 15 Feb 2019 08:47:14: 7000000 INFO @ Fri, 15 Feb 2019 08:47:19: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 08:47:19: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 08:47:19: #1 total tags in treatment: 3798749 INFO @ Fri, 15 Feb 2019 08:47:19: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 08:47:19: #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 08:47:19: #1 tags after filtering in treatment: 3292209 INFO @ Fri, 15 Feb 2019 08:47:19: #1 Redundant rate of treatment: 0.13 INFO @ Fri, 15 Feb 2019 08:47:19: #1 finished! INFO @ Fri, 15 Feb 2019 08:47:19: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 08:47:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 08:47:19: #2 number of paired peaks: 30 WARNING @ Fri, 15 Feb 2019 08:47:19: Too few paired peaks (30) 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 08:47:19: Process for pairing-model is terminated! cat: ERX1236100.05_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 `ERX1236100.05_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 `ERX1236100.05_*.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 `ERX1236100.05_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 @ Fri, 15 Feb 2019 08:47:21: 7000000 INFO @ Fri, 15 Feb 2019 08:47:21: 7000000 INFO @ Fri, 15 Feb 2019 08:47:26: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 08:47:26: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 08:47:26: #1 total tags in treatment: 3798749 INFO @ Fri, 15 Feb 2019 08:47:26: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 08:47:26: #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 08:47:26: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 08:47:26: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 08:47:26: #1 total tags in treatment: 3798749 INFO @ Fri, 15 Feb 2019 08:47:26: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 08:47:26: #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 08:47:26: #1 tags after filtering in treatment: 3292209 INFO @ Fri, 15 Feb 2019 08:47:26: #1 Redundant rate of treatment: 0.13 INFO @ Fri, 15 Feb 2019 08:47:26: #1 finished! INFO @ Fri, 15 Feb 2019 08:47:26: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 08:47:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 08:47:26: #1 tags after filtering in treatment: 3292209 INFO @ Fri, 15 Feb 2019 08:47:26: #1 Redundant rate of treatment: 0.13 INFO @ Fri, 15 Feb 2019 08:47:26: #1 finished! INFO @ Fri, 15 Feb 2019 08:47:26: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 08:47:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 08:47:26: #2 number of paired peaks: 30 WARNING @ Fri, 15 Feb 2019 08:47:26: Too few paired peaks (30) 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 08:47:26: Process for pairing-model is terminated! INFO @ Fri, 15 Feb 2019 08:47:26: #2 number of paired peaks: 30 WARNING @ Fri, 15 Feb 2019 08:47:26: Too few paired peaks (30) 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 08:47:26: Process for pairing-model is terminated! cat: ERX1236100.20_peaks.narrowPeak: そのようなファイルやディレクトリはありません cat: ERX1236100.10_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) pass1 - making usageList (0 chroms): 2 millis rm: cannot remove `ERX1236100.20_model.r'needLargeMem: trying to allocate 0 bytes (limit: 17179869184) : 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 `ERX1236100.20_*.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 `ERX1236100.20_peaks.narrowPeak': そのようなファイルやディレクトリはありません rm: cannot remove `ERX1236100.10_model.r': そのようなファイルやディレクトリはありません CompletedMACS2peakCalling rm: cannot remove `ERX1236100.10_*.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 `ERX1236100.10_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。