Job ID = 1298880 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T08:39:52 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 ) 2019-06-03T08:39:56 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 ) 2019-06-03T08:40:33 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 ) 2019-06-03T08:42:15 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 ) 2019-06-03T08:46:15 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 : 29,206,592 reads read : 29,206,592 reads written : 29,206,592 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: 00:10:21 29206592 reads; of these: 29206592 (100.00%) were unpaired; of these: 909631 (3.11%) aligned 0 times 22185880 (75.96%) aligned exactly 1 time 6111081 (20.92%) aligned >1 times 96.89% overall alignment rate Time searching: 00:10:21 Overall time: 00:10:21 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] 6072917 / 28296961 = 0.2146 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 18:11:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467057/SRX467057.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467057/SRX467057.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467057/SRX467057.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467057/SRX467057.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 18:11:22: #1 read tag files... INFO @ Mon, 03 Jun 2019 18:11:22: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 18:11:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467057/SRX467057.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467057/SRX467057.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467057/SRX467057.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467057/SRX467057.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 18:11:23: #1 read tag files... INFO @ Mon, 03 Jun 2019 18:11:23: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 18:11:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467057/SRX467057.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467057/SRX467057.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467057/SRX467057.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467057/SRX467057.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 18:11:23: #1 read tag files... INFO @ Mon, 03 Jun 2019 18:11:23: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 18:11:32: 1000000 INFO @ Mon, 03 Jun 2019 18:11:32: 1000000 INFO @ Mon, 03 Jun 2019 18:11:34: 1000000 INFO @ Mon, 03 Jun 2019 18:11:41: 2000000 INFO @ Mon, 03 Jun 2019 18:11:42: 2000000 INFO @ Mon, 03 Jun 2019 18:11:44: 2000000 INFO @ Mon, 03 Jun 2019 18:11:49: 3000000 INFO @ Mon, 03 Jun 2019 18:11:51: 3000000 INFO @ Mon, 03 Jun 2019 18:11:54: 3000000 INFO @ Mon, 03 Jun 2019 18:11:56: 4000000 INFO @ Mon, 03 Jun 2019 18:12:00: 4000000 INFO @ Mon, 03 Jun 2019 18:12:03: 5000000 INFO @ Mon, 03 Jun 2019 18:12:04: 4000000 INFO @ Mon, 03 Jun 2019 18:12:09: 5000000 INFO @ Mon, 03 Jun 2019 18:12:11: 6000000 INFO @ Mon, 03 Jun 2019 18:12:14: 5000000 INFO @ Mon, 03 Jun 2019 18:12:18: 6000000 INFO @ Mon, 03 Jun 2019 18:12:20: 7000000 INFO @ Mon, 03 Jun 2019 18:12:24: 6000000 INFO @ Mon, 03 Jun 2019 18:12:27: 7000000 INFO @ Mon, 03 Jun 2019 18:12:28: 8000000 INFO @ Mon, 03 Jun 2019 18:12:34: 7000000 INFO @ Mon, 03 Jun 2019 18:12:36: 9000000 INFO @ Mon, 03 Jun 2019 18:12:36: 8000000 INFO @ Mon, 03 Jun 2019 18:12:43: 10000000 INFO @ Mon, 03 Jun 2019 18:12:44: 8000000 INFO @ Mon, 03 Jun 2019 18:12:45: 9000000 INFO @ Mon, 03 Jun 2019 18:12:51: 11000000 INFO @ Mon, 03 Jun 2019 18:12:54: 10000000 INFO @ Mon, 03 Jun 2019 18:12:55: 9000000 INFO @ Mon, 03 Jun 2019 18:12:59: 12000000 INFO @ Mon, 03 Jun 2019 18:13:03: 11000000 INFO @ Mon, 03 Jun 2019 18:13:05: 10000000 INFO @ Mon, 03 Jun 2019 18:13:06: 13000000 INFO @ Mon, 03 Jun 2019 18:13:12: 12000000 INFO @ Mon, 03 Jun 2019 18:13:13: 14000000 INFO @ Mon, 03 Jun 2019 18:13:17: 11000000 INFO @ Mon, 03 Jun 2019 18:13:20: 15000000 INFO @ Mon, 03 Jun 2019 18:13:21: 13000000 INFO @ Mon, 03 Jun 2019 18:13:27: 16000000 INFO @ Mon, 03 Jun 2019 18:13:28: 12000000 INFO @ Mon, 03 Jun 2019 18:13:30: 14000000 INFO @ Mon, 03 Jun 2019 18:13:35: 17000000 INFO @ Mon, 03 Jun 2019 18:13:38: 13000000 INFO @ Mon, 03 Jun 2019 18:13:39: 15000000 INFO @ Mon, 03 Jun 2019 18:13:42: 18000000 INFO @ Mon, 03 Jun 2019 18:13:49: 16000000 INFO @ Mon, 03 Jun 2019 18:13:49: 14000000 INFO @ Mon, 03 Jun 2019 18:13:50: 19000000 INFO @ Mon, 03 Jun 2019 18:13:58: 17000000 INFO @ Mon, 03 Jun 2019 18:13:58: 20000000 INFO @ Mon, 03 Jun 2019 18:13:59: 15000000 INFO @ Mon, 03 Jun 2019 18:14:06: 21000000 INFO @ Mon, 03 Jun 2019 18:14:06: 18000000 INFO @ Mon, 03 Jun 2019 18:14:10: 16000000 INFO @ Mon, 03 Jun 2019 18:14:13: 22000000 INFO @ Mon, 03 Jun 2019 18:14:15: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 18:14:15: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 18:14:15: #1 total tags in treatment: 22224044 INFO @ Mon, 03 Jun 2019 18:14:15: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:14:15: #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 18:14:15: #1 tags after filtering in treatment: 22224044 INFO @ Mon, 03 Jun 2019 18:14:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 18:14:15: #1 finished! INFO @ Mon, 03 Jun 2019 18:14:15: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:14:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:14:15: 19000000 INFO @ Mon, 03 Jun 2019 18:14:17: #2 number of paired peaks: 26 WARNING @ Mon, 03 Jun 2019 18:14:17: Too few paired peaks (26) 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 18:14:17: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX467057/SRX467057.10_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/SRX467057/SRX467057.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467057/SRX467057.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467057/SRX467057.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 18:14:20: 17000000 INFO @ Mon, 03 Jun 2019 18:14:24: 20000000 INFO @ Mon, 03 Jun 2019 18:14:30: 18000000 INFO @ Mon, 03 Jun 2019 18:14:33: 21000000 INFO @ Mon, 03 Jun 2019 18:14:41: 19000000 INFO @ Mon, 03 Jun 2019 18:14:42: 22000000 INFO @ Mon, 03 Jun 2019 18:14:44: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 18:14:44: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 18:14:44: #1 total tags in treatment: 22224044 INFO @ Mon, 03 Jun 2019 18:14:44: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:14:44: #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 18:14:44: #1 tags after filtering in treatment: 22224044 INFO @ Mon, 03 Jun 2019 18:14:44: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 18:14:44: #1 finished! INFO @ Mon, 03 Jun 2019 18:14:44: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:14:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:14:46: #2 number of paired peaks: 26 WARNING @ Mon, 03 Jun 2019 18:14:46: Too few paired peaks (26) 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 18:14:46: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX467057/SRX467057.05_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/SRX467057/SRX467057.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467057/SRX467057.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467057/SRX467057.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 18:14:51: 20000000 INFO @ Mon, 03 Jun 2019 18:15:00: 21000000 INFO @ Mon, 03 Jun 2019 18:15:10: 22000000 INFO @ Mon, 03 Jun 2019 18:15:12: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 18:15:12: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 18:15:12: #1 total tags in treatment: 22224044 INFO @ Mon, 03 Jun 2019 18:15:12: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:15:12: #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 18:15:13: #1 tags after filtering in treatment: 22224044 INFO @ Mon, 03 Jun 2019 18:15:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 18:15:13: #1 finished! INFO @ Mon, 03 Jun 2019 18:15:13: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:15:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:15:15: #2 number of paired peaks: 26 WARNING @ Mon, 03 Jun 2019 18:15:15: Too few paired peaks (26) 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 18:15:15: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX467057/SRX467057.20_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/SRX467057/SRX467057.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467057/SRX467057.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467057/SRX467057.20_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。