Job ID = 1298550 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T08:28:33 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 ) 2019-06-03T08:30:14 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 : 25,052,980 reads read : 25,052,980 reads written : 25,052,980 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: 00:06:09 25052980 reads; of these: 25052980 (100.00%) were unpaired; of these: 2792094 (11.14%) aligned 0 times 19706523 (78.66%) aligned exactly 1 time 2554363 (10.20%) aligned >1 times 88.86% overall alignment rate Time searching: 00:06:09 Overall time: 00:06:09 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 12 files... [bam_rmdupse_core] 5471134 / 22260886 = 0.2458 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 17:53:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467041/SRX467041.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467041/SRX467041.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467041/SRX467041.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467041/SRX467041.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 17:53:06: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:53:06: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:53:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467041/SRX467041.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467041/SRX467041.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467041/SRX467041.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467041/SRX467041.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 17:53:06: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:53:06: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:53:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467041/SRX467041.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467041/SRX467041.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467041/SRX467041.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467041/SRX467041.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 17:53:06: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:53:06: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:53:13: 1000000 INFO @ Mon, 03 Jun 2019 17:53:14: 1000000 INFO @ Mon, 03 Jun 2019 17:53:15: 1000000 INFO @ Mon, 03 Jun 2019 17:53:19: 2000000 INFO @ Mon, 03 Jun 2019 17:53:21: 2000000 INFO @ Mon, 03 Jun 2019 17:53:22: 2000000 INFO @ Mon, 03 Jun 2019 17:53:26: 3000000 INFO @ Mon, 03 Jun 2019 17:53:28: 3000000 INFO @ Mon, 03 Jun 2019 17:53:30: 3000000 INFO @ Mon, 03 Jun 2019 17:53:32: 4000000 INFO @ Mon, 03 Jun 2019 17:53:35: 4000000 INFO @ Mon, 03 Jun 2019 17:53:38: 4000000 INFO @ Mon, 03 Jun 2019 17:53:39: 5000000 INFO @ Mon, 03 Jun 2019 17:53:42: 5000000 INFO @ Mon, 03 Jun 2019 17:53:45: 6000000 INFO @ Mon, 03 Jun 2019 17:53:45: 5000000 INFO @ Mon, 03 Jun 2019 17:53:49: 6000000 INFO @ Mon, 03 Jun 2019 17:53:51: 7000000 INFO @ Mon, 03 Jun 2019 17:53:53: 6000000 INFO @ Mon, 03 Jun 2019 17:53:55: 7000000 INFO @ Mon, 03 Jun 2019 17:53:58: 8000000 INFO @ Mon, 03 Jun 2019 17:54:01: 7000000 INFO @ Mon, 03 Jun 2019 17:54:03: 8000000 INFO @ Mon, 03 Jun 2019 17:54:04: 9000000 INFO @ Mon, 03 Jun 2019 17:54:08: 8000000 INFO @ Mon, 03 Jun 2019 17:54:10: 9000000 INFO @ Mon, 03 Jun 2019 17:54:11: 10000000 INFO @ Mon, 03 Jun 2019 17:54:16: 9000000 INFO @ Mon, 03 Jun 2019 17:54:17: 11000000 INFO @ Mon, 03 Jun 2019 17:54:17: 10000000 INFO @ Mon, 03 Jun 2019 17:54:23: 12000000 INFO @ Mon, 03 Jun 2019 17:54:23: 10000000 INFO @ Mon, 03 Jun 2019 17:54:24: 11000000 INFO @ Mon, 03 Jun 2019 17:54:30: 13000000 INFO @ Mon, 03 Jun 2019 17:54:31: 12000000 INFO @ Mon, 03 Jun 2019 17:54:31: 11000000 INFO @ Mon, 03 Jun 2019 17:54:36: 14000000 INFO @ Mon, 03 Jun 2019 17:54:38: 13000000 INFO @ Mon, 03 Jun 2019 17:54:39: 12000000 INFO @ Mon, 03 Jun 2019 17:54:43: 15000000 INFO @ Mon, 03 Jun 2019 17:54:45: 14000000 INFO @ Mon, 03 Jun 2019 17:54:46: 13000000 INFO @ Mon, 03 Jun 2019 17:54:50: 16000000 INFO @ Mon, 03 Jun 2019 17:54:52: 15000000 INFO @ Mon, 03 Jun 2019 17:54:54: 14000000 INFO @ Mon, 03 Jun 2019 17:54:55: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 17:54:55: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 17:54:55: #1 total tags in treatment: 16789752 INFO @ Mon, 03 Jun 2019 17:54:55: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:54:55: #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 17:54:56: #1 tags after filtering in treatment: 16789752 INFO @ Mon, 03 Jun 2019 17:54:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 17:54:56: #1 finished! INFO @ Mon, 03 Jun 2019 17:54:56: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:54:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:54:57: #2 number of paired peaks: 49 WARNING @ Mon, 03 Jun 2019 17:54:57: Too few paired peaks (49) 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 17:54:57: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX467041/SRX467041.05_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/SRX467041/SRX467041.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467041/SRX467041.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467041/SRX467041.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 17:54:59: 16000000 INFO @ Mon, 03 Jun 2019 17:55:02: 15000000 INFO @ Mon, 03 Jun 2019 17:55:05: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 17:55:05: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 17:55:05: #1 total tags in treatment: 16789752 INFO @ Mon, 03 Jun 2019 17:55:05: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:55:05: #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 17:55:05: #1 tags after filtering in treatment: 16789752 INFO @ Mon, 03 Jun 2019 17:55:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 17:55:05: #1 finished! INFO @ Mon, 03 Jun 2019 17:55:05: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:55:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:55:07: #2 number of paired peaks: 49 WARNING @ Mon, 03 Jun 2019 17:55:07: Too few paired peaks (49) 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 17:55:07: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX467041/SRX467041.20_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/SRX467041/SRX467041.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467041/SRX467041.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467041/SRX467041.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 17:55:09: 16000000 INFO @ Mon, 03 Jun 2019 17:55:16: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 17:55:16: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 17:55:16: #1 total tags in treatment: 16789752 INFO @ Mon, 03 Jun 2019 17:55:16: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:55:16: #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 17:55:16: #1 tags after filtering in treatment: 16789752 INFO @ Mon, 03 Jun 2019 17:55:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 17:55:16: #1 finished! INFO @ Mon, 03 Jun 2019 17:55:16: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:55:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:55:17: #2 number of paired peaks: 49 WARNING @ Mon, 03 Jun 2019 17:55:17: Too few paired peaks (49) 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 17:55:17: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX467041/SRX467041.10_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/SRX467041/SRX467041.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467041/SRX467041.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467041/SRX467041.10_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。