Job ID = 2640931 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T11:05:01 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 ) 2019-08-24T11:07:41 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 ) 2019-08-24T11:07:41 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 ) 2019-08-24T11:07:41 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 : 37,869,376 reads read : 37,869,376 reads written : 37,869,376 rm: cannot remove ‘[DSE]RR*’: 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: 00:12:43 37869376 reads; of these: 37869376 (100.00%) were unpaired; of these: 1015583 (2.68%) aligned 0 times 33679985 (88.94%) aligned exactly 1 time 3173808 (8.38%) aligned >1 times 97.32% overall alignment rate Time searching: 00:12:43 Overall time: 00:12:43 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 23339842 / 36853793 = 0.6333 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 20:50:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4703453/SRX4703453.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4703453/SRX4703453.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4703453/SRX4703453.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4703453/SRX4703453.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Sat, 24 Aug 2019 20:50:10: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:50:10: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:50:21: 1000000 INFO @ Sat, 24 Aug 2019 20:50:33: 2000000 INFO @ Sat, 24 Aug 2019 20:50:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4703453/SRX4703453.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4703453/SRX4703453.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4703453/SRX4703453.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4703453/SRX4703453.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Sat, 24 Aug 2019 20:50:39: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:50:39: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:50:45: 3000000 INFO @ Sat, 24 Aug 2019 20:50:49: 1000000 INFO @ Sat, 24 Aug 2019 20:50:56: 4000000 INFO @ Sat, 24 Aug 2019 20:50:59: 2000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 20:51:07: 5000000 INFO @ Sat, 24 Aug 2019 20:51:08: 3000000 INFO @ Sat, 24 Aug 2019 20:51:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4703453/SRX4703453.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4703453/SRX4703453.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4703453/SRX4703453.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4703453/SRX4703453.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Sat, 24 Aug 2019 20:51:09: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:51:09: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:51:18: 4000000 INFO @ Sat, 24 Aug 2019 20:51:19: 6000000 INFO @ Sat, 24 Aug 2019 20:51:21: 1000000 INFO @ Sat, 24 Aug 2019 20:51:28: 5000000 INFO @ Sat, 24 Aug 2019 20:51:30: 7000000 INFO @ Sat, 24 Aug 2019 20:51:33: 2000000 INFO @ Sat, 24 Aug 2019 20:51:39: 6000000 INFO @ Sat, 24 Aug 2019 20:51:41: 8000000 INFO @ Sat, 24 Aug 2019 20:51:46: 3000000 INFO @ Sat, 24 Aug 2019 20:51:50: 7000000 INFO @ Sat, 24 Aug 2019 20:51:52: 9000000 INFO @ Sat, 24 Aug 2019 20:51:58: 4000000 INFO @ Sat, 24 Aug 2019 20:52:00: 8000000 INFO @ Sat, 24 Aug 2019 20:52:04: 10000000 INFO @ Sat, 24 Aug 2019 20:52:10: 9000000 INFO @ Sat, 24 Aug 2019 20:52:10: 5000000 INFO @ Sat, 24 Aug 2019 20:52:15: 11000000 INFO @ Sat, 24 Aug 2019 20:52:20: 10000000 INFO @ Sat, 24 Aug 2019 20:52:23: 6000000 INFO @ Sat, 24 Aug 2019 20:52:26: 12000000 INFO @ Sat, 24 Aug 2019 20:52:30: 11000000 INFO @ Sat, 24 Aug 2019 20:52:36: 7000000 INFO @ Sat, 24 Aug 2019 20:52:38: 13000000 INFO @ Sat, 24 Aug 2019 20:52:40: 12000000 INFO @ Sat, 24 Aug 2019 20:52:44: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 20:52:44: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 20:52:44: #1 total tags in treatment: 13513951 INFO @ Sat, 24 Aug 2019 20:52:44: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:52:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 20:52:44: #1 tags after filtering in treatment: 13513951 INFO @ Sat, 24 Aug 2019 20:52:44: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 20:52:44: #1 finished! INFO @ Sat, 24 Aug 2019 20:52:44: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:52:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:52:45: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 20:52:45: Too few paired peaks (0) 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 @ Sat, 24 Aug 2019 20:52:45: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4703453/SRX4703453.05_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/sacCer3/SRX4703453/SRX4703453.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4703453/SRX4703453.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4703453/SRX4703453.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 20:52:50: 8000000 INFO @ Sat, 24 Aug 2019 20:52:51: 13000000 INFO @ Sat, 24 Aug 2019 20:52:56: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 20:52:56: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 20:52:56: #1 total tags in treatment: 13513951 INFO @ Sat, 24 Aug 2019 20:52:56: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:52:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 20:52:56: #1 tags after filtering in treatment: 13513951 INFO @ Sat, 24 Aug 2019 20:52:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 20:52:56: #1 finished! INFO @ Sat, 24 Aug 2019 20:52:56: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:52:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:52:57: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 20:52:57: Too few paired peaks (0) 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 @ Sat, 24 Aug 2019 20:52:57: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4703453/SRX4703453.10_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/sacCer3/SRX4703453/SRX4703453.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4703453/SRX4703453.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4703453/SRX4703453.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 20:53:03: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 20:53:16: 10000000 BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 20:53:28: 11000000 INFO @ Sat, 24 Aug 2019 20:53:41: 12000000 INFO @ Sat, 24 Aug 2019 20:53:54: 13000000 INFO @ Sat, 24 Aug 2019 20:54:01: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 20:54:01: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 20:54:01: #1 total tags in treatment: 13513951 INFO @ Sat, 24 Aug 2019 20:54:01: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:54:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 20:54:01: #1 tags after filtering in treatment: 13513951 INFO @ Sat, 24 Aug 2019 20:54:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 20:54:01: #1 finished! INFO @ Sat, 24 Aug 2019 20:54:01: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:54:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:54:02: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 20:54:02: Too few paired peaks (0) 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 @ Sat, 24 Aug 2019 20:54:02: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4703453/SRX4703453.20_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/sacCer3/SRX4703453/SRX4703453.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4703453/SRX4703453.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4703453/SRX4703453.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling