Job ID = 1293728 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T16:59:44 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 : 19,278,042 reads read : 19,278,042 reads written : 19,278,042 2019-06-02T17:02:17 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 ) 2019-06-02T17:02:17 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 ) 2019-06-02T17:03:39 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 : 20,582,740 reads read : 20,582,740 reads written : 20,582,740 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: 00:15:39 39860782 reads; of these: 39860782 (100.00%) were unpaired; of these: 5546299 (13.91%) aligned 0 times 22879222 (57.40%) aligned exactly 1 time 11435261 (28.69%) aligned >1 times 86.09% overall alignment rate Time searching: 00:15:39 Overall time: 00:15:39 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 12 files... [bam_rmdupse_core] 12910082 / 34314483 = 0.3762 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 02:30:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX111812/SRX111812.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX111812/SRX111812.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX111812/SRX111812.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX111812/SRX111812.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 02:30:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX111812/SRX111812.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX111812/SRX111812.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX111812/SRX111812.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX111812/SRX111812.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 02:30:34: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:30:34: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:30:34: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:30:34: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:30:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX111812/SRX111812.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX111812/SRX111812.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX111812/SRX111812.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX111812/SRX111812.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 02:30:34: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:30:34: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:30:43: 1000000 INFO @ Mon, 03 Jun 2019 02:30:44: 1000000 INFO @ Mon, 03 Jun 2019 02:30:45: 1000000 INFO @ Mon, 03 Jun 2019 02:30:51: 2000000 INFO @ Mon, 03 Jun 2019 02:30:54: 2000000 INFO @ Mon, 03 Jun 2019 02:30:54: 2000000 INFO @ Mon, 03 Jun 2019 02:30:59: 3000000 INFO @ Mon, 03 Jun 2019 02:31:03: 3000000 INFO @ Mon, 03 Jun 2019 02:31:04: 3000000 INFO @ Mon, 03 Jun 2019 02:31:06: 4000000 INFO @ Mon, 03 Jun 2019 02:31:12: 4000000 INFO @ Mon, 03 Jun 2019 02:31:14: 5000000 INFO @ Mon, 03 Jun 2019 02:31:14: 4000000 INFO @ Mon, 03 Jun 2019 02:31:22: 6000000 INFO @ Mon, 03 Jun 2019 02:31:22: 5000000 INFO @ Mon, 03 Jun 2019 02:31:24: 5000000 INFO @ Mon, 03 Jun 2019 02:31:30: 7000000 INFO @ Mon, 03 Jun 2019 02:31:31: 6000000 INFO @ Mon, 03 Jun 2019 02:31:34: 6000000 INFO @ Mon, 03 Jun 2019 02:31:37: 8000000 INFO @ Mon, 03 Jun 2019 02:31:41: 7000000 INFO @ Mon, 03 Jun 2019 02:31:43: 7000000 INFO @ Mon, 03 Jun 2019 02:31:45: 9000000 INFO @ Mon, 03 Jun 2019 02:31:50: 8000000 INFO @ Mon, 03 Jun 2019 02:31:52: 8000000 INFO @ Mon, 03 Jun 2019 02:31:52: 10000000 INFO @ Mon, 03 Jun 2019 02:31:58: 9000000 INFO @ Mon, 03 Jun 2019 02:32:00: 11000000 INFO @ Mon, 03 Jun 2019 02:32:01: 9000000 INFO @ Mon, 03 Jun 2019 02:32:07: 10000000 INFO @ Mon, 03 Jun 2019 02:32:08: 12000000 INFO @ Mon, 03 Jun 2019 02:32:09: 10000000 INFO @ Mon, 03 Jun 2019 02:32:15: 13000000 INFO @ Mon, 03 Jun 2019 02:32:16: 11000000 INFO @ Mon, 03 Jun 2019 02:32:18: 11000000 INFO @ Mon, 03 Jun 2019 02:32:23: 14000000 INFO @ Mon, 03 Jun 2019 02:32:24: 12000000 INFO @ Mon, 03 Jun 2019 02:32:27: 12000000 INFO @ Mon, 03 Jun 2019 02:32:30: 15000000 INFO @ Mon, 03 Jun 2019 02:32:33: 13000000 INFO @ Mon, 03 Jun 2019 02:32:35: 13000000 INFO @ Mon, 03 Jun 2019 02:32:38: 16000000 INFO @ Mon, 03 Jun 2019 02:32:42: 14000000 INFO @ Mon, 03 Jun 2019 02:32:44: 14000000 INFO @ Mon, 03 Jun 2019 02:32:45: 17000000 INFO @ Mon, 03 Jun 2019 02:32:50: 15000000 INFO @ Mon, 03 Jun 2019 02:32:53: 15000000 INFO @ Mon, 03 Jun 2019 02:32:53: 18000000 INFO @ Mon, 03 Jun 2019 02:32:59: 16000000 INFO @ Mon, 03 Jun 2019 02:33:01: 19000000 INFO @ Mon, 03 Jun 2019 02:33:02: 16000000 INFO @ Mon, 03 Jun 2019 02:33:08: 17000000 INFO @ Mon, 03 Jun 2019 02:33:09: 20000000 INFO @ Mon, 03 Jun 2019 02:33:11: 17000000 INFO @ Mon, 03 Jun 2019 02:33:16: 21000000 INFO @ Mon, 03 Jun 2019 02:33:17: 18000000 INFO @ Mon, 03 Jun 2019 02:33:19: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 02:33:19: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 02:33:19: #1 total tags in treatment: 21404401 INFO @ Mon, 03 Jun 2019 02:33:19: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:33:19: #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 02:33:19: 18000000 INFO @ Mon, 03 Jun 2019 02:33:20: #1 tags after filtering in treatment: 21404401 INFO @ Mon, 03 Jun 2019 02:33:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:33:20: #1 finished! INFO @ Mon, 03 Jun 2019 02:33:20: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:33:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:33:22: #2 number of paired peaks: 9 WARNING @ Mon, 03 Jun 2019 02:33:22: Too few paired peaks (9) 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 02:33:22: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX111812/SRX111812.05_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/dm3/SRX111812/SRX111812.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111812/SRX111812.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111812/SRX111812.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:33:26: 19000000 INFO @ Mon, 03 Jun 2019 02:33:28: 19000000 INFO @ Mon, 03 Jun 2019 02:33:34: 20000000 INFO @ Mon, 03 Jun 2019 02:33:37: 20000000 INFO @ Mon, 03 Jun 2019 02:33:43: 21000000 INFO @ Mon, 03 Jun 2019 02:33:46: 21000000 INFO @ Mon, 03 Jun 2019 02:33:47: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 02:33:47: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 02:33:47: #1 total tags in treatment: 21404401 INFO @ Mon, 03 Jun 2019 02:33:47: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:33:47: #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 02:33:47: #1 tags after filtering in treatment: 21404401 INFO @ Mon, 03 Jun 2019 02:33:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:33:47: #1 finished! INFO @ Mon, 03 Jun 2019 02:33:47: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:33:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:33:49: #2 number of paired peaks: 9 WARNING @ Mon, 03 Jun 2019 02:33:49: Too few paired peaks (9) 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 02:33:49: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX111812/SRX111812.20_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/SRX111812/SRX111812.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111812/SRX111812.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111812/SRX111812.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:33:49: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 02:33:49: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 02:33:49: #1 total tags in treatment: 21404401 INFO @ Mon, 03 Jun 2019 02:33:49: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:33:49: #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 02:33:50: #1 tags after filtering in treatment: 21404401 INFO @ Mon, 03 Jun 2019 02:33:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:33:50: #1 finished! INFO @ Mon, 03 Jun 2019 02:33:50: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:33:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:33:52: #2 number of paired peaks: 9 WARNING @ Mon, 03 Jun 2019 02:33:52: Too few paired peaks (9) 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 02:33:52: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX111812/SRX111812.10_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/SRX111812/SRX111812.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111812/SRX111812.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111812/SRX111812.10_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。