Job ID = 11245185 sra ファイルのダウンロード中... Completed: 19603K bytes transferred in 3 seconds (50945K bits/sec), in 1 file. Completed: 127877K bytes transferred in 4 seconds (244582K 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 415375 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669626/SRR7818220.sra Written 415375 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669626/SRR7818220.sra Read 3394262 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669626/SRR7818221.sra Written 3394262 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669626/SRR7818221.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 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: 00:02:56 3809637 reads; of these: 3809637 (100.00%) were paired; of these: 386133 (10.14%) aligned concordantly 0 times 3006491 (78.92%) aligned concordantly exactly 1 time 417013 (10.95%) aligned concordantly >1 times ---- 386133 pairs aligned concordantly 0 times; of these: 14773 (3.83%) aligned discordantly 1 time ---- 371360 pairs aligned 0 times concordantly or discordantly; of these: 742720 mates make up the pairs; of these: 602155 (81.07%) aligned 0 times 98070 (13.20%) aligned exactly 1 time 42495 (5.72%) aligned >1 times 92.10% overall alignment rate Time searching: 00:02:56 Overall time: 00:02:56 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] 524335 / 3435679 = 0.1526 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 @ Tue, 09 Oct 2018 23:49:00: # Command line: callpeak -t SRX4669626.bam -f BAM -g 12100000 -n SRX4669626.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4669626.20 # format = BAM # ChIP-seq file = ['SRX4669626.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 @ Tue, 09 Oct 2018 23:49:00: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:49:00: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:49:00: # Command line: callpeak -t SRX4669626.bam -f BAM -g 12100000 -n SRX4669626.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4669626.10 # format = BAM # ChIP-seq file = ['SRX4669626.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 @ Tue, 09 Oct 2018 23:49:00: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:49:00: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:49:00: # Command line: callpeak -t SRX4669626.bam -f BAM -g 12100000 -n SRX4669626.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4669626.05 # format = BAM # ChIP-seq file = ['SRX4669626.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 @ Tue, 09 Oct 2018 23:49:00: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:49:00: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:49:07: 1000000 INFO @ Tue, 09 Oct 2018 23:49:08: 1000000 INFO @ Tue, 09 Oct 2018 23:49:10: 1000000 INFO @ Tue, 09 Oct 2018 23:49:15: 2000000 INFO @ Tue, 09 Oct 2018 23:49:17: 2000000 INFO @ Tue, 09 Oct 2018 23:49:20: 2000000 INFO @ Tue, 09 Oct 2018 23:49:23: 3000000 INFO @ Tue, 09 Oct 2018 23:49:26: 3000000 INFO @ Tue, 09 Oct 2018 23:49:31: 4000000 INFO @ Tue, 09 Oct 2018 23:49:31: 3000000 INFO @ Tue, 09 Oct 2018 23:49:35: 4000000 INFO @ Tue, 09 Oct 2018 23:49:39: 5000000 INFO @ Tue, 09 Oct 2018 23:49:42: 4000000 INFO @ Tue, 09 Oct 2018 23:49:44: 5000000 INFO @ Tue, 09 Oct 2018 23:49:47: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:49:47: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:49:47: #1 total tags in treatment: 2901117 INFO @ Tue, 09 Oct 2018 23:49:47: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:49:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:49:47: #1 tags after filtering in treatment: 2507080 INFO @ Tue, 09 Oct 2018 23:49:47: #1 Redundant rate of treatment: 0.14 INFO @ Tue, 09 Oct 2018 23:49:47: #1 finished! INFO @ Tue, 09 Oct 2018 23:49:47: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:49:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:49:47: #2 number of paired peaks: 45 WARNING @ Tue, 09 Oct 2018 23:49:47: Too few paired peaks (45) 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 @ Tue, 09 Oct 2018 23:49:47: Process for pairing-model is terminated! cat: SRX4669626.10_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): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4669626.10_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 `SRX4669626.10_*.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 `SRX4669626.10_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 @ Tue, 09 Oct 2018 23:49:53: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:49:53: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:49:53: #1 total tags in treatment: 2901117 INFO @ Tue, 09 Oct 2018 23:49:53: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:49:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:49:53: #1 tags after filtering in treatment: 2507080 INFO @ Tue, 09 Oct 2018 23:49:53: #1 Redundant rate of treatment: 0.14 INFO @ Tue, 09 Oct 2018 23:49:53: #1 finished! INFO @ Tue, 09 Oct 2018 23:49:53: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:49:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:49:53: 5000000 INFO @ Tue, 09 Oct 2018 23:49:53: #2 number of paired peaks: 45 WARNING @ Tue, 09 Oct 2018 23:49:53: Too few paired peaks (45) 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 @ Tue, 09 Oct 2018 23:49:53: Process for pairing-model is terminated! cat: SRX4669626.05_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 `SRX4669626.05_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 `SRX4669626.05_*.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 `SRX4669626.05_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 @ Tue, 09 Oct 2018 23:50:03: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:50:03: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:50:03: #1 total tags in treatment: 2901117 INFO @ Tue, 09 Oct 2018 23:50:03: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:50:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:50:03: #1 tags after filtering in treatment: 2507080 INFO @ Tue, 09 Oct 2018 23:50:03: #1 Redundant rate of treatment: 0.14 INFO @ Tue, 09 Oct 2018 23:50:03: #1 finished! INFO @ Tue, 09 Oct 2018 23:50:03: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:50:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:50:03: #2 number of paired peaks: 45 WARNING @ Tue, 09 Oct 2018 23:50:03: Too few paired peaks (45) 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 @ Tue, 09 Oct 2018 23:50:03: Process for pairing-model is terminated! cat: SRX4669626.20_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 `SRX4669626.20_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 `SRX4669626.20_*.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 `SRX4669626.20_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。