Job ID = 1304115 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T11:40:06 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 ) 2019-06-03T11:40:06 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 ) 2019-06-03T11:40:06 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 ) 2019-06-03T11:40:06 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 ) 2019-06-03T11:43:23 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 ) 2019-06-03T11:43:34 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 ) 2019-06-03T11:44:46 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 ) 2019-06-03T11:46:07 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 ) spots read : 22,157,841 reads read : 22,157,841 reads written : 22,157,841 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: 00:07:34 22157841 reads; of these: 22157841 (100.00%) were unpaired; of these: 1763433 (7.96%) aligned 0 times 15388234 (69.45%) aligned exactly 1 time 5006174 (22.59%) aligned >1 times 92.04% overall alignment rate Time searching: 00:07:34 Overall time: 00:07:34 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] 4548628 / 20394408 = 0.2230 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 21:03:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495176/SRX495176.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495176/SRX495176.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495176/SRX495176.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495176/SRX495176.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 21:03:12: #1 read tag files... INFO @ Mon, 03 Jun 2019 21:03:12: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 21:03:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495176/SRX495176.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495176/SRX495176.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495176/SRX495176.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495176/SRX495176.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 21:03:12: #1 read tag files... INFO @ Mon, 03 Jun 2019 21:03:12: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 21:03:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495176/SRX495176.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495176/SRX495176.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495176/SRX495176.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495176/SRX495176.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 21:03:12: #1 read tag files... INFO @ Mon, 03 Jun 2019 21:03:12: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 21:03:19: 1000000 INFO @ Mon, 03 Jun 2019 21:03:20: 1000000 INFO @ Mon, 03 Jun 2019 21:03:22: 1000000 INFO @ Mon, 03 Jun 2019 21:03:27: 2000000 INFO @ Mon, 03 Jun 2019 21:03:27: 2000000 INFO @ Mon, 03 Jun 2019 21:03:31: 2000000 INFO @ Mon, 03 Jun 2019 21:03:34: 3000000 INFO @ Mon, 03 Jun 2019 21:03:35: 3000000 INFO @ Mon, 03 Jun 2019 21:03:40: 3000000 INFO @ Mon, 03 Jun 2019 21:03:41: 4000000 INFO @ Mon, 03 Jun 2019 21:03:42: 4000000 INFO @ Mon, 03 Jun 2019 21:03:48: 5000000 INFO @ Mon, 03 Jun 2019 21:03:49: 4000000 INFO @ Mon, 03 Jun 2019 21:03:50: 5000000 INFO @ Mon, 03 Jun 2019 21:03:55: 6000000 INFO @ Mon, 03 Jun 2019 21:03:57: 6000000 INFO @ Mon, 03 Jun 2019 21:03:58: 5000000 INFO @ Mon, 03 Jun 2019 21:04:03: 7000000 INFO @ Mon, 03 Jun 2019 21:04:05: 7000000 INFO @ Mon, 03 Jun 2019 21:04:07: 6000000 INFO @ Mon, 03 Jun 2019 21:04:10: 8000000 INFO @ Mon, 03 Jun 2019 21:04:12: 8000000 INFO @ Mon, 03 Jun 2019 21:04:16: 7000000 INFO @ Mon, 03 Jun 2019 21:04:17: 9000000 INFO @ Mon, 03 Jun 2019 21:04:20: 9000000 INFO @ Mon, 03 Jun 2019 21:04:25: 10000000 INFO @ Mon, 03 Jun 2019 21:04:25: 8000000 INFO @ Mon, 03 Jun 2019 21:04:28: 10000000 INFO @ Mon, 03 Jun 2019 21:04:32: 11000000 INFO @ Mon, 03 Jun 2019 21:04:35: 9000000 INFO @ Mon, 03 Jun 2019 21:04:35: 11000000 INFO @ Mon, 03 Jun 2019 21:04:39: 12000000 INFO @ Mon, 03 Jun 2019 21:04:43: 12000000 INFO @ Mon, 03 Jun 2019 21:04:44: 10000000 INFO @ Mon, 03 Jun 2019 21:04:46: 13000000 INFO @ Mon, 03 Jun 2019 21:04:51: 13000000 INFO @ Mon, 03 Jun 2019 21:04:53: 11000000 INFO @ Mon, 03 Jun 2019 21:04:54: 14000000 INFO @ Mon, 03 Jun 2019 21:04:58: 14000000 INFO @ Mon, 03 Jun 2019 21:05:01: 15000000 INFO @ Mon, 03 Jun 2019 21:05:01: 12000000 INFO @ Mon, 03 Jun 2019 21:05:06: 15000000 INFO @ Mon, 03 Jun 2019 21:05:07: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 21:05:07: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 21:05:07: #1 total tags in treatment: 15845780 INFO @ Mon, 03 Jun 2019 21:05:07: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 21:05:07: #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 21:05:07: #1 tags after filtering in treatment: 15845780 INFO @ Mon, 03 Jun 2019 21:05:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 21:05:07: #1 finished! INFO @ Mon, 03 Jun 2019 21:05:07: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 21:05:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 21:05:09: #2 number of paired peaks: 51 WARNING @ Mon, 03 Jun 2019 21:05:09: Too few paired peaks (51) 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 21:05:09: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX495176/SRX495176.10_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/SRX495176/SRX495176.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495176/SRX495176.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495176/SRX495176.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 21:05:09: 13000000 INFO @ Mon, 03 Jun 2019 21:05:12: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 21:05:12: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 21:05:12: #1 total tags in treatment: 15845780 INFO @ Mon, 03 Jun 2019 21:05:12: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 21:05:12: #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 21:05:13: #1 tags after filtering in treatment: 15845780 INFO @ Mon, 03 Jun 2019 21:05:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 21:05:13: #1 finished! INFO @ Mon, 03 Jun 2019 21:05:13: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 21:05:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 21:05:14: #2 number of paired peaks: 51 WARNING @ Mon, 03 Jun 2019 21:05:14: Too few paired peaks (51) 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 21:05:14: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX495176/SRX495176.20_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/SRX495176/SRX495176.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495176/SRX495176.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495176/SRX495176.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 21:05:17: 14000000 INFO @ Mon, 03 Jun 2019 21:05:25: 15000000 INFO @ Mon, 03 Jun 2019 21:05:32: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 21:05:32: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 21:05:32: #1 total tags in treatment: 15845780 INFO @ Mon, 03 Jun 2019 21:05:32: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 21:05:32: #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 21:05:32: #1 tags after filtering in treatment: 15845780 INFO @ Mon, 03 Jun 2019 21:05:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 21:05:32: #1 finished! INFO @ Mon, 03 Jun 2019 21:05:32: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 21:05:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 21:05:33: #2 number of paired peaks: 51 WARNING @ Mon, 03 Jun 2019 21:05:33: Too few paired peaks (51) 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 21:05:33: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX495176/SRX495176.05_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/SRX495176/SRX495176.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495176/SRX495176.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495176/SRX495176.05_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。