Job ID = 9161975 sra ファイルのダウンロード中... Completed: 1115951K bytes transferred in 12 seconds (706010K bits/sec), in 1 file, 2 directories. 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 25380703 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1423707/SRR2930996.sra Written 25380703 spots total 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: 00:19:28 25380703 reads; of these: 25380703 (100.00%) were paired; of these: 1615828 (6.37%) aligned concordantly 0 times 20903015 (82.36%) aligned concordantly exactly 1 time 2861860 (11.28%) aligned concordantly >1 times ---- 1615828 pairs aligned concordantly 0 times; of these: 43390 (2.69%) aligned discordantly 1 time ---- 1572438 pairs aligned 0 times concordantly or discordantly; of these: 3144876 mates make up the pairs; of these: 2420591 (76.97%) aligned 0 times 626003 (19.91%) aligned exactly 1 time 98282 (3.13%) aligned >1 times 95.23% overall alignment rate Time searching: 00:19:28 Overall time: 00:19:28 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] 20743286 / 23774826 = 0.8725 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 @ Wed, 28 Jun 2017 05:37:26: # Command line: callpeak -t SRX1423707.bam -f BAM -g 12100000 -n SRX1423707.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1423707.10 # format = BAM # ChIP-seq file = ['SRX1423707.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 @ Wed, 28 Jun 2017 05:37:26: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:37:26: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:37:26: # Command line: callpeak -t SRX1423707.bam -f BAM -g 12100000 -n SRX1423707.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1423707.20 # format = BAM # ChIP-seq file = ['SRX1423707.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 @ Wed, 28 Jun 2017 05:37:26: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:37:26: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:37:26: # Command line: callpeak -t SRX1423707.bam -f BAM -g 12100000 -n SRX1423707.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1423707.05 # format = BAM # ChIP-seq file = ['SRX1423707.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 @ Wed, 28 Jun 2017 05:37:26: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:37:26: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:37:32: 1000000 INFO @ Wed, 28 Jun 2017 05:37:32: 1000000 INFO @ Wed, 28 Jun 2017 05:37:32: 1000000 INFO @ Wed, 28 Jun 2017 05:37:39: 2000000 INFO @ Wed, 28 Jun 2017 05:37:39: 2000000 INFO @ Wed, 28 Jun 2017 05:37:39: 2000000 INFO @ Wed, 28 Jun 2017 05:37:46: 3000000 INFO @ Wed, 28 Jun 2017 05:37:46: 3000000 INFO @ Wed, 28 Jun 2017 05:37:46: 3000000 INFO @ Wed, 28 Jun 2017 05:37:53: 4000000 INFO @ Wed, 28 Jun 2017 05:37:53: 4000000 INFO @ Wed, 28 Jun 2017 05:37:53: 4000000 INFO @ Wed, 28 Jun 2017 05:37:59: 5000000 INFO @ Wed, 28 Jun 2017 05:38:00: 5000000 INFO @ Wed, 28 Jun 2017 05:38:00: 5000000 INFO @ Wed, 28 Jun 2017 05:38:06: 6000000 INFO @ Wed, 28 Jun 2017 05:38:06: 6000000 INFO @ Wed, 28 Jun 2017 05:38:07: 6000000 INFO @ Wed, 28 Jun 2017 05:38:12: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:38:12: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:38:12: #1 total tags in treatment: 3028713 INFO @ Wed, 28 Jun 2017 05:38:12: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:38:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 05:38:12: #1 tags after filtering in treatment: 2617717 INFO @ Wed, 28 Jun 2017 05:38:12: #1 Redundant rate of treatment: 0.14 INFO @ Wed, 28 Jun 2017 05:38:12: #1 finished! INFO @ Wed, 28 Jun 2017 05:38:12: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:38:12: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:38:12: #2 number of paired peaks: 33 WARNING @ Wed, 28 Jun 2017 05:38:12: Too few paired peaks (33) 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 @ Wed, 28 Jun 2017 05:38:12: Process for pairing-model is terminated! cat: SRX1423707.05_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 `SRX1423707.05_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 `SRX1423707.05_*.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 `SRX1423707.05_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 @ Wed, 28 Jun 2017 05:38:12: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:38:12: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:38:12: #1 total tags in treatment: 3028713 INFO @ Wed, 28 Jun 2017 05:38:12: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:38:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 05:38:12: #1 tags after filtering in treatment: 2617717 INFO @ Wed, 28 Jun 2017 05:38:12: #1 Redundant rate of treatment: 0.14 INFO @ Wed, 28 Jun 2017 05:38:12: #1 finished! INFO @ Wed, 28 Jun 2017 05:38:12: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:38:12: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:38:12: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:38:12: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:38:12: #1 total tags in treatment: 3028713 INFO @ Wed, 28 Jun 2017 05:38:12: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:38:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 05:38:12: #2 number of paired peaks: 33 WARNING @ Wed, 28 Jun 2017 05:38:12: Too few paired peaks (33) 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 @ Wed, 28 Jun 2017 05:38:12: Process for pairing-model is terminated! cat: SRX1423707.20_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): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX1423707.20_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 `SRX1423707.20_*.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 `SRX1423707.20_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 @ Wed, 28 Jun 2017 05:38:12: #1 tags after filtering in treatment: 2617717 INFO @ Wed, 28 Jun 2017 05:38:12: #1 Redundant rate of treatment: 0.14 INFO @ Wed, 28 Jun 2017 05:38:12: #1 finished! INFO @ Wed, 28 Jun 2017 05:38:12: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:38:12: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:38:13: #2 number of paired peaks: 33 WARNING @ Wed, 28 Jun 2017 05:38:13: Too few paired peaks (33) 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 @ Wed, 28 Jun 2017 05:38:13: Process for pairing-model is terminated! cat: SRX1423707.10_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 `SRX1423707.10_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 `SRX1423707.10_*.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 `SRX1423707.10_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。