Job ID = 11193124 sra ファイルのダウンロード中... Completed: 558480K bytes transferred in 13 seconds (335618K 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 17500280 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4337716/SRR7467887.sra Written 17500280 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4337716/SRR7467887.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: 00:10:06 17500280 reads; of these: 17500280 (100.00%) were paired; of these: 10617657 (60.67%) aligned concordantly 0 times 5313776 (30.36%) aligned concordantly exactly 1 time 1568847 (8.96%) aligned concordantly >1 times ---- 10617657 pairs aligned concordantly 0 times; of these: 1048872 (9.88%) aligned discordantly 1 time ---- 9568785 pairs aligned 0 times concordantly or discordantly; of these: 19137570 mates make up the pairs; of these: 15034066 (78.56%) aligned 0 times 2853187 (14.91%) aligned exactly 1 time 1250317 (6.53%) aligned >1 times 57.05% overall alignment rate Time searching: 00:10:06 Overall time: 00:10:06 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] 1667618 / 7431838 = 0.2244 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 @ Sat, 15 Sep 2018 11:15:12: # Command line: callpeak -t SRX4337716.bam -f BAM -g 12100000 -n SRX4337716.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4337716.20 # format = BAM # ChIP-seq file = ['SRX4337716.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 @ Sat, 15 Sep 2018 11:15:12: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:15:12: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:15:12: # Command line: callpeak -t SRX4337716.bam -f BAM -g 12100000 -n SRX4337716.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4337716.10 # format = BAM # ChIP-seq file = ['SRX4337716.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 @ Sat, 15 Sep 2018 11:15:12: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:15:12: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:15:12: # Command line: callpeak -t SRX4337716.bam -f BAM -g 12100000 -n SRX4337716.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4337716.05 # format = BAM # ChIP-seq file = ['SRX4337716.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 @ Sat, 15 Sep 2018 11:15:12: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:15:12: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:15:18: 1000000 INFO @ Sat, 15 Sep 2018 11:15:18: 1000000 INFO @ Sat, 15 Sep 2018 11:15:18: 1000000 INFO @ Sat, 15 Sep 2018 11:15:24: 2000000 INFO @ Sat, 15 Sep 2018 11:15:25: 2000000 INFO @ Sat, 15 Sep 2018 11:15:25: 2000000 INFO @ Sat, 15 Sep 2018 11:15:31: 3000000 INFO @ Sat, 15 Sep 2018 11:15:31: 3000000 INFO @ Sat, 15 Sep 2018 11:15:31: 3000000 INFO @ Sat, 15 Sep 2018 11:15:37: 4000000 INFO @ Sat, 15 Sep 2018 11:15:37: 4000000 INFO @ Sat, 15 Sep 2018 11:15:37: 4000000 INFO @ Sat, 15 Sep 2018 11:15:43: 5000000 INFO @ Sat, 15 Sep 2018 11:15:43: 5000000 INFO @ Sat, 15 Sep 2018 11:15:43: 5000000 INFO @ Sat, 15 Sep 2018 11:15:49: 6000000 INFO @ Sat, 15 Sep 2018 11:15:49: 6000000 INFO @ Sat, 15 Sep 2018 11:15:50: 6000000 INFO @ Sat, 15 Sep 2018 11:15:56: 7000000 INFO @ Sat, 15 Sep 2018 11:15:56: 7000000 INFO @ Sat, 15 Sep 2018 11:15:56: 7000000 INFO @ Sat, 15 Sep 2018 11:16:02: 8000000 INFO @ Sat, 15 Sep 2018 11:16:02: 8000000 INFO @ Sat, 15 Sep 2018 11:16:03: 8000000 INFO @ Sat, 15 Sep 2018 11:16:07: 9000000 INFO @ Sat, 15 Sep 2018 11:16:09: 9000000 INFO @ Sat, 15 Sep 2018 11:16:10: 9000000 INFO @ Sat, 15 Sep 2018 11:16:13: 10000000 INFO @ Sat, 15 Sep 2018 11:16:16: 10000000 INFO @ Sat, 15 Sep 2018 11:16:17: 10000000 INFO @ Sat, 15 Sep 2018 11:16:18: 11000000 INFO @ Sat, 15 Sep 2018 11:16:23: 11000000 INFO @ Sat, 15 Sep 2018 11:16:24: 12000000 INFO @ Sat, 15 Sep 2018 11:16:24: 11000000 INFO @ Sat, 15 Sep 2018 11:16:30: 13000000 INFO @ Sat, 15 Sep 2018 11:16:30: 12000000 INFO @ Sat, 15 Sep 2018 11:16:32: 12000000 INFO @ Sat, 15 Sep 2018 11:16:35: 14000000 