Job ID = 1295400 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T04:36:03 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 : 24,349,077 reads read : 24,349,077 reads written : 24,349,077 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: 00:05:16 24349077 reads; of these: 24349077 (100.00%) were unpaired; of these: 9772086 (40.13%) aligned 0 times 11813183 (48.52%) aligned exactly 1 time 2763808 (11.35%) aligned >1 times 59.87% overall alignment rate Time searching: 00:05:16 Overall time: 00:05:16 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_rmdupse_core] 2467042 / 14576991 = 0.1692 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 13:49:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX336277/SRX336277.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX336277/SRX336277.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX336277/SRX336277.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX336277/SRX336277.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 13:49:10: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:49:10: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:49:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX336277/SRX336277.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX336277/SRX336277.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX336277/SRX336277.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX336277/SRX336277.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 13:49:10: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:49:10: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:49:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX336277/SRX336277.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX336277/SRX336277.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX336277/SRX336277.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX336277/SRX336277.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 13:49:10: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:49:10: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:49:20: 1000000 INFO @ Mon, 03 Jun 2019 13:49:20: 1000000 INFO @ Mon, 03 Jun 2019 13:49:20: 1000000 INFO @ Mon, 03 Jun 2019 13:49:28: 2000000 INFO @ Mon, 03 Jun 2019 13:49:28: 2000000 INFO @ Mon, 03 Jun 2019 13:49:29: 2000000 INFO @ Mon, 03 Jun 2019 13:49:36: 3000000 INFO @ Mon, 03 Jun 2019 13:49:37: 3000000 INFO @ Mon, 03 Jun 2019 13:49:37: 3000000 INFO @ Mon, 03 Jun 2019 13:49:44: 4000000 INFO @ Mon, 03 Jun 2019 13:49:45: 4000000 INFO @ Mon, 03 Jun 2019 13:49:46: 4000000 INFO @ Mon, 03 Jun 2019 13:49:52: 5000000 INFO @ Mon, 03 Jun 2019 13:49:53: 5000000 INFO @ Mon, 03 Jun 2019 13:49:54: 5000000 INFO @ Mon, 03 Jun 2019 13:50:00: 6000000 INFO @ Mon, 03 Jun 2019 13:50:02: 6000000 INFO @ Mon, 03 Jun 2019 13:50:03: 6000000 INFO @ Mon, 03 Jun 2019 13:50:08: 7000000 INFO @ Mon, 03 Jun 2019 13:50:10: 7000000 INFO @ Mon, 03 Jun 2019 13:50:12: 7000000 INFO @ Mon, 03 Jun 2019 13:50:15: 8000000 INFO @ Mon, 03 Jun 2019 13:50:18: 8000000 INFO @ Mon, 03 Jun 2019 13:50:20: 8000000 INFO @ Mon, 03 Jun 2019 13:50:23: 9000000 INFO @ Mon, 03 Jun 2019 13:50:26: 9000000 INFO @ Mon, 03 Jun 2019 13:50:29: 9000000 INFO @ Mon, 03 Jun 2019 13:50:31: 10000000 INFO @ Mon, 03 Jun 2019 13:50:34: 10000000 INFO @ Mon, 03 Jun 2019 13:50:37: 10000000 INFO @ Mon, 03 Jun 2019 13:50:40: 11000000 INFO @ Mon, 03 Jun 2019 13:50:43: 11000000 INFO @ Mon, 03 Jun 2019 13:50:46: 11000000 INFO @ Mon, 03 Jun 2019 13:50:48: 12000000 INFO @ Mon, 03 Jun 2019 13:50:49: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 13:50:49: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 13:50:49: #1 total tags in treatment: 12109949 INFO @ Mon, 03 Jun 2019 13:50:49: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:50:49: #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 13:50:49: #1 tags after filtering in treatment: 12109949 INFO @ Mon, 03 Jun 2019 13:50:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 13:50:49: #1 finished! INFO @ Mon, 03 Jun 2019 13:50:49: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:50:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:50:50: #2 number of paired peaks: 54 WARNING @ Mon, 03 Jun 2019 13:50:50: Too few paired peaks (54) 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 13:50:50: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX336277/SRX336277.20_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/SRX336277/SRX336277.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX336277/SRX336277.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX336277/SRX336277.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 13:50:51: 12000000 INFO @ Mon, 03 Jun 2019 13:50:52: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 13:50:52: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 13:50:52: #1 total tags in treatment: 12109949 INFO @ Mon, 03 Jun 2019 13:50:52: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:50:52: #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 13:50:52: #1 tags after filtering in treatment: 12109949 INFO @ Mon, 03 Jun 2019 13:50:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 13:50:52: #1 finished! INFO @ Mon, 03 Jun 2019 13:50:52: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:50:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:50:53: #2 number of paired peaks: 54 WARNING @ Mon, 03 Jun 2019 13:50:53: Too few paired peaks (54) 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 13:50:53: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX336277/SRX336277.05_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/SRX336277/SRX336277.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX336277/SRX336277.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX336277/SRX336277.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 13:50:54: 12000000 INFO @ Mon, 03 Jun 2019 13:50:55: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 13:50:55: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 13:50:55: #1 total tags in treatment: 12109949 INFO @ Mon, 03 Jun 2019 13:50:55: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:50:55: #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 13:50:55: #1 tags after filtering in treatment: 12109949 INFO @ Mon, 03 Jun 2019 13:50:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 13:50:55: #1 finished! INFO @ Mon, 03 Jun 2019 13:50:55: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:50:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:50:56: #2 number of paired peaks: 54 WARNING @ Mon, 03 Jun 2019 13:50:56: Too few paired peaks (54) 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 13:50:56: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX336277/SRX336277.10_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/SRX336277/SRX336277.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX336277/SRX336277.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX336277/SRX336277.10_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。