Job ID = 10937487 sra ファイルのダウンロード中... Completed: 433791K bytes transferred in 27 seconds (128509K 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 4574288 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3010304/SRR5833297.sra Written 4574288 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3010304/SRR5833297.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: 00:05:47 4574288 reads; of these: 4574288 (100.00%) were paired; of these: 463083 (10.12%) aligned concordantly 0 times 3563712 (77.91%) aligned concordantly exactly 1 time 547493 (11.97%) aligned concordantly >1 times ---- 463083 pairs aligned concordantly 0 times; of these: 59196 (12.78%) aligned discordantly 1 time ---- 403887 pairs aligned 0 times concordantly or discordantly; of these: 807774 mates make up the pairs; of these: 720313 (89.17%) aligned 0 times 57263 (7.09%) aligned exactly 1 time 30198 (3.74%) aligned >1 times 92.13% overall alignment rate Time searching: 00:05:47 Overall time: 00:05:47 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] 67499 / 4148057 = 0.0163 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 02:31:55: # Command line: callpeak -t SRX3010304.bam -f BAM -g 12100000 -n SRX3010304.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3010304.10 # format = BAM # ChIP-seq file = ['SRX3010304.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 02:31:55: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:31:55: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:31:55: # Command line: callpeak -t SRX3010304.bam -f BAM -g 12100000 -n SRX3010304.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3010304.20 # format = BAM # ChIP-seq file = ['SRX3010304.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 02:31:55: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:31:55: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:31:55: # Command line: callpeak -t SRX3010304.bam -f BAM -g 12100000 -n SRX3010304.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3010304.05 # format = BAM # ChIP-seq file = ['SRX3010304.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 02:31:55: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:31:55: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:32:02: 1000000 INFO @ Fri, 10 Aug 2018 02:32:02: 1000000 INFO @ Fri, 10 Aug 2018 02:32:02: 1000000 INFO @ Fri, 10 Aug 2018 02:32:09: 2000000 INFO @ Fri, 10 Aug 2018 02:32:10: 2000000 INFO @ Fri, 10 Aug 2018 02:32:10: 2000000 INFO @ Fri, 10 Aug 2018 02:32:15: 3000000 INFO @ Fri, 10 Aug 2018 02:32:18: 3000000 INFO @ Fri, 10 Aug 2018 02:32:19: 3000000 INFO @ Fri, 10 Aug 2018 02:32:22: 4000000 INFO @ Fri, 10 Aug 2018 02:32:26: 4000000 INFO @ Fri, 10 Aug 2018 02:32:28: 5000000 INFO @ Fri, 10 Aug 2018 02:32:29: 4000000 INFO @ Fri, 10 Aug 2018 02:32:35: 5000000 INFO @ Fri, 10 Aug 2018 02:32:35: 6000000 INFO @ Fri, 10 Aug 2018 02:32:39: 5000000 INFO @ Fri, 10 Aug 2018 02:32:41: 7000000 INFO @ Fri, 10 Aug 2018 02:32:43: 6000000 INFO @ Fri, 10 Aug 2018 02:32:48: 6000000 INFO @ Fri, 10 Aug 2018 02:32:49: 8000000 INFO @ Fri, 10 Aug 2018 02:32:50: 7000000 INFO @ Fri, 10 Aug 2018 02:32:51: #1 tag size is determined as 101 bps INFO @ Fri, 10 Aug 2018 02:32:51: #1 tag size = 101 INFO @ Fri, 10 Aug 2018 02:32:51: #1 total tags in treatment: 4043959 INFO @ Fri, 10 Aug 2018 02:32:51: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:32:51: #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 02:32:51: #1 tags after filtering in treatment: 3378311 INFO @ Fri, 10 Aug 2018 02:32:51: #1 Redundant rate of treatment: 0.16 INFO @ Fri, 10 Aug 2018 02:32:51: #1 finished! INFO @ Fri, 10 Aug 2018 02:32:51: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:32:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:32:51: #2 number of paired peaks: 71 WARNING @ Fri, 10 Aug 2018 02:32:51: Too few paired peaks (71) 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 02:32:51: Process for pairing-model is terminated! cat: SRX3010304.10_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3010304.10_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 `SRX3010304.10_*.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 `SRX3010304.10_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 @ Fri, 10 Aug 2018 02:32:56: 7000000 INFO @ Fri, 10 Aug 2018 02:32:57: 8000000 INFO @ Fri, 10 Aug 2018 02:32:59: #1 tag size is determined as 101 bps INFO @ Fri, 10 Aug 2018 02:32:59: #1 tag size = 101 INFO @ Fri, 10 Aug 2018 02:32:59: #1 total tags in treatment: 4043959 INFO @ Fri, 10 Aug 2018 02:32:59: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:32:59: #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 02:33:00: #1 tags after filtering in treatment: 3378311 INFO @ Fri, 10 Aug 2018 02:33:00: #1 Redundant rate of treatment: 0.16 INFO @ Fri, 10 Aug 2018 02:33:00: #1 finished! INFO @ Fri, 10 Aug 2018 02:33:00: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:33:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:33:00: #2 number of paired peaks: 71 WARNING @ Fri, 10 Aug 2018 02:33:00: Too few paired peaks (71) 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 02:33:00: Process for pairing-model is terminated! cat: SRX3010304.05_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3010304.05_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 `SRX3010304.05_*.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 `SRX3010304.05_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 02:33:03: 8000000 INFO @ Fri, 10 Aug 2018 02:33:05: #1 tag size is determined as 101 bps INFO @ Fri, 10 Aug 2018 02:33:05: #1 tag size = 101 INFO @ Fri, 10 Aug 2018 02:33:05: #1 total tags in treatment: 4043959 INFO @ Fri, 10 Aug 2018 02:33:05: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:33:05: #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 02:33:05: #1 tags after filtering in treatment: 3378311 INFO @ Fri, 10 Aug 2018 02:33:05: #1 Redundant rate of treatment: 0.16 INFO @ Fri, 10 Aug 2018 02:33:05: #1 finished! INFO @ Fri, 10 Aug 2018 02:33:05: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:33:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:33:05: #2 number of paired peaks: 71 WARNING @ Fri, 10 Aug 2018 02:33:05: Too few paired peaks (71) 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 02:33:05: Process for pairing-model is terminated! cat: SRX3010304.20_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3010304.20_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 `SRX3010304.20_*.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 `SRX3010304.20_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。