Job ID = 1294657 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T00:29:49 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 ) 2019-06-03T00:30:08 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 ) 2019-06-03T00:31:44 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 ) 2019-06-03T00:32:52 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 ) 2019-06-03T00:35:07 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 ) 2019-06-03T00:35:07 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 ) 2019-06-03T00:36:16 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 : 15,263,721 reads read : 15,263,721 reads written : 15,263,721 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: 00:04:34 15263721 reads; of these: 15263721 (100.00%) were unpaired; of these: 1007355 (6.60%) aligned 0 times 11401938 (74.70%) aligned exactly 1 time 2854428 (18.70%) aligned >1 times 93.40% overall alignment rate Time searching: 00:04:34 Overall time: 00:04:34 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] 709401 / 14256366 = 0.0498 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 09:47:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287808/SRX287808.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287808/SRX287808.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287808/SRX287808.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287808/SRX287808.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 09:47:44: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:47:44: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:47:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287808/SRX287808.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287808/SRX287808.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287808/SRX287808.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287808/SRX287808.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 09:47:44: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:47:44: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:47:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287808/SRX287808.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287808/SRX287808.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287808/SRX287808.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287808/SRX287808.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 09:47:44: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:47:44: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:47:54: 1000000 INFO @ Mon, 03 Jun 2019 09:47:55: 1000000 INFO @ Mon, 03 Jun 2019 09:47:56: 1000000 INFO @ Mon, 03 Jun 2019 09:48:04: 2000000 INFO @ Mon, 03 Jun 2019 09:48:06: 2000000 INFO @ Mon, 03 Jun 2019 09:48:08: 2000000 INFO @ Mon, 03 Jun 2019 09:48:13: 3000000 INFO @ Mon, 03 Jun 2019 09:48:16: 3000000 INFO @ Mon, 03 Jun 2019 09:48:19: 3000000 INFO @ Mon, 03 Jun 2019 09:48:22: 4000000 INFO @ Mon, 03 Jun 2019 09:48:27: 4000000 INFO @ Mon, 03 Jun 2019 09:48:30: 4000000 INFO @ Mon, 03 Jun 2019 09:48:32: 5000000 INFO @ Mon, 03 Jun 2019 09:48:37: 5000000 INFO @ Mon, 03 Jun 2019 09:48:40: 5000000 INFO @ Mon, 03 Jun 2019 09:48:42: 6000000 INFO @ Mon, 03 Jun 2019 09:48:47: 6000000 INFO @ Mon, 03 Jun 2019 09:48:51: 6000000 INFO @ Mon, 03 Jun 2019 09:48:53: 7000000 INFO @ Mon, 03 Jun 2019 09:48:57: 7000000 INFO @ Mon, 03 Jun 2019 09:49:02: 7000000 INFO @ Mon, 03 Jun 2019 09:49:03: 8000000 INFO @ Mon, 03 Jun 2019 09:49:07: 8000000 INFO @ Mon, 03 Jun 2019 09:49:13: 8000000 INFO @ Mon, 03 Jun 2019 09:49:14: 9000000 INFO @ Mon, 03 Jun 2019 09:49:17: 9000000 INFO @ Mon, 03 Jun 2019 09:49:23: 9000000 INFO @ Mon, 03 Jun 2019 09:49:24: 10000000 INFO @ Mon, 03 Jun 2019 09:49:27: 10000000 INFO @ Mon, 03 Jun 2019 09:49:34: 10000000 INFO @ Mon, 03 Jun 2019 09:49:35: 11000000 INFO @ Mon, 03 Jun 2019 09:49:38: 11000000 INFO @ Mon, 03 Jun 2019 09:49:45: 11000000 INFO @ Mon, 03 Jun 2019 09:49:46: 12000000 INFO @ Mon, 03 Jun 2019 09:49:48: 12000000 INFO @ Mon, 03 Jun 2019 09:49:55: 12000000 INFO @ Mon, 03 Jun 2019 09:49:57: 13000000 INFO @ Mon, 03 Jun 2019 09:49:59: 13000000 INFO @ Mon, 03 Jun 2019 09:50:03: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:50:03: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:50:03: #1 total tags in treatment: 13546965 INFO @ Mon, 03 Jun 2019 09:50:03: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:50:03: #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 09:50:03: #1 tags after filtering in treatment: 13546965 INFO @ Mon, 03 Jun 2019 09:50:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:50:03: #1 finished! INFO @ Mon, 03 Jun 2019 09:50:03: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:50:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:50:04: #2 number of paired peaks: 2 WARNING @ Mon, 03 Jun 2019 09:50:04: Too few paired peaks (2) 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 09:50:04: Process for pairing-model is terminated! INFO @ Mon, 03 Jun 2019 09:50:04: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:50:04: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:50:04: #1 total tags in treatment: 13546965 INFO @ Mon, 03 Jun 2019 09:50:04: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:50:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) cut: /home/okishinya/chipatlas/results/dm3/SRX287808/SRX287808.05_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/SRX287808/SRX287808.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX287808/SRX287808.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX287808/SRX287808.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:50:05: #1 tags after filtering in treatment: 13546965 INFO @ Mon, 03 Jun 2019 09:50:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:50:05: #1 finished! INFO @ Mon, 03 Jun 2019 09:50:05: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:50:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:50:06: #2 number of paired peaks: 2 WARNING @ Mon, 03 Jun 2019 09:50:06: Too few paired peaks (2) 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 09:50:06: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX287808/SRX287808.10_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/SRX287808/SRX287808.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX287808/SRX287808.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX287808/SRX287808.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:50:06: 13000000 INFO @ Mon, 03 Jun 2019 09:50:12: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:50:12: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:50:12: #1 total tags in treatment: 13546965 INFO @ Mon, 03 Jun 2019 09:50:12: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:50:12: #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 09:50:12: #1 tags after filtering in treatment: 13546965 INFO @ Mon, 03 Jun 2019 09:50:12: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:50:12: #1 finished! INFO @ Mon, 03 Jun 2019 09:50:12: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:50:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:50:13: #2 number of paired peaks: 2 WARNING @ Mon, 03 Jun 2019 09:50:13: Too few paired peaks (2) 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 09:50:13: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX287808/SRX287808.20_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/SRX287808/SRX287808.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX287808/SRX287808.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX287808/SRX287808.20_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。