Job ID = 11244872 sra ファイルのダウンロード中... Completed: 1031962K bytes transferred in 13 seconds (643778K 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 10517043 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3765664/SRR6807387.sra Written 10517043 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3765664/SRR6807387.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: 00:15:42 10517043 reads; of these: 10517043 (100.00%) were paired; of these: 462551 (4.40%) aligned concordantly 0 times 8172842 (77.71%) aligned concordantly exactly 1 time 1881650 (17.89%) aligned concordantly >1 times ---- 462551 pairs aligned concordantly 0 times; of these: 156999 (33.94%) aligned discordantly 1 time ---- 305552 pairs aligned 0 times concordantly or discordantly; of these: 611104 mates make up the pairs; of these: 378195 (61.89%) aligned 0 times 128667 (21.05%) aligned exactly 1 time 104242 (17.06%) aligned >1 times 98.20% overall alignment rate Time searching: 00:15:42 Overall time: 00:15:42 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 12 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] 1304961 / 10186190 = 0.1281 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 22:41:55: # Command line: callpeak -t SRX3765664.bam -f BAM -g 12100000 -n SRX3765664.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3765664.20 # format = BAM # ChIP-seq file = ['SRX3765664.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 22:41:55: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:41:55: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:41:55: # Command line: callpeak -t SRX3765664.bam -f BAM -g 12100000 -n SRX3765664.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3765664.05 # format = BAM # ChIP-seq file = ['SRX3765664.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 22:41:55: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:41:55: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:41:55: # Command line: callpeak -t SRX3765664.bam -f BAM -g 12100000 -n SRX3765664.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3765664.10 # format = BAM # ChIP-seq file = ['SRX3765664.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 22:41:55: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:41:55: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:42:04: 1000000 INFO @ Tue, 09 Oct 2018 22:42:04: 1000000 INFO @ Tue, 09 Oct 2018 22:42:06: 1000000 INFO @ Tue, 09 Oct 2018 22:42:12: 2000000 INFO @ Tue, 09 Oct 2018 22:42:12: 2000000 INFO @ Tue, 09 Oct 2018 22:42:17: 2000000 INFO @ Tue, 09 Oct 2018 22:42:22: 3000000 INFO @ Tue, 09 Oct 2018 22:42:22: 3000000 INFO @ Tue, 09 Oct 2018 22:42:28: 3000000 INFO @ Tue, 09 Oct 2018 22:42:31: 4000000 INFO @ Tue, 09 Oct 2018 22:42:31: 4000000 INFO @ Tue, 09 Oct 2018 22:42:38: 4000000 INFO @ Tue, 09 Oct 2018 22:42:41: 5000000 INFO @ Tue, 09 Oct 2018 22:42:41: 5000000 INFO @ Tue, 09 Oct 2018 22:42:49: 5000000 INFO @ Tue, 09 Oct 2018 22:42:50: 6000000 INFO @ Tue, 09 Oct 2018 22:42:50: 6000000 INFO @ Tue, 09 Oct 2018 22:42:59: 6000000 INFO @ Tue, 09 Oct 2018 22:43:00: 7000000 INFO @ Tue, 09 Oct 2018 22:43:00: 7000000 INFO @ Tue, 09 Oct 2018 22:43:09: 7000000 INFO @ Tue, 09 Oct 2018 22:43:10: 8000000 INFO @ Tue, 09 Oct 2018 22:43:10: 8000000 INFO @ Tue, 09 Oct 2018 22:43:19: 9000000 INFO @ Tue, 09 Oct 2018 22:43:19: 9000000 INFO @ Tue, 09 Oct 2018 22:43:20: 8000000 INFO @ Tue, 09 Oct 2018 22:43:29: 10000000 INFO @ Tue, 09 Oct 2018 22:43:29: 10000000 INFO @ Tue, 09 Oct 2018 22:43:30: 9000000 INFO @ Tue, 09 Oct 2018 22:43:38: 11000000 INFO @ Tue, 09 Oct 2018 22:43:38: 11000000 INFO @ Tue, 09 Oct 2018 22:43:40: 10000000 INFO @ Tue, 09 Oct 2018 22:43:48: 12000000 INFO @ Tue, 09 Oct 2018 22:43:48: 12000000 INFO @ Tue, 09 Oct 2018 22:43:51: 11000000 INFO @ Tue, 09 Oct 2018 22:43:57: 13000000 INFO @ Tue, 09 Oct 2018 22:43:57: 13000000 INFO @ Tue, 09 Oct 2018 22:44:01: 12000000 INFO @ Tue, 09 Oct 2018 22:44:07: 14000000 INFO @ Tue, 09 Oct 2018 22:44:07: 14000000 INFO @ Tue, 