Job ID = 1295367 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T04:21:38 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 ) 2019-06-03T04:21:38 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 ) 2019-06-03T04:21:38 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 ) 2019-06-03T04:24:12 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 ) 2019-06-03T04:24:12 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 ) 2019-06-03T04:24:12 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 : 28,614,306 reads read : 28,614,306 reads written : 28,614,306 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:04 28614306 reads; of these: 28614306 (100.00%) were unpaired; of these: 9276556 (32.42%) aligned 0 times 15616135 (54.57%) aligned exactly 1 time 3721615 (13.01%) aligned >1 times 67.58% overall alignment rate Time searching: 00:08:05 Overall time: 00:08:05 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] 3029561 / 19337750 = 0.1567 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 13:44:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX335504/SRX335504.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX335504/SRX335504.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX335504/SRX335504.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX335504/SRX335504.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 13:44:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:44:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:44:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX335504/SRX335504.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX335504/SRX335504.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX335504/SRX335504.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX335504/SRX335504.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 13:44:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:44:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:44:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX335504/SRX335504.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX335504/SRX335504.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX335504/SRX335504.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX335504/SRX335504.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 13:44:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:44:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:44:18: 1000000 INFO @ Mon, 03 Jun 2019 13:44:18: 1000000 INFO @ Mon, 03 Jun 2019 13:44:21: 1000000 INFO @ Mon, 03 Jun 2019 13:44:28: 2000000 INFO @ Mon, 03 Jun 2019 13:44:28: 2000000 INFO @ Mon, 03 Jun 2019 13:44:34: 2000000 INFO @ Mon, 03 Jun 2019 13:44:37: 3000000 INFO @ Mon, 03 Jun 2019 13:44:37: 3000000 INFO @ Mon, 03 Jun 2019 13:44:46: 3000000 INFO @ Mon, 03 Jun 2019 13:44:46: 4000000 INFO @ Mon, 03 Jun 2019 13:44:46: 4000000 INFO @ Mon, 03 Jun 2019 13:44:55: 5000000 INFO @ Mon, 03 Jun 2019 13:44:55: 5000000 INFO @ Mon, 03 Jun 2019 13:44:57: 4000000 INFO @ Mon, 03 Jun 2019 13:45:03: 6000000 INFO @ Mon, 03 Jun 2019 13:45:04: 6000000 INFO @ Mon, 03 Jun 2019 13:45:09: 5000000 INFO @ Mon, 03 Jun 2019 13:45:11: 7000000 INFO @ Mon, 03 Jun 2019 13:45:13: 7000000 INFO @ Mon, 03 Jun 2019 13:45:20: 8000000 INFO @ Mon, 03 Jun 2019 13:45:20: 6000000 INFO @ Mon, 03 Jun 2019 13:45:22: 8000000 INFO @ Mon, 03 Jun 2019 13:45:28: 9000000 INFO @ Mon, 03 Jun 2019 13:45:31: 9000000 INFO @ Mon, 03 Jun 2019 13:45:32: 7000000 INFO @ Mon, 03 Jun 2019 13:45:36: 10000000 INFO @ Mon, 03 Jun 2019 13:45:40: 10000000 INFO @ Mon, 03 Jun 2019 13:45:43: 8000000 INFO @ Mon, 03 Jun 2019 13:45:44: 11000000 INFO @ Mon, 03 Jun 2019 13:45:49: 11000000 INFO @ Mon, 03 Jun 2019 13:45:55: 12000000 INFO @ Mon, 03 Jun 2019 13:45:55: 9000000 INFO @ Mon, 03 Jun 2019 13:45:59: 12000000 INFO @ Mon, 03 Jun 2019 13:46:04: 13000000 INFO @ Mon, 03 Jun 2019 13:46:07: 10000000 INFO @ Mon, 03 Jun 2019 13:46:08: 13000000 INFO @ Mon, 03 Jun 2019 13:46:13: 14000000 INFO @ Mon, 03 Jun 2019 13:46:17: 14000000 INFO @ Mon, 03 Jun 2019 13:46:19: 11000000 INFO @ Mon, 03 Jun 2019 13:46:21: 15000000 INFO @ Mon, 03 Jun 2019 13:46:26: 15000000 INFO @ Mon, 03 Jun 2019 13:46:30: 16000000 INFO @ Mon, 03 Jun 2019 13:46:30: 12000000 INFO @ Mon, 03 Jun 2019 13:46:32: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 13:46:32: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 13:46:32: #1 total tags in treatment: 16308189 INFO @ Mon, 03 Jun 2019 13:46:32: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:46:32: #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 13:46:33: #1 tags after filtering in treatment: 16308189 INFO @ Mon, 03 Jun 2019 13:46:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 13:46:33: #1 finished! INFO @ Mon, 03 Jun 2019 13:46:33: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:46:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:46:34: #2 number of paired peaks: 12 WARNING @ Mon, 03 Jun 2019 13:46:34: Too few paired peaks (12) 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 13:46:34: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX335504/SRX335504.10_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/SRX335504/SRX335504.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX335504/SRX335504.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX335504/SRX335504.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 13:46:34: 16000000 INFO @ Mon, 03 Jun 2019 13:46:37: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 13:46:37: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 13:46:37: #1 total tags in treatment: 16308189 INFO @ Mon, 03 Jun 2019 13:46:37: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:46:37: #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 13:46:37: #1 tags after filtering in treatment: 16308189 INFO @ Mon, 03 Jun 2019 13:46:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 13:46:37: #1 finished! INFO @ Mon, 03 Jun 2019 13:46:37: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:46:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:46:39: #2 number of paired peaks: 12 WARNING @ Mon, 03 Jun 2019 13:46:39: Too few paired peaks (12) 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 13:46:39: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX335504/SRX335504.05_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/SRX335504/SRX335504.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX335504/SRX335504.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX335504/SRX335504.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 13:46:42: 13000000 INFO @ Mon, 03 Jun 2019 13:46:53: 14000000 INFO @ Mon, 03 Jun 2019 13:47:05: 15000000 INFO @ Mon, 03 Jun 2019 13:47:16: 16000000 INFO @ Mon, 03 Jun 2019 13:47:20: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 13:47:20: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 13:47:20: #1 total tags in treatment: 16308189 INFO @ Mon, 03 Jun 2019 13:47:20: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:47:20: #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 13:47:20: #1 tags after filtering in treatment: 16308189 INFO @ Mon, 03 Jun 2019 13:47:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 13:47:20: #1 finished! INFO @ Mon, 03 Jun 2019 13:47:20: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:47:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:47:22: #2 number of paired peaks: 12 WARNING @ Mon, 03 Jun 2019 13:47:22: Too few paired peaks (12) 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 13:47:22: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX335504/SRX335504.20_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/SRX335504/SRX335504.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX335504/SRX335504.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX335504/SRX335504.20_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。