Job ID = 1293718 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T16:54:29 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-06-02T16:54:29 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 18,246,387 reads read : 18,246,387 reads written : 18,246,387 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: No such file or directory 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: 00:05:16 18246387 reads; of these: 18246387 (100.00%) were unpaired; of these: 177677 (0.97%) aligned 0 times 14809107 (81.16%) aligned exactly 1 time 3259603 (17.86%) aligned >1 times 99.03% overall alignment rate Time searching: 00:05:16 Overall time: 00:05:16 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 3737647 / 18068710 = 0.2069 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 @ Mon, 03 Jun 2019 02:08:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX111796/SRX111796.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX111796/SRX111796.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX111796/SRX111796.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX111796/SRX111796.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 02:08:11: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:08:11: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:08:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX111796/SRX111796.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX111796/SRX111796.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX111796/SRX111796.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX111796/SRX111796.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 02:08:11: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:08:11: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:08:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX111796/SRX111796.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX111796/SRX111796.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX111796/SRX111796.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX111796/SRX111796.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 02:08:11: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:08:11: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:08:20: 1000000 INFO @ Mon, 03 Jun 2019 02:08:21: 1000000 INFO @ Mon, 03 Jun 2019 02:08:21: 1000000 INFO @ Mon, 03 Jun 2019 02:08:28: 2000000 INFO @ Mon, 03 Jun 2019 02:08:29: 2000000 INFO @ Mon, 03 Jun 2019 02:08:30: 2000000 INFO @ Mon, 03 Jun 2019 02:08:37: 3000000 INFO @ Mon, 03 Jun 2019 02:08:38: 3000000 INFO @ Mon, 03 Jun 2019 02:08:39: 3000000 INFO @ Mon, 03 Jun 2019 02:08:45: 4000000 INFO @ Mon, 03 Jun 2019 02:08:47: 4000000 INFO @ Mon, 03 Jun 2019 02:08:49: 4000000 INFO @ Mon, 03 Jun 2019 02:08:54: 5000000 INFO @ Mon, 03 Jun 2019 02:08:56: 5000000 INFO @ Mon, 03 Jun 2019 02:08:58: 5000000 INFO @ Mon, 03 Jun 2019 02:09:03: 6000000 INFO @ Mon, 03 Jun 2019 02:09:05: 6000000 INFO @ Mon, 03 Jun 2019 02:09:08: 6000000 INFO @ Mon, 03 Jun 2019 02:09:11: 7000000 INFO @ Mon, 03 Jun 2019 02:09:14: 7000000 INFO @ Mon, 03 Jun 2019 02:09:17: 7000000 INFO @ Mon, 03 Jun 2019 02:09:19: 8000000 INFO @ Mon, 03 Jun 2019 02:09:23: 8000000 INFO @ Mon, 03 Jun 2019 02:09:27: 8000000 INFO @ Mon, 03 Jun 2019 02:09:28: 9000000 INFO @ Mon, 03 Jun 2019 02:09:32: 9000000 INFO @ Mon, 03 Jun 2019 02:09:36: 10000000 INFO @ Mon, 03 Jun 2019 02:09:37: 9000000 INFO @ Mon, 03 Jun 2019 02:09:41: 10000000 INFO @ Mon, 03 Jun 2019 02:09:44: 11000000 INFO @ Mon, 03 Jun 2019 02:09:46: 10000000 INFO @ Mon, 03 Jun 2019 02:09:50: 11000000 INFO @ Mon, 03 Jun 2019 02:09:53: 12000000 INFO @ Mon, 03 Jun 2019 02:09:56: 11000000 INFO @ Mon, 03 Jun 2019 02:09:59: 12000000 INFO @ Mon, 03 Jun 2019 02:10:01: 13000000 INFO @ Mon, 03 Jun 2019 02:10:05: 12000000 INFO @ Mon, 03 Jun 2019 02:10:08: 13000000 INFO @ Mon, 03 Jun 2019 02:10:10: 14000000 INFO @ Mon, 03 Jun 2019 02:10:13: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 02:10:13: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 02:10:13: #1 total tags in treatment: 14331063 INFO @ Mon, 03 Jun 2019 02:10:13: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:10:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 02:10:13: #1 tags after filtering in treatment: 14331063 INFO @ Mon, 03 Jun 2019 02:10:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:10:13: #1 finished! INFO @ Mon, 03 Jun 2019 02:10:13: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:10:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:10:14: 13000000 INFO @ Mon, 03 Jun 2019 02:10:14: #2 number of paired peaks: 46 WARNING @ Mon, 03 Jun 2019 02:10:14: Too few paired peaks (46) 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 @ Mon, 03 Jun 2019 02:10:14: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX111796/SRX111796.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111796/SRX111796.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111796/SRX111796.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111796/SRX111796.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:10:17: 14000000 INFO @ Mon, 03 Jun 2019 02:10:20: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 02:10:20: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 02:10:20: #1 total tags in treatment: 14331063 INFO @ Mon, 03 Jun 2019 02:10:20: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:10:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 02:10:20: #1 tags after filtering in treatment: 14331063 INFO @ Mon, 03 Jun 2019 02:10:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:10:20: #1 finished! INFO @ Mon, 03 Jun 2019 02:10:20: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:10:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:10:21: #2 number of paired peaks: 46 WARNING @ Mon, 03 Jun 2019 02:10:21: Too few paired peaks (46) 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 @ Mon, 03 Jun 2019 02:10:21: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX111796/SRX111796.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111796/SRX111796.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111796/SRX111796.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111796/SRX111796.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:10:23: 14000000 INFO @ Mon, 03 Jun 2019 02:10:27: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 02:10:27: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 02:10:27: #1 total tags in treatment: 14331063 INFO @ Mon, 03 Jun 2019 02:10:27: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:10:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 02:10:27: #1 tags after filtering in treatment: 14331063 INFO @ Mon, 03 Jun 2019 02:10:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:10:27: #1 finished! INFO @ Mon, 03 Jun 2019 02:10:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:10:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:10:28: #2 number of paired peaks: 46 WARNING @ Mon, 03 Jun 2019 02:10:28: Too few paired peaks (46) 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 @ Mon, 03 Jun 2019 02:10:28: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX111796/SRX111796.10_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111796/SRX111796.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111796/SRX111796.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111796/SRX111796.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。