Job ID = 1293787 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 20,576,294 reads read : 20,576,294 reads written : 20,576,294 2019-06-02T17:22:56 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 ) 2019-06-02T17:26:13 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 : 17,170,791 reads read : 17,170,791 reads written : 17,170,791 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: 00:09:31 37747085 reads; of these: 37747085 (100.00%) were unpaired; of these: 3044896 (8.07%) aligned 0 times 24907631 (65.99%) aligned exactly 1 time 9794558 (25.95%) aligned >1 times 91.93% overall alignment rate Time searching: 00:09:31 Overall time: 00:09:31 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] 12330416 / 34702189 = 0.3553 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 02:49:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX113336/SRX113336.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX113336/SRX113336.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX113336/SRX113336.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX113336/SRX113336.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 02:49:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:49:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:49:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX113336/SRX113336.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX113336/SRX113336.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX113336/SRX113336.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX113336/SRX113336.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 02:49:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:49:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:49:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX113336/SRX113336.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX113336/SRX113336.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX113336/SRX113336.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX113336/SRX113336.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 02:49:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:49:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:49:18: 1000000 INFO @ Mon, 03 Jun 2019 02:49:18: 1000000 INFO @ Mon, 03 Jun 2019 02:49:18: 1000000 INFO @ Mon, 03 Jun 2019 02:49:27: 2000000 INFO @ Mon, 03 Jun 2019 02:49:27: 2000000 INFO @ Mon, 03 Jun 2019 02:49:27: 2000000 INFO @ Mon, 03 Jun 2019 02:49:36: 3000000 INFO @ Mon, 03 Jun 2019 02:49:37: 3000000 INFO @ Mon, 03 Jun 2019 02:49:37: 3000000 INFO @ Mon, 03 Jun 2019 02:49:46: 4000000 INFO @ Mon, 03 Jun 2019 02:49:46: 4000000 INFO @ Mon, 03 Jun 2019 02:49:46: 4000000 INFO @ Mon, 03 Jun 2019 02:49:55: 5000000 INFO @ Mon, 03 Jun 2019 02:49:55: 5000000 INFO @ Mon, 03 Jun 2019 02:49:55: 5000000 INFO @ Mon, 03 Jun 2019 02:50:04: 6000000 INFO @ Mon, 03 Jun 2019 02:50:04: 6000000 INFO @ Mon, 03 Jun 2019 02:50:05: 6000000 INFO @ Mon, 03 Jun 2019 02:50:13: 7000000 INFO @ Mon, 03 Jun 2019 02:50:13: 7000000 INFO @ Mon, 03 Jun 2019 02:50:15: 7000000 INFO @ Mon, 03 Jun 2019 02:50:22: 8000000 INFO @ Mon, 03 Jun 2019 02:50:23: 8000000 INFO @ Mon, 03 Jun 2019 02:50:24: 8000000 INFO @ Mon, 03 Jun 2019 02:50:32: 9000000 INFO @ Mon, 03 Jun 2019 02:50:32: 9000000 INFO @ Mon, 03 Jun 2019 02:50:33: 9000000 INFO @ Mon, 03 Jun 2019 02:50:41: 10000000 INFO @ Mon, 03 Jun 2019 02:50:41: 10000000 INFO @ Mon, 03 Jun 2019 02:50:42: 10000000 INFO @ Mon, 03 Jun 2019 02:50:50: 11000000 INFO @ Mon, 03 Jun 2019 02:50:50: 11000000 INFO @ Mon, 03 Jun 2019 02:50:52: 11000000 INFO @ Mon, 03 Jun 2019 02:50:59: 12000000 INFO @ Mon, 03 Jun 2019 02:50:59: 12000000 INFO @ Mon, 03 Jun 2019 02:51:01: 12000000 INFO @ Mon, 03 Jun 2019 02:51:08: 13000000 INFO @ Mon, 03 Jun 2019 02:51:09: 13000000 INFO @ Mon, 03 Jun 2019 02:51:10: 13000000 INFO @ Mon, 03 Jun 2019 02:51:18: 14000000 INFO @ Mon, 03 Jun 2019 02:51:18: 14000000 INFO @ Mon, 03 Jun 2019 02:51:19: 14000000 INFO @ Mon, 03 Jun 2019 02:51:27: 15000000 INFO @ Mon, 03 Jun 2019 02:51:27: 15000000 INFO @ Mon, 03 Jun 2019 02:51:29: 15000000 INFO @ Mon, 03 Jun 2019 02:51:36: 16000000 INFO @ Mon, 03 Jun 2019 02:51:36: 16000000 INFO @ Mon, 03 Jun 2019 02:51:39: 16000000 INFO @ Mon, 03 Jun 2019 02:51:45: 17000000 INFO @ Mon, 03 Jun 2019 02:51:45: 17000000 INFO @ Mon, 03 Jun 2019 02:51:48: 17000000 INFO @ Mon, 03 Jun 2019 02:51:54: 18000000 INFO @ Mon, 03 Jun 2019 02:51:55: 18000000 INFO @ Mon, 03 Jun 2019 02:51:57: 18000000 INFO @ Mon, 03 Jun 2019 02:52:04: 19000000 INFO @ Mon, 03 Jun 2019 02:52:04: 19000000 INFO @ Mon, 03 Jun 2019 02:52:07: 19000000 INFO @ Mon, 03 Jun 2019 02:52:13: 20000000 INFO @ Mon, 03 Jun 2019 02:52:13: 20000000 INFO @ Mon, 03 Jun 2019 02:52:16: 20000000 INFO @ Mon, 03 Jun 2019 02:52:22: 21000000 INFO @ Mon, 03 Jun 2019 02:52:22: 21000000 INFO @ Mon, 03 Jun 2019 02:52:25: 21000000 INFO @ Mon, 03 Jun 2019 02:52:31: 22000000 INFO @ Mon, 03 Jun 2019 02:52:31: 22000000 INFO @ Mon, 03 Jun 2019 02:52:34: 22000000 INFO @ Mon, 03 Jun 2019 02:52:35: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 02:52:35: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 02:52:35: #1 total tags in treatment: 22371773 INFO @ Mon, 03 Jun 2019 02:52:35: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:52:35: #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 02:52:35: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 02:52:35: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 02:52:35: #1 total tags in treatment: 22371773 INFO @ Mon, 03 Jun 2019 02:52:35: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:52:35: #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 02:52:35: #1 tags after filtering in treatment: 22371773 INFO @ Mon, 03 Jun 2019 02:52:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:52:35: #1 finished! INFO @ Mon, 03 Jun 2019 02:52:35: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:52:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:52:36: #1 tags after filtering in treatment: 22371773 INFO @ Mon, 03 Jun 2019 02:52:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:52:36: #1 finished! INFO @ Mon, 03 Jun 2019 02:52:36: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:52:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:52:38: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 02:52:38: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 02:52:38: #1 total tags in treatment: 22371773 INFO @ Mon, 03 Jun 2019 02:52:38: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:52:38: #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 02:52:38: #2 number of paired peaks: 58 WARNING @ Mon, 03 Jun 2019 02:52:38: Too few paired peaks (58) 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 02:52:38: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX113336/SRX113336.20_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/SRX113336/SRX113336.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX113336/SRX113336.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX113336/SRX113336.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:52:38: #2 number of paired peaks: 58 WARNING @ Mon, 03 Jun 2019 02:52:38: Too few paired peaks (58) 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 02:52:38: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX113336/SRX113336.05_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/SRX113336/SRX113336.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX113336/SRX113336.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX113336/SRX113336.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:52:38: #1 tags after filtering in treatment: 22371773 INFO @ Mon, 03 Jun 2019 02:52:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:52:38: #1 finished! INFO @ Mon, 03 Jun 2019 02:52:38: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:52:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:52:41: #2 number of paired peaks: 58 WARNING @ Mon, 03 Jun 2019 02:52:41: Too few paired peaks (58) 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 02:52:41: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX113336/SRX113336.10_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/SRX113336/SRX113336.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX113336/SRX113336.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX113336/SRX113336.10_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。