09 Oct 2018 22:44:11: 13000000 INFO @ Tue, 09 Oct 2018 22:44:16: 15000000 INFO @ Tue, 09 Oct 2018 22:44:16: 15000000 INFO @ Tue, 09 Oct 2018 22:44:22: 14000000 INFO @ Tue, 09 Oct 2018 22:44:26: 16000000 INFO @ Tue, 09 Oct 2018 22:44:26: 16000000 INFO @ Tue, 09 Oct 2018 22:44:32: 15000000 INFO @ Tue, 09 Oct 2018 22:44:35: 17000000 INFO @ Tue, 09 Oct 2018 22:44:35: 17000000 INFO @ Tue, 09 Oct 2018 22:44:42: 16000000 INFO @ Tue, 09 Oct 2018 22:44:45: 18000000 INFO @ Tue, 09 Oct 2018 22:44:45: 18000000 INFO @ Tue, 09 Oct 2018 22:44:45: #1 tag size is determined as 100 bps INFO @ Tue, 09 Oct 2018 22:44:45: #1 tag size = 100 INFO @ Tue, 09 Oct 2018 22:44:45: #1 total tags in treatment: 8757942 INFO @ Tue, 09 Oct 2018 22:44:45: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:44:45: #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 22:44:45: #1 tag size is determined as 100 bps INFO @ Tue, 09 Oct 2018 22:44:45: #1 tag size = 100 INFO @ Tue, 09 Oct 2018 22:44:45: #1 total tags in treatment: 8757942 INFO @ Tue, 09 Oct 2018 22:44:45: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:44:45: #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 22:44:45: #1 tags after filtering in treatment: 6347269 INFO @ Tue, 09 Oct 2018 22:44:45: #1 Redundant rate of treatment: 0.28 INFO @ Tue, 09 Oct 2018 22:44:45: #1 finished! INFO @ Tue, 09 Oct 2018 22:44:45: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:44:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:44:46: #1 tags after filtering in treatment: 6347269 INFO @ Tue, 09 Oct 2018 22:44:46: #1 Redundant rate of treatment: 0.28 INFO @ Tue, 09 Oct 2018 22:44:46: #1 finished! INFO @ Tue, 09 Oct 2018 22:44:46: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:44:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:44:46: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 22:44:46: Too few paired peaks (0) 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 22:44:46: Process for pairing-model is terminated! cat: SRX3765664.20_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 `SRX3765664.20_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 `SRX3765664.20_*.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 `SRX3765664.20_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 @ Tue, 09 Oct 2018 22:44:46: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 22:44:46: Too few paired peaks (0) 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 22:44:46: Process for pairing-model is terminated! cat: SRX3765664.05_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 `SRX3765664.05_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 `SRX3765664.05_*.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 `SRX3765664.05_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 22:44:53: 17000000 INFO @ Tue, 09 Oct 2018 22:45:02: 18000000 INFO @ Tue, 09 Oct 2018 22:45:03: #1 tag size is determined as 100 bps INFO @ Tue, 09 Oct 2018 22:45:03: #1 tag size = 100 INFO @ Tue, 09 Oct 2018 22:45:03: #1 total tags in treatment: 8757942 INFO @ Tue, 09 Oct 2018 22:45:03: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:45:03: #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 22:45:03: #1 tags after filtering in treatment: 6347269 INFO @ Tue, 09 Oct 2018 22:45:03: #1 Redundant rate of treatment: 0.28 INFO @ Tue, 09 Oct 2018 22:45:03: #1 finished! INFO @ Tue, 09 Oct 2018 22:45:03: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:45:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:45:03: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 22:45:03: Too few paired peaks (0) 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 22:45:03: Process for pairing-model is terminated! cat: SRX3765664.10_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 `SRX3765664.10_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 `SRX3765664.10_*.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 `SRX3765664.10_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。