Job ID = 1293783 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T17:22:56 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 ) 2019-06-02T17:22:56 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 ) 2019-06-02T17:22:56 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 ) 2019-06-02T17:24:43 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 ) 2019-06-02T17:24:43 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 ) 2019-06-02T17:24:54 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 : 12,127,697 reads read : 12,127,697 reads written : 12,127,697 spots read : 28,441,419 reads read : 28,441,419 reads written : 28,441,419 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: 00:08:47 40569116 reads; of these: 40569116 (100.00%) were unpaired; of these: 13901062 (34.27%) aligned 0 times 22397357 (55.21%) aligned exactly 1 time 4270697 (10.53%) aligned >1 times 65.73% overall alignment rate Time searching: 00:08:47 Overall time: 00:08:47 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] 6152543 / 26668054 = 0.2307 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 02:56:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX113333/SRX113333.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX113333/SRX113333.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX113333/SRX113333.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX113333/SRX113333.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 02:56:51: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:56:51: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:56:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX113333/SRX113333.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX113333/SRX113333.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX113333/SRX113333.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX113333/SRX113333.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 02:56:51: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:56:51: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:56:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX113333/SRX113333.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX113333/SRX113333.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX113333/SRX113333.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX113333/SRX113333.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 02:56:51: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:56:51: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:57:03: 1000000 INFO @ Mon, 03 Jun 2019 02:57:03: 1000000 INFO @ Mon, 03 Jun 2019 02:57:04: 1000000 INFO @ Mon, 03 Jun 2019 02:57:13: 2000000 INFO @ Mon, 03 Jun 2019 02:57:15: 2000000 INFO @ Mon, 03 Jun 2019 02:57:16: 2000000 INFO @ Mon, 03 Jun 2019 02:57:24: 3000000 INFO @ Mon, 03 Jun 2019 02:57:26: 3000000 INFO @ Mon, 03 Jun 2019 02:57:28: 3000000 INFO @ Mon, 03 Jun 2019 02:57:34: 4000000 INFO @ Mon, 03 Jun 2019 02:57:38: 4000000 INFO @ Mon, 03 Jun 2019 02:57:40: 4000000 INFO @ Mon, 03 Jun 2019 02:57:45: 5000000 INFO @ Mon, 03 Jun 2019 02:57:49: 5000000 INFO @ Mon, 03 Jun 2019 02:57:52: 5000000 INFO @ Mon, 03 Jun 2019 02:57:55: 6000000 INFO @ Mon, 03 Jun 2019 02:58:00: 6000000 INFO @ Mon, 03 Jun 2019 02:58:04: 6000000 INFO @ Mon, 03 Jun 2019 02:58:06: 7000000 INFO @ Mon, 03 Jun 2019 02:58:11: 7000000 INFO @ Mon, 03 Jun 2019 02:58:16: 7000000 INFO @ Mon, 03 Jun 2019 02:58:16: 8000000 INFO @ Mon, 03 Jun 2019 02:58:22: 8000000 INFO @ Mon, 03 Jun 2019 02:58:27: 9000000 INFO @ Mon, 03 Jun 2019 02:58:28: 8000000 INFO @ Mon, 03 Jun 2019 02:58:34: 9000000 INFO @ Mon, 03 Jun 2019 02:58:37: 10000000 INFO @ Mon, 03 Jun 2019 02:58:40: 9000000 INFO @ Mon, 03 Jun 2019 02:58:45: 10000000 INFO @ Mon, 03 Jun 2019 02:58:48: 11000000 INFO @ Mon, 03 Jun 2019 02:58:51: 10000000 INFO @ Mon, 03 Jun 2019 02:58:56: 11000000 INFO @ Mon, 03 Jun 2019 02:58:58: 12000000 INFO @ Mon, 03 Jun 2019 02:59:03: 11000000 INFO @ Mon, 03 Jun 2019 02:59:07: 12000000 INFO @ Mon, 03 Jun 2019 02:59:09: 13000000 INFO @ Mon, 03 Jun 2019 02:59:15: 12000000 INFO @ Mon, 03 Jun 2019 02:59:18: 13000000 INFO @ Mon, 03 Jun 2019 02:59:19: 14000000 INFO @ Mon, 03 Jun 2019 02:59:26: 13000000 INFO @ Mon, 03 Jun 2019 02:59:29: 15000000 INFO @ Mon, 03 Jun 2019 02:59:30: 14000000 INFO @ Mon, 03 Jun 2019 02:59:38: 14000000 INFO @ Mon, 03 Jun 2019 02:59:40: 16000000 INFO @ Mon, 03 Jun 2019 02:59:41: 15000000 INFO @ Mon, 03 Jun 2019 02:59:50: 15000000 INFO @ Mon, 03 Jun 2019 02:59:51: 17000000 INFO @ Mon, 03 Jun 2019 02:59:52: 16000000 INFO @ Mon, 03 Jun 2019 03:00:02: 16000000 INFO @ Mon, 03 Jun 2019 03:00:02: 18000000 INFO @ Mon, 03 Jun 2019 03:00:04: 17000000 INFO @ Mon, 03 Jun 2019 03:00:13: 19000000 INFO @ Mon, 03 Jun 2019 03:00:14: 17000000 INFO @ Mon, 03 Jun 2019 03:00:16: 18000000 INFO @ Mon, 03 Jun 2019 03:00:24: 20000000 INFO @ Mon, 03 Jun 2019 03:00:27: 18000000 INFO @ Mon, 03 Jun 2019 03:00:28: 19000000 INFO @ Mon, 03 Jun 2019 03:00:30: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 03:00:30: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 03:00:30: #1 total tags in treatment: 20515511 INFO @ Mon, 03 Jun 2019 03:00:30: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:00:30: #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 03:00:30: #1 tags after filtering in treatment: 20515511 INFO @ Mon, 03 Jun 2019 03:00:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:00:30: #1 finished! INFO @ Mon, 03 Jun 2019 03:00:30: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:00:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:00:32: #2 number of paired peaks: 2 WARNING @ Mon, 03 Jun 2019 03:00:32: Too few paired peaks (2) 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 03:00:32: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX113333/SRX113333.10_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/SRX113333/SRX113333.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX113333/SRX113333.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX113333/SRX113333.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:00:40: 20000000 INFO @ Mon, 03 Jun 2019 03:00:40: 19000000 INFO @ Mon, 03 Jun 2019 03:00:46: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 03:00:46: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 03:00:46: #1 total tags in treatment: 20515511 INFO @ Mon, 03 Jun 2019 03:00:46: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:00:46: #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 03:00:46: #1 tags after filtering in treatment: 20515511 INFO @ Mon, 03 Jun 2019 03:00:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:00:46: #1 finished! INFO @ Mon, 03 Jun 2019 03:00:46: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:00:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:00:48: #2 number of paired peaks: 2 WARNING @ Mon, 03 Jun 2019 03:00:48: Too few paired peaks (2) 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 03:00:48: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX113333/SRX113333.20_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/SRX113333/SRX113333.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX113333/SRX113333.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX113333/SRX113333.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:00:52: 20000000 INFO @ Mon, 03 Jun 2019 03:00:59: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 03:00:59: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 03:00:59: #1 total tags in treatment: 20515511 INFO @ Mon, 03 Jun 2019 03:00:59: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:00:59: #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 03:00:59: #1 tags after filtering in treatment: 20515511 INFO @ Mon, 03 Jun 2019 03:00:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:00:59: #1 finished! INFO @ Mon, 03 Jun 2019 03:00:59: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:00:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:01:01: #2 number of paired peaks: 2 WARNING @ Mon, 03 Jun 2019 03:01:01: Too few paired peaks (2) 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 03:01:01: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX113333/SRX113333.05_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/SRX113333/SRX113333.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX113333/SRX113333.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX113333/SRX113333.05_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。