Job ID = 10937371 sra ファイルのダウンロード中... Completed: 363948K bytes transferred in 6 seconds (480436K 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 5081938 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2198715/SRR4304445.sra Written 5081938 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2198715/SRR4304445.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: 00:04:40 5081938 reads; of these: 5081938 (100.00%) were paired; of these: 301645 (5.94%) aligned concordantly 0 times 3840649 (75.57%) aligned concordantly exactly 1 time 939644 (18.49%) aligned concordantly >1 times ---- 301645 pairs aligned concordantly 0 times; of these: 82026 (27.19%) aligned discordantly 1 time ---- 219619 pairs aligned 0 times concordantly or discordantly; of these: 439238 mates make up the pairs; of these: 270391 (61.56%) aligned 0 times 108157 (24.62%) aligned exactly 1 time 60690 (13.82%) aligned >1 times 97.34% overall alignment rate Time searching: 00:04:40 Overall time: 00:04:40 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] 499353 / 4834834 = 0.1033 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 02:01:15: # Command line: callpeak -t SRX2198715.bam -f BAM -g 12100000 -n SRX2198715.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2198715.05 # format = BAM # ChIP-seq file = ['SRX2198715.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 02:01:15: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:01:15: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:01:15: # Command line: callpeak -t SRX2198715.bam -f BAM -g 12100000 -n SRX2198715.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2198715.10 # format = BAM # ChIP-seq file = ['SRX2198715.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 02:01:15: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:01:15: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:01:15: # Command line: callpeak -t SRX2198715.bam -f BAM -g 12100000 -n SRX2198715.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2198715.20 # format = BAM # ChIP-seq file = ['SRX2198715.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 02:01:15: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:01:15: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:01:24: 1000000 INFO @ Fri, 10 Aug 2018 02:01:24: 1000000 INFO @ Fri, 10 Aug 2018 02:01:24: 1000000 INFO @ Fri, 10 Aug 2018 02:01:32: 2000000 INFO @ Fri, 10 Aug 2018 02:01:32: 2000000 INFO @ Fri, 10 Aug 2018 02:01:33: 2000000 INFO @ Fri, 10 Aug 2018 02:01:41: 3000000 INFO @ Fri, 10 Aug 2018 02:01:41: 3000000 INFO @ Fri, 10 Aug 2018 02:01:42: 3000000 INFO @ Fri, 10 Aug 2018 02:01:49: 4000000 INFO @ Fri, 10 Aug 2018 02:01:49: 4000000 INFO @ Fri, 10 Aug 2018 02:01:52: 4000000 INFO @ Fri, 10 Aug 2018 02:01:58: 5000000 INFO @ Fri, 10 Aug 2018 02:01:58: 5000000 INFO @ Fri, 10 Aug 2018 02:02:01: 5000000 INFO @ Fri, 10 Aug 2018 02:02:06: 6000000 INFO @ Fri, 10 Aug 2018 02:02:06: 6000000 INFO @ Fri, 10 Aug 2018 02:02:10: 6000000 INFO @ Fri, 10 Aug 2018 02:02:15: 7000000 INFO @ Fri, 10 Aug 2018 02:02:15: 7000000 INFO @ Fri, 10 Aug 2018 02:02:19: 7000000 INFO @ Fri, 10 Aug 2018 02:02:23: 8000000 INFO @ Fri, 10 Aug 2018 02:02:23: 8000000 INFO @ Fri, 10 Aug 2018 02:02:29: 8000000 INFO @ Fri, 10 Aug 2018 02:02:31: #1 tag size is determined as 51 bps INFO @ Fri, 10 Aug 2018 02:02:31: #1 tag size = 51 INFO @ Fri, 10 Aug 2018 02:02:31: #1 total tags in treatment: 4302620 INFO @ Fri, 10 Aug 2018 02:02:31: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:02:31: #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 02:02:31: #1 tag size is determined as 51 bps INFO @ Fri, 10 Aug 2018 02:02:31: #1 tag size = 51 INFO @ Fri, 10 Aug 2018 02:02:31: #1 total tags in treatment: 4302620 INFO @ Fri, 10 Aug 2018 02:02:31: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:02:31: #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 02:02:31: #1 tags after filtering in treatment: 3269000 INFO @ Fri, 10 Aug 2018 02:02:31: #1 Redundant rate of treatment: 0.24 INFO @ Fri, 10 Aug 2018 02:02:31: #1 finished! INFO @ Fri, 10 Aug 2018 02:02:31: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:02:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:02:31: #1 tags after filtering in treatment: 3269000 INFO @ Fri, 10 Aug 2018 02:02:31: #1 Redundant rate of treatment: 0.24 INFO @ Fri, 10 Aug 2018 02:02:31: #1 finished! INFO @ Fri, 10 Aug 2018 02:02:31: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:02:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:02:31: #2 number of paired peaks: 35 WARNING @ Fri, 10 Aug 2018 02:02:31: Too few paired peaks (35) 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 02:02:31: Process for pairing-model is terminated! INFO @ Fri, 10 Aug 2018 02:02:31: #2 number of paired peaks: 35 WARNING @ Fri, 10 Aug 2018 02:02:31: Too few paired peaks (35) 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 02:02:31: Process for pairing-model is terminated! cat: SRX2198715.20_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: SRX2198715.05_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) pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2198715.20_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 `SRX2198715.20_*.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 `SRX2198715.20_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 rm: cannot remove `SRX2198715.05_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 `SRX2198715.05_*.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 `SRX2198715.05_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, 10 Aug 2018 02:02:37: #1 tag size is determined as 51 bps INFO @ Fri, 10 Aug 2018 02:02:37: #1 tag size = 51 INFO @ Fri, 10 Aug 2018 02:02:37: #1 total tags in treatment: 4302620 INFO @ Fri, 10 Aug 2018 02:02:37: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:02:37: #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 02:02:37: #1 tags after filtering in treatment: 3269000 INFO @ Fri, 10 Aug 2018 02:02:37: #1 Redundant rate of treatment: 0.24 INFO @ Fri, 10 Aug 2018 02:02:37: #1 finished! INFO @ Fri, 10 Aug 2018 02:02:37: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:02:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:02:37: #2 number of paired peaks: 35 WARNING @ Fri, 10 Aug 2018 02:02:37: Too few paired peaks (35) 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 02:02:37: Process for pairing-model is terminated! cat: SRX2198715.10_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 `SRX2198715.10_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 `SRX2198715.10_*.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 `SRX2198715.10_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。