Job ID = 1298443 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T08:29:54 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 ) 2019-06-03T08:30:45 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 ) 2019-06-03T08:40:02 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 : 29,175,008 reads read : 29,175,008 reads written : 29,175,008 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: 00:07:44 29175008 reads; of these: 29175008 (100.00%) were unpaired; of these: 2082664 (7.14%) aligned 0 times 24234387 (83.07%) aligned exactly 1 time 2857957 (9.80%) aligned >1 times 92.86% overall alignment rate Time searching: 00:07:44 Overall time: 00:07:44 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] 7455195 / 27092344 = 0.2752 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 17:57:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467034/SRX467034.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467034/SRX467034.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467034/SRX467034.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467034/SRX467034.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 17:57:23: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:57:23: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:57:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467034/SRX467034.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467034/SRX467034.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467034/SRX467034.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467034/SRX467034.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 17:57:23: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:57:23: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:57:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467034/SRX467034.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467034/SRX467034.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467034/SRX467034.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467034/SRX467034.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 17:57:23: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:57:23: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:57:33: 1000000 INFO @ Mon, 03 Jun 2019 17:57:33: 1000000 INFO @ Mon, 03 Jun 2019 17:57:34: 1000000 INFO @ Mon, 03 Jun 2019 17:57:43: 2000000 INFO @ Mon, 03 Jun 2019 17:57:43: 2000000 INFO @ Mon, 03 Jun 2019 17:57:44: 2000000 INFO @ Mon, 03 Jun 2019 17:57:53: 3000000 INFO @ Mon, 03 Jun 2019 17:57:53: 3000000 INFO @ Mon, 03 Jun 2019 17:57:53: 3000000 INFO @ Mon, 03 Jun 2019 17:58:02: 4000000 INFO @ Mon, 03 Jun 2019 17:58:03: 4000000 INFO @ Mon, 03 Jun 2019 17:58:03: 4000000 INFO @ Mon, 03 Jun 2019 17:58:12: 5000000 INFO @ Mon, 03 Jun 2019 17:58:12: 5000000 INFO @ Mon, 03 Jun 2019 17:58:12: 5000000 INFO @ Mon, 03 Jun 2019 17:58:21: 6000000 INFO @ Mon, 03 Jun 2019 17:58:22: 6000000 INFO @ Mon, 03 Jun 2019 17:58:22: 6000000 INFO @ Mon, 03 Jun 2019 17:58:31: 7000000 INFO @ Mon, 03 Jun 2019 17:58:31: 7000000 INFO @ Mon, 03 Jun 2019 17:58:31: 7000000 INFO @ Mon, 03 Jun 2019 17:58:40: 8000000 INFO @ Mon, 03 Jun 2019 17:58:41: 8000000 INFO @ Mon, 03 Jun 2019 17:58:41: 8000000 INFO @ Mon, 03 Jun 2019 17:58:50: 9000000 INFO @ Mon, 03 Jun 2019 17:58:50: 9000000 INFO @ Mon, 03 Jun 2019 17:58:50: 9000000 INFO @ Mon, 03 Jun 2019 17:58:59: 10000000 INFO @ Mon, 03 Jun 2019 17:58:59: 10000000 INFO @ Mon, 03 Jun 2019 17:59:00: 10000000 INFO @ Mon, 03 Jun 2019 17:59:08: 11000000 INFO @ Mon, 03 Jun 2019 17:59:09: 11000000 INFO @ Mon, 03 Jun 2019 17:59:09: 11000000 INFO @ Mon, 03 Jun 2019 17:59:18: 12000000 INFO @ Mon, 03 Jun 2019 17:59:18: 12000000 INFO @ Mon, 03 Jun 2019 17:59:19: 12000000 INFO @ Mon, 03 Jun 2019 17:59:27: 13000000 INFO @ Mon, 03 Jun 2019 17:59:27: 13000000 INFO @ Mon, 03 Jun 2019 17:59:28: 13000000 INFO @ Mon, 03 Jun 2019 17:59:36: 14000000 INFO @ Mon, 03 Jun 2019 17:59:37: 14000000 INFO @ Mon, 03 Jun 2019 17:59:37: 14000000 INFO @ Mon, 03 Jun 2019 17:59:46: 15000000 INFO @ Mon, 03 Jun 2019 17:59:46: 15000000 INFO @ Mon, 03 Jun 2019 17:59:46: 15000000 INFO @ Mon, 03 Jun 2019 17:59:55: 16000000 INFO @ Mon, 03 Jun 2019 17:59:55: 16000000 INFO @ Mon, 03 Jun 2019 17:59:57: 16000000 INFO @ Mon, 03 Jun 2019 18:00:04: 17000000 INFO @ Mon, 03 Jun 2019 18:00:05: 17000000 INFO @ Mon, 03 Jun 2019 18:00:07: 17000000 INFO @ Mon, 03 Jun 2019 18:00:13: 18000000 INFO @ Mon, 03 Jun 2019 18:00:14: 18000000 INFO @ Mon, 03 Jun 2019 18:00:17: 18000000 INFO @ Mon, 03 Jun 2019 18:00:22: 19000000 INFO @ Mon, 03 Jun 2019 18:00:23: 19000000 INFO @ Mon, 03 Jun 2019 18:00:27: 19000000 INFO @ Mon, 03 Jun 2019 18:00:28: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 18:00:28: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 18:00:28: #1 total tags in treatment: 19637149 INFO @ Mon, 03 Jun 2019 18:00:28: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:00:28: #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 18:00:28: #1 tags after filtering in treatment: 19637149 INFO @ Mon, 03 Jun 2019 18:00:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 18:00:28: #1 finished! INFO @ Mon, 03 Jun 2019 18:00:28: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:00:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:00:29: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 18:00:29: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 18:00:29: #1 total tags in treatment: 19637149 INFO @ Mon, 03 Jun 2019 18:00:29: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:00:29: #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 18:00:30: #1 tags after filtering in treatment: 19637149 INFO @ Mon, 03 Jun 2019 18:00:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 18:00:30: #1 finished! INFO @ Mon, 03 Jun 2019 18:00:30: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:00:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:00:30: #2 number of paired peaks: 17 WARNING @ Mon, 03 Jun 2019 18:00:30: Too few paired peaks (17) 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 18:00:30: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX467034/SRX467034.10_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/SRX467034/SRX467034.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467034/SRX467034.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467034/SRX467034.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 18:00:31: #2 number of paired peaks: 17 WARNING @ Mon, 03 Jun 2019 18:00:31: Too few paired peaks (17) 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 18:00:31: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX467034/SRX467034.05_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/SRX467034/SRX467034.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467034/SRX467034.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467034/SRX467034.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 18:00:34: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 18:00:34: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 18:00:34: #1 total tags in treatment: 19637149 INFO @ Mon, 03 Jun 2019 18:00:34: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:00:34: #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 18:00:34: #1 tags after filtering in treatment: 19637149 INFO @ Mon, 03 Jun 2019 18:00:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 18:00:34: #1 finished! INFO @ Mon, 03 Jun 2019 18:00:34: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:00:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:00:36: #2 number of paired peaks: 17 WARNING @ Mon, 03 Jun 2019 18:00:36: Too few paired peaks (17) 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 18:00:36: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX467034/SRX467034.20_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/SRX467034/SRX467034.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467034/SRX467034.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467034/SRX467034.20_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。