Job ID = 1301918 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T11:05:03 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 ) 2019-06-03T11:05:03 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 ) 2019-06-03T11:06:27 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 ) 2019-06-03T11:13:46 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 ) 2019-06-03T11:14:14 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 : 40,009,774 reads read : 40,009,774 reads written : 40,009,774 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: 00:15:13 40009774 reads; of these: 40009774 (100.00%) were unpaired; of these: 9548813 (23.87%) aligned 0 times 21276113 (53.18%) aligned exactly 1 time 9184848 (22.96%) aligned >1 times 76.13% overall alignment rate Time searching: 00:15:13 Overall time: 00:15:13 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 16 files... [bam_rmdupse_core] 11352985 / 30460961 = 0.3727 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 20:45:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4933873/SRX4933873.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4933873/SRX4933873.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4933873/SRX4933873.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4933873/SRX4933873.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 20:45:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:45:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:45:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4933873/SRX4933873.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4933873/SRX4933873.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4933873/SRX4933873.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4933873/SRX4933873.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 20:45:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:45:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:45:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4933873/SRX4933873.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4933873/SRX4933873.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4933873/SRX4933873.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4933873/SRX4933873.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 20:45:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:45:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:45:46: 1000000 INFO @ Mon, 03 Jun 2019 20:45:47: 1000000 INFO @ Mon, 03 Jun 2019 20:45:48: 1000000 INFO @ Mon, 03 Jun 2019 20:45:55: 2000000 INFO @ Mon, 03 Jun 2019 20:45:58: 2000000 INFO @ Mon, 03 Jun 2019 20:46:00: 2000000 INFO @ Mon, 03 Jun 2019 20:46:03: 3000000 INFO @ Mon, 03 Jun 2019 20:46:08: 3000000 INFO @ Mon, 03 Jun 2019 20:46:11: 3000000 INFO @ Mon, 03 Jun 2019 20:46:12: 4000000 INFO @ Mon, 03 Jun 2019 20:46:19: 4000000 INFO @ Mon, 03 Jun 2019 20:46:21: 5000000 INFO @ Mon, 03 Jun 2019 20:46:22: 4000000 INFO @ Mon, 03 Jun 2019 20:46:29: 6000000 INFO @ Mon, 03 Jun 2019 20:46:29: 5000000 INFO @ Mon, 03 Jun 2019 20:46:34: 5000000 INFO @ Mon, 03 Jun 2019 20:46:38: 7000000 INFO @ Mon, 03 Jun 2019 20:46:40: 6000000 INFO @ Mon, 03 Jun 2019 20:46:45: 6000000 INFO @ Mon, 03 Jun 2019 20:46:47: 8000000 INFO @ Mon, 03 Jun 2019 20:46:50: 7000000 INFO @ Mon, 03 Jun 2019 20:46:55: 9000000 INFO @ Mon, 03 Jun 2019 20:46:56: 7000000 INFO @ Mon, 03 Jun 2019 20:47:01: 8000000 INFO @ Mon, 03 Jun 2019 20:47:04: 10000000 INFO @ Mon, 03 Jun 2019 20:47:07: 8000000 INFO @ Mon, 03 Jun 2019 20:47:11: 9000000 INFO @ Mon, 03 Jun 2019 20:47:12: 11000000 INFO @ Mon, 03 Jun 2019 20:47:18: 9000000 INFO @ Mon, 03 Jun 2019 20:47:21: 12000000 INFO @ Mon, 03 Jun 2019 20:47:22: 10000000 INFO @ Mon, 03 Jun 2019 20:47:29: 10000000 INFO @ Mon, 03 Jun 2019 20:47:30: 13000000 INFO @ Mon, 03 Jun 2019 20:47:32: 11000000 INFO @ Mon, 03 Jun 2019 20:47:40: 11000000 INFO @ Mon, 03 Jun 2019 20:47:40: 14000000 INFO @ Mon, 03 Jun 2019 20:47:43: 12000000 INFO @ Mon, 03 Jun 2019 20:47:49: 15000000 INFO @ Mon, 03 Jun 2019 20:47:50: 12000000 INFO @ Mon, 03 Jun 2019 20:47:54: 13000000 INFO @ Mon, 03 Jun 2019 20:47:59: 16000000 INFO @ Mon, 03 Jun 2019 20:48:01: 13000000 INFO @ Mon, 03 Jun 2019 20:48:05: 14000000 INFO @ Mon, 03 Jun 2019 20:48:08: 17000000 INFO @ Mon, 03 Jun 2019 20:48:12: 14000000 INFO @ Mon, 03 Jun 2019 20:48:16: 15000000 INFO @ Mon, 03 Jun 2019 20:48:18: 18000000 INFO @ Mon, 03 Jun 2019 20:48:23: 15000000 INFO @ Mon, 03 Jun 2019 20:48:26: 16000000 INFO @ Mon, 03 Jun 2019 20:48:28: 19000000 INFO @ Mon, 03 Jun 2019 20:48:29: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 20:48:29: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 20:48:29: #1 total tags in treatment: 19107976 INFO @ Mon, 03 Jun 2019 20:48:29: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:48:29: #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 20:48:29: #1 tags after filtering in treatment: 19107976 INFO @ Mon, 03 Jun 2019 20:48:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:48:29: #1 finished! INFO @ Mon, 03 Jun 2019 20:48:29: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:48:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:48:31: #2 number of paired peaks: 91 WARNING @ Mon, 03 Jun 2019 20:48:31: Too few paired peaks (91) 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 20:48:31: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX4933873/SRX4933873.10_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/SRX4933873/SRX4933873.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX4933873/SRX4933873.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX4933873/SRX4933873.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:48:34: 16000000 INFO @ Mon, 03 Jun 2019 20:48:37: 17000000 INFO @ Mon, 03 Jun 2019 20:48:44: 17000000 INFO @ Mon, 03 Jun 2019 20:48:48: 18000000 INFO @ Mon, 03 Jun 2019 20:48:55: 18000000 INFO @ Mon, 03 Jun 2019 20:48:58: 19000000 INFO @ Mon, 03 Jun 2019 20:49:00: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 20:49:00: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 20:49:00: #1 total tags in treatment: 19107976 INFO @ Mon, 03 Jun 2019 20:49:00: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:49:00: #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 20:49:00: #1 tags after filtering in treatment: 19107976 INFO @ Mon, 03 Jun 2019 20:49:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:49:00: #1 finished! INFO @ Mon, 03 Jun 2019 20:49:00: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:49:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:49:02: #2 number of paired peaks: 91 WARNING @ Mon, 03 Jun 2019 20:49:02: Too few paired peaks (91) 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 20:49:02: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX4933873/SRX4933873.20_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/SRX4933873/SRX4933873.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX4933873/SRX4933873.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX4933873/SRX4933873.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:49:05: 19000000 INFO @ Mon, 03 Jun 2019 20:49:06: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 20:49:06: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 20:49:06: #1 total tags in treatment: 19107976 INFO @ Mon, 03 Jun 2019 20:49:06: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:49:06: #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 20:49:07: #1 tags after filtering in treatment: 19107976 INFO @ Mon, 03 Jun 2019 20:49:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:49:07: #1 finished! INFO @ Mon, 03 Jun 2019 20:49:07: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:49:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:49:08: #2 number of paired peaks: 91 WARNING @ Mon, 03 Jun 2019 20:49:08: Too few paired peaks (91) 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 20:49:08: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX4933873/SRX4933873.05_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/SRX4933873/SRX4933873.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX4933873/SRX4933873.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX4933873/SRX4933873.05_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。