Job ID = 1303806 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T11:31:14 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 ) 2019-06-03T11:31:14 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 ) 2019-06-03T11:31:14 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 ) 2019-06-03T11:31:38 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 ) 2019-06-03T11:35:32 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 ) 2019-06-03T11:38:35 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 ) 2019-06-03T11:40:55 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 : 19,927,623 reads read : 19,927,623 reads written : 19,927,623 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: 00:08:19 19927623 reads; of these: 19927623 (100.00%) were unpaired; of these: 222105 (1.11%) aligned 0 times 14963131 (75.09%) aligned exactly 1 time 4742387 (23.80%) aligned >1 times 98.89% overall alignment rate Time searching: 00:08:19 Overall time: 00:08:19 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] 4260581 / 19705518 = 0.2162 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 20:55:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495165/SRX495165.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495165/SRX495165.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495165/SRX495165.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495165/SRX495165.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 20:55:19: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:55:19: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:55:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495165/SRX495165.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495165/SRX495165.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495165/SRX495165.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495165/SRX495165.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 20:55:19: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:55:19: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:55:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495165/SRX495165.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495165/SRX495165.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495165/SRX495165.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495165/SRX495165.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 20:55:19: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:55:19: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:55:28: 1000000 INFO @ Mon, 03 Jun 2019 20:55:29: 1000000 INFO @ Mon, 03 Jun 2019 20:55:29: 1000000 INFO @ Mon, 03 Jun 2019 20:55:36: 2000000 INFO @ Mon, 03 Jun 2019 20:55:37: 2000000 INFO @ Mon, 03 Jun 2019 20:55:39: 2000000 INFO @ Mon, 03 Jun 2019 20:55:45: 3000000 INFO @ Mon, 03 Jun 2019 20:55:46: 3000000 INFO @ Mon, 03 Jun 2019 20:55:48: 3000000 INFO @ Mon, 03 Jun 2019 20:55:53: 4000000 INFO @ Mon, 03 Jun 2019 20:55:55: 4000000 INFO @ Mon, 03 Jun 2019 20:55:58: 4000000 INFO @ Mon, 03 Jun 2019 20:56:02: 5000000 INFO @ Mon, 03 Jun 2019 20:56:03: 5000000 INFO @ Mon, 03 Jun 2019 20:56:08: 5000000 INFO @ Mon, 03 Jun 2019 20:56:11: 6000000 INFO @ Mon, 03 Jun 2019 20:56:12: 6000000 INFO @ Mon, 03 Jun 2019 20:56:17: 6000000 INFO @ Mon, 03 Jun 2019 20:56:19: 7000000 INFO @ Mon, 03 Jun 2019 20:56:21: 7000000 INFO @ Mon, 03 Jun 2019 20:56:27: 7000000 INFO @ Mon, 03 Jun 2019 20:56:28: 8000000 INFO @ Mon, 03 Jun 2019 20:56:29: 8000000 INFO @ Mon, 03 Jun 2019 20:56:36: 9000000 INFO @ Mon, 03 Jun 2019 20:56:37: 8000000 INFO @ Mon, 03 Jun 2019 20:56:38: 9000000 INFO @ Mon, 03 Jun 2019 20:56:44: 10000000 INFO @ Mon, 03 Jun 2019 20:56:46: 10000000 INFO @ Mon, 03 Jun 2019 20:56:46: 9000000 INFO @ Mon, 03 Jun 2019 20:56:53: 11000000 INFO @ Mon, 03 Jun 2019 20:56:55: 11000000 INFO @ Mon, 03 Jun 2019 20:56:56: 10000000 INFO @ Mon, 03 Jun 2019 20:57:01: 12000000 INFO @ Mon, 03 Jun 2019 20:57:03: 12000000 INFO @ Mon, 03 Jun 2019 20:57:05: 11000000 INFO @ Mon, 03 Jun 2019 20:57:10: 13000000 INFO @ Mon, 03 Jun 2019 20:57:12: 13000000 INFO @ Mon, 03 Jun 2019 20:57:15: 12000000 INFO @ Mon, 03 Jun 2019 20:57:18: 14000000 INFO @ Mon, 03 Jun 2019 20:57:21: 14000000 INFO @ Mon, 03 Jun 2019 20:57:24: 13000000 INFO @ Mon, 03 Jun 2019 20:57:27: 15000000 INFO @ Mon, 03 Jun 2019 20:57:30: 15000000 INFO @ Mon, 03 Jun 2019 20:57:31: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 20:57:31: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 20:57:31: #1 total tags in treatment: 15444937 INFO @ Mon, 03 Jun 2019 20:57:31: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:57:31: #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 20:57:31: #1 tags after filtering in treatment: 15444937 INFO @ Mon, 03 Jun 2019 20:57:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:57:31: #1 finished! INFO @ Mon, 03 Jun 2019 20:57:31: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:57:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:57:33: #2 number of paired peaks: 40 WARNING @ Mon, 03 Jun 2019 20:57:33: Too few paired peaks (40) 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 20:57:33: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX495165/SRX495165.20_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/SRX495165/SRX495165.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495165/SRX495165.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495165/SRX495165.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:57:33: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 20:57:33: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 20:57:33: #1 total tags in treatment: 15444937 INFO @ Mon, 03 Jun 2019 20:57:33: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:57:33: #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 20:57:34: #1 tags after filtering in treatment: 15444937 INFO @ Mon, 03 Jun 2019 20:57:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:57:34: #1 finished! INFO @ Mon, 03 Jun 2019 20:57:34: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:57:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:57:34: 14000000 INFO @ Mon, 03 Jun 2019 20:57:35: #2 number of paired peaks: 40 WARNING @ Mon, 03 Jun 2019 20:57:35: Too few paired peaks (40) 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 20:57:35: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX495165/SRX495165.10_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/SRX495165/SRX495165.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495165/SRX495165.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495165/SRX495165.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:57:44: 15000000 INFO @ Mon, 03 Jun 2019 20:57:48: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 20:57:48: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 20:57:48: #1 total tags in treatment: 15444937 INFO @ Mon, 03 Jun 2019 20:57:48: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:57:48: #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 20:57:48: #1 tags after filtering in treatment: 15444937 INFO @ Mon, 03 Jun 2019 20:57:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:57:48: #1 finished! INFO @ Mon, 03 Jun 2019 20:57:48: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:57:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:57:49: #2 number of paired peaks: 40 WARNING @ Mon, 03 Jun 2019 20:57:49: Too few paired peaks (40) 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 20:57:49: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX495165/SRX495165.05_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/SRX495165/SRX495165.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495165/SRX495165.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495165/SRX495165.05_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。