INFO @ Sat, 15 Sep 2018 11:16:37: 13000000 INFO @ Sat, 15 Sep 2018 11:16:39: 13000000 INFO @ Sat, 15 Sep 2018 11:16:41: 15000000 INFO @ Sat, 15 Sep 2018 11:16:44: 14000000 INFO @ Sat, 15 Sep 2018 11:16:46: 14000000 INFO @ Sat, 15 Sep 2018 11:16:47: 16000000 INFO @ Sat, 15 Sep 2018 11:16:51: #1 tag size is determined as 41 bps INFO @ Sat, 15 Sep 2018 11:16:51: #1 tag size = 41 INFO @ Sat, 15 Sep 2018 11:16:51: #1 total tags in treatment: 5430422 INFO @ Sat, 15 Sep 2018 11:16:51: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:16:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 11:16:51: 15000000 INFO @ Sat, 15 Sep 2018 11:16:51: #1 tags after filtering in treatment: 4029005 INFO @ Sat, 15 Sep 2018 11:16:51: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 15 Sep 2018 11:16:51: #1 finished! INFO @ Sat, 15 Sep 2018 11:16:51: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:16:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:16:51: #2 number of paired peaks: 30 WARNING @ Sat, 15 Sep 2018 11:16:51: Too few paired peaks (30) 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 @ Sat, 15 Sep 2018 11:16:51: Process for pairing-model is terminated! cat: SRX4337716.10_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 `SRX4337716.10_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 `SRX4337716.10_*.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 `SRX4337716.10_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 @ Sat, 15 Sep 2018 11:16:53: 15000000 INFO @ Sat, 15 Sep 2018 11:16:57: 16000000 INFO @ Sat, 15 Sep 2018 11:16:59: 16000000 INFO @ Sat, 15 Sep 2018 11:17:01: #1 tag size is determined as 41 bps INFO @ Sat, 15 Sep 2018 11:17:01: #1 tag size = 41 INFO @ Sat, 15 Sep 2018 11:17:01: #1 total tags in treatment: 5430422 INFO @ Sat, 15 Sep 2018 11:17:01: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:17:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 11:17:01: #1 tags after filtering in treatment: 4029005 INFO @ Sat, 15 Sep 2018 11:17:01: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 15 Sep 2018 11:17:01: #1 finished! INFO @ Sat, 15 Sep 2018 11:17:01: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:17:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:17:02: #2 number of paired peaks: 30 WARNING @ Sat, 15 Sep 2018 11:17:02: Too few paired peaks (30) 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 @ Sat, 15 Sep 2018 11:17:02: Process for pairing-model is terminated! cat: SRX4337716.20_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 `SRX4337716.20_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 `SRX4337716.20_*.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 `SRX4337716.20_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 @ Sat, 15 Sep 2018 11:17:03: #1 tag size is determined as 41 bps INFO @ Sat, 15 Sep 2018 11:17:03: #1 tag size = 41 INFO @ Sat, 15 Sep 2018 11:17:03: #1 total tags in treatment: 5430422 INFO @ Sat, 15 Sep 2018 11:17:03: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:17:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 11:17:03: #1 tags after filtering in treatment: 4029005 INFO @ Sat, 15 Sep 2018 11:17:03: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 15 Sep 2018 11:17:03: #1 finished! INFO @ Sat, 15 Sep 2018 11:17:03: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:17:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:17:04: #2 number of paired peaks: 30 WARNING @ Sat, 15 Sep 2018 11:17:04: Too few paired peaks (30) 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 @ Sat, 15 Sep 2018 11:17:04: Process for pairing-model is terminated! cat: SRX4337716.05_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 `SRX4337716.05_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 `SRX4337716.05_*.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 `SRX4337716.05_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。