Job ID = 2010751 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T15:21:17 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-07-05T15:21:37 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 ) 2019-07-05T15:21:47 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 : 43,513,709 reads read : 43,513,709 reads written : 43,513,709 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: 00:07:24 43513709 reads; of these: 43513709 (100.00%) were unpaired; of these: 1357240 (3.12%) aligned 0 times 36272570 (83.36%) aligned exactly 1 time 5883899 (13.52%) aligned >1 times 96.88% overall alignment rate Time searching: 00:07:24 Overall time: 00:07:24 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 20 files... [bam_rmdupse_core] 25470670 / 42156469 = 0.6042 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 @ Sat, 06 Jul 2019 01:01:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX387210/SRX387210.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX387210/SRX387210.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX387210/SRX387210.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX387210/SRX387210.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, 06 Jul 2019 01:01:04: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:01:04: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:01:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX387210/SRX387210.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX387210/SRX387210.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX387210/SRX387210.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX387210/SRX387210.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, 06 Jul 2019 01:01:05: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:01:05: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:01:14: 1000000 INFO @ Sat, 06 Jul 2019 01:01:15: 1000000 INFO @ Sat, 06 Jul 2019 01:01:24: 2000000 INFO @ Sat, 06 Jul 2019 01:01:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX387210/SRX387210.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX387210/SRX387210.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX387210/SRX387210.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX387210/SRX387210.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, 06 Jul 2019 01:01:24: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:01:24: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:01:25: 2000000 INFO @ Sat, 06 Jul 2019 01:01:33: 3000000 INFO @ Sat, 06 Jul 2019 01:01:35: 1000000 INFO @ Sat, 06 Jul 2019 01:01:35: 3000000 INFO @ Sat, 06 Jul 2019 01:01:43: 4000000 INFO @ Sat, 06 Jul 2019 01:01:45: 4000000 INFO @ Sat, 06 Jul 2019 01:01:46: 2000000 INFO @ Sat, 06 Jul 2019 01:01:53: 5000000 INFO @ Sat, 06 Jul 2019 01:01:55: 5000000 INFO @ Sat, 06 Jul 2019 01:01:56: 3000000 INFO @ Sat, 06 Jul 2019 01:02:02: 6000000 INFO @ Sat, 06 Jul 2019 01:02:06: 6000000 INFO @ Sat, 06 Jul 2019 01:02:07: 4000000 INFO @ Sat, 06 Jul 2019 01:02:12: 7000000 INFO @ Sat, 06 Jul 2019 01:02:16: 7000000 INFO @ Sat, 06 Jul 2019 01:02:18: 5000000 INFO @ Sat, 06 Jul 2019 01:02:21: 8000000 INFO @ Sat, 06 Jul 2019 01:02:26: 8000000 INFO @ Sat, 06 Jul 2019 01:02:28: 6000000 INFO @ Sat, 06 Jul 2019 01:02:31: 9000000 INFO @ Sat, 06 Jul 2019 01:02:37: 9000000 INFO @ Sat, 06 Jul 2019 01:02:39: 7000000 INFO @ Sat, 06 Jul 2019 01:02:40: 10000000 INFO @ Sat, 06 Jul 2019 01:02:47: 10000000 INFO @ Sat, 06 Jul 2019 01:02:49: 8000000 INFO @ Sat, 06 Jul 2019 01:02:50: 11000000 INFO @ Sat, 06 Jul 2019 01:02:58: 11000000 INFO @ Sat, 06 Jul 2019 01:02:59: 12000000 INFO @ Sat, 06 Jul 2019 01:03:00: 9000000 INFO @ Sat, 06 Jul 2019 01:03:08: 12000000 INFO @ Sat, 06 Jul 2019 01:03:09: 13000000 INFO @ Sat, 06 Jul 2019 01:03:11: 10000000 INFO @ Sat, 06 Jul 2019 01:03:19: 14000000 INFO @ Sat, 06 Jul 2019 01:03:19: 13000000 INFO @ Sat, 06 Jul 2019 01:03:21: 11000000 INFO @ Sat, 06 Jul 2019 01:03:28: 15000000 INFO @ Sat, 06 Jul 2019 01:03:29: 14000000 INFO @ Sat, 06 Jul 2019 01:03:32: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 01:03:38: 16000000 INFO @ Sat, 06 Jul 2019 01:03:40: 15000000 INFO @ Sat, 06 Jul 2019 01:03:43: 13000000 INFO @ Sat, 06 Jul 2019 01:03:45: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 01:03:45: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 01:03:45: #1 total tags in treatment: 16685799 INFO @ Sat, 06 Jul 2019 01:03:45: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:03:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 01:03:45: #1 tags after filtering in treatment: 16685799 INFO @ Sat, 06 Jul 2019 01:03:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 01:03:45: #1 finished! INFO @ Sat, 06 Jul 2019 01:03:45: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:03:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:03:46: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 01:03:46: 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, 06 Jul 2019 01:03:46: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX387210/SRX387210.05_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/sacCer3/SRX387210/SRX387210.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX387210/SRX387210.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX387210/SRX387210.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 01:03:52: 16000000 INFO @ Sat, 06 Jul 2019 01:03:54: 14000000 INFO @ Sat, 06 Jul 2019 01:04:01: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 01:04:01: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 01:04:01: #1 total tags in treatment: 16685799 INFO @ Sat, 06 Jul 2019 01:04:01: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:04:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 01:04:01: #1 tags after filtering in treatment: 16685799 INFO @ Sat, 06 Jul 2019 01:04:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 01:04:01: #1 finished! INFO @ Sat, 06 Jul 2019 01:04:01: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:04:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:04:02: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 01:04:02: 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, 06 Jul 2019 01:04:02: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX387210/SRX387210.10_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/sacCer3/SRX387210/SRX387210.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX387210/SRX387210.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX387210/SRX387210.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 01:04:05: 15000000 INFO @ Sat, 06 Jul 2019 01:04:14: 16000000 INFO @ Sat, 06 Jul 2019 01:04:21: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 01:04:21: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 01:04:21: #1 total tags in treatment: 16685799 INFO @ Sat, 06 Jul 2019 01:04:21: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:04:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 01:04:22: #1 tags after filtering in treatment: 16685799 INFO @ Sat, 06 Jul 2019 01:04:22: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 01:04:22: #1 finished! INFO @ Sat, 06 Jul 2019 01:04:22: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:04:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:04:23: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 01:04:23: 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, 06 Jul 2019 01:04:23: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX387210/SRX387210.20_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/SRX387210/SRX387210.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX387210/SRX387210.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX387210/SRX387210.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling