Job ID = 1304520 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T11:49:31 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 ) 2019-06-03T11:49:31 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 : 16,205,479 reads read : 16,205,479 reads written : 16,205,479 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: 00:05:29 16205479 reads; of these: 16205479 (100.00%) were unpaired; of these: 144661 (0.89%) aligned 0 times 13248743 (81.75%) aligned exactly 1 time 2812075 (17.35%) aligned >1 times 99.11% overall alignment rate Time searching: 00:05:29 Overall time: 00:05:29 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] 2669863 / 16060818 = 0.1662 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 21:05:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495190/SRX495190.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495190/SRX495190.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495190/SRX495190.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495190/SRX495190.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 21:05:47: #1 read tag files... INFO @ Mon, 03 Jun 2019 21:05:47: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 21:05:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495190/SRX495190.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495190/SRX495190.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495190/SRX495190.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495190/SRX495190.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 21:05:47: #1 read tag files... INFO @ Mon, 03 Jun 2019 21:05:47: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 21:05:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495190/SRX495190.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495190/SRX495190.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495190/SRX495190.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495190/SRX495190.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 21:05:47: #1 read tag files... INFO @ Mon, 03 Jun 2019 21:05:47: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 21:05:54: 1000000 INFO @ Mon, 03 Jun 2019 21:05:55: 1000000 INFO @ Mon, 03 Jun 2019 21:05:57: 1000000 INFO @ Mon, 03 Jun 2019 21:06:01: 2000000 INFO @ Mon, 03 Jun 2019 21:06:02: 2000000 INFO @ Mon, 03 Jun 2019 21:06:06: 2000000 INFO @ Mon, 03 Jun 2019 21:06:08: 3000000 INFO @ Mon, 03 Jun 2019 21:06:09: 3000000 INFO @ Mon, 03 Jun 2019 21:06:14: 4000000 INFO @ Mon, 03 Jun 2019 21:06:15: 3000000 INFO @ Mon, 03 Jun 2019 21:06:16: 4000000 INFO @ Mon, 03 Jun 2019 21:06:21: 5000000 INFO @ Mon, 03 Jun 2019 21:06:23: 5000000 INFO @ Mon, 03 Jun 2019 21:06:23: 4000000 INFO @ Mon, 03 Jun 2019 21:06:28: 6000000 INFO @ Mon, 03 Jun 2019 21:06:30: 6000000 INFO @ Mon, 03 Jun 2019 21:06:31: 5000000 INFO @ Mon, 03 Jun 2019 21:06:34: 7000000 INFO @ Mon, 03 Jun 2019 21:06:37: 7000000 INFO @ Mon, 03 Jun 2019 21:06:39: 6000000 INFO @ Mon, 03 Jun 2019 21:06:41: 8000000 INFO @ Mon, 03 Jun 2019 21:06:44: 8000000 INFO @ Mon, 03 Jun 2019 21:06:47: 7000000 INFO @ Mon, 03 Jun 2019 21:06:48: 9000000 INFO @ Mon, 03 Jun 2019 21:06:50: 9000000 INFO @ Mon, 03 Jun 2019 21:06:54: 10000000 INFO @ Mon, 03 Jun 2019 21:06:55: 8000000 INFO @ Mon, 03 Jun 2019 21:06:57: 10000000 INFO @ Mon, 03 Jun 2019 21:07:01: 11000000 INFO @ Mon, 03 Jun 2019 21:07:03: 9000000 INFO @ Mon, 03 Jun 2019 21:07:04: 11000000 INFO @ Mon, 03 Jun 2019 21:07:07: 12000000 INFO @ Mon, 03 Jun 2019 21:07:11: 10000000 INFO @ Mon, 03 Jun 2019 21:07:11: 12000000 INFO @ Mon, 03 Jun 2019 21:07:14: 13000000 INFO @ Mon, 03 Jun 2019 21:07:17: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 21:07:17: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 21:07:17: #1 total tags in treatment: 13390955 INFO @ Mon, 03 Jun 2019 21:07:17: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 21:07:17: #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 21:07:17: #1 tags after filtering in treatment: 13390955 INFO @ Mon, 03 Jun 2019 21:07:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 21:07:17: #1 finished! INFO @ Mon, 03 Jun 2019 21:07:17: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 21:07:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 21:07:18: 13000000 INFO @ Mon, 03 Jun 2019 21:07:18: 11000000 INFO @ Mon, 03 Jun 2019 21:07:18: #2 number of paired peaks: 41 WARNING @ Mon, 03 Jun 2019 21:07:18: Too few paired peaks (41) 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 21:07:18: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX495190/SRX495190.20_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/SRX495190/SRX495190.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495190/SRX495190.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495190/SRX495190.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 21:07:21: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 21:07:21: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 21:07:21: #1 total tags in treatment: 13390955 INFO @ Mon, 03 Jun 2019 21:07:21: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 21:07:21: #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 21:07:21: #1 tags after filtering in treatment: 13390955 INFO @ Mon, 03 Jun 2019 21:07:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 21:07:21: #1 finished! INFO @ Mon, 03 Jun 2019 21:07:21: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 21:07:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 21:07:22: #2 number of paired peaks: 41 WARNING @ Mon, 03 Jun 2019 21:07:22: Too few paired peaks (41) 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 21:07:22: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX495190/SRX495190.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495190/SRX495190.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495190/SRX495190.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495190/SRX495190.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 21:07:26: 12000000 INFO @ Mon, 03 Jun 2019 21:07:33: 13000000 INFO @ Mon, 03 Jun 2019 21:07:36: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 21:07:36: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 21:07:36: #1 total tags in treatment: 13390955 INFO @ Mon, 03 Jun 2019 21:07:36: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 21:07:36: #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 21:07:37: #1 tags after filtering in treatment: 13390955 INFO @ Mon, 03 Jun 2019 21:07:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 21:07:37: #1 finished! INFO @ Mon, 03 Jun 2019 21:07:37: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 21:07:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 21:07:38: #2 number of paired peaks: 41 WARNING @ Mon, 03 Jun 2019 21:07:38: Too few paired peaks (41) 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 21:07:38: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX495190/SRX495190.10_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/SRX495190/SRX495190.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495190/SRX495190.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495190/SRX495190.10_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。