Job ID = 1293705 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,728,174 reads read : 19,728,174 reads written : 19,728,174 2019-06-02T16:54:29 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 ) 2019-06-02T16:54:29 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 ) 2019-06-02T16:54:29 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 ) 2019-06-02T16:57:38 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 ) 2019-06-02T16:58:06 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 ) 2019-06-02T16:58:59 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 ) 2019-06-02T17:01:57 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 ) 2019-06-02T17:02:22 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 ‘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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:10:26 44077251 reads; of these: 44077251 (100.00%) were unpaired; of these: 13072348 (29.66%) aligned 0 times 25243463 (57.27%) aligned exactly 1 time 5761440 (13.07%) aligned >1 times 70.34% overall alignment rate Time searching: 00:10:27 Overall time: 00:10:27 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] 8420364 / 31004903 = 0.2716 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 02:26:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX111785/SRX111785.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX111785/SRX111785.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX111785/SRX111785.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX111785/SRX111785.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 02:26:54: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:26:54: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:26:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX111785/SRX111785.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX111785/SRX111785.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX111785/SRX111785.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX111785/SRX111785.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 02:26:54: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:26:54: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:26:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX111785/SRX111785.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX111785/SRX111785.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX111785/SRX111785.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX111785/SRX111785.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 02:26:54: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:26:54: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:27:03: 1000000 INFO @ Mon, 03 Jun 2019 02:27:04: 1000000 INFO @ Mon, 03 Jun 2019 02:27:04: 1000000 INFO @ Mon, 03 Jun 2019 02:27:10: 2000000 INFO @ Mon, 03 Jun 2019 02:27:13: 2000000 INFO @ Mon, 03 Jun 2019 02:27:13: 2000000 INFO @ Mon, 03 Jun 2019 02:27:19: 3000000 INFO @ Mon, 03 Jun 2019 02:27:22: 3000000 INFO @ Mon, 03 Jun 2019 02:27:22: 3000000 INFO @ Mon, 03 Jun 2019 02:27:27: 4000000 INFO @ Mon, 03 Jun 2019 02:27:31: 4000000 INFO @ Mon, 03 Jun 2019 02:27:31: 4000000 INFO @ Mon, 03 Jun 2019 02:27:35: 5000000 INFO @ Mon, 03 Jun 2019 02:27:39: 5000000 INFO @ Mon, 03 Jun 2019 02:27:39: 5000000 INFO @ Mon, 03 Jun 2019 02:27:43: 6000000 INFO @ Mon, 03 Jun 2019 02:27:48: 6000000 INFO @ Mon, 03 Jun 2019 02:27:48: 6000000 INFO @ Mon, 03 Jun 2019 02:27:50: 7000000 INFO @ Mon, 03 Jun 2019 02:27:57: 7000000 INFO @ Mon, 03 Jun 2019 02:27:57: 7000000 INFO @ Mon, 03 Jun 2019 02:27:57: 8000000 INFO @ Mon, 03 Jun 2019 02:28:05: 9000000 INFO @ Mon, 03 Jun 2019 02:28:06: 8000000 INFO @ Mon, 03 Jun 2019 02:28:07: 8000000 INFO @ Mon, 03 Jun 2019 02:28:12: 10000000 INFO @ Mon, 03 Jun 2019 02:28:16: 9000000 INFO @ Mon, 03 Jun 2019 02:28:16: 9000000 INFO @ Mon, 03 Jun 2019 02:28:19: 11000000 INFO @ Mon, 03 Jun 2019 02:28:25: 10000000 INFO @ Mon, 03 Jun 2019 02:28:26: 10000000 INFO @ Mon, 03 Jun 2019 02:28:26: 12000000 INFO @ Mon, 03 Jun 2019 02:28:33: 13000000 INFO @ Mon, 03 Jun 2019 02:28:34: 11000000 INFO @ Mon, 03 Jun 2019 02:28:36: 11000000 INFO @ Mon, 03 Jun 2019 02:28:42: 14000000 INFO @ Mon, 03 Jun 2019 02:28:44: 12000000 INFO @ Mon, 03 Jun 2019 02:28:47: 12000000 INFO @ Mon, 03 Jun 2019 02:28:50: 15000000 INFO @ Mon, 03 Jun 2019 02:28:53: 13000000 INFO @ Mon, 03 Jun 2019 02:28:56: 13000000 INFO @ Mon, 03 Jun 2019 02:28:58: 16000000 INFO @ Mon, 03 Jun 2019 02:29:02: 14000000 INFO @ Mon, 03 Jun 2019 02:29:05: 14000000 INFO @ Mon, 03 Jun 2019 02:29:05: 17000000 INFO @ Mon, 03 Jun 2019 02:29:11: 15000000 INFO @ Mon, 03 Jun 2019 02:29:12: 18000000 INFO @ Mon, 03 Jun 2019 02:29:14: 15000000 INFO @ Mon, 03 Jun 2019 02:29:19: 19000000 INFO @ Mon, 03 Jun 2019 02:29:20: 16000000 INFO @ Mon, 03 Jun 2019 02:29:23: 16000000 INFO @ Mon, 03 Jun 2019 02:29:26: 20000000 INFO @ Mon, 03 Jun 2019 02:29:29: 17000000 INFO @ Mon, 03 Jun 2019 02:29:32: 17000000 INFO @ Mon, 03 Jun 2019 02:29:34: 21000000 INFO @ Mon, 03 Jun 2019 02:29:38: 18000000 INFO @ Mon, 03 Jun 2019 02:29:41: 22000000 INFO @ Mon, 03 Jun 2019 02:29:41: 18000000 INFO @ Mon, 03 Jun 2019 02:29:45: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 02:29:45: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 02:29:45: #1 total tags in treatment: 22584539 INFO @ Mon, 03 Jun 2019 02:29:45: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:29:45: #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 02:29:45: #1 tags after filtering in treatment: 22584539 INFO @ Mon, 03 Jun 2019 02:29:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:29:45: #1 finished! INFO @ Mon, 03 Jun 2019 02:29:45: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:29:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:29:47: #2 number of paired peaks: 26 WARNING @ Mon, 03 Jun 2019 02:29:47: Too few paired peaks (26) 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 02:29:47: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX111785/SRX111785.20_peaks.narrowPeak: No such file or directory INFO @ Mon, 03 Jun 2019 02:29:47: 19000000 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111785/SRX111785.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111785/SRX111785.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111785/SRX111785.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:29:50: 19000000 INFO @ Mon, 03 Jun 2019 02:29:56: 20000000 INFO @ Mon, 03 Jun 2019 02:29:59: 20000000 INFO @ Mon, 03 Jun 2019 02:30:05: 21000000 INFO @ Mon, 03 Jun 2019 02:30:08: 21000000 INFO @ Mon, 03 Jun 2019 02:30:14: 22000000 INFO @ Mon, 03 Jun 2019 02:30:18: 22000000 INFO @ Mon, 03 Jun 2019 02:30:19: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 02:30:19: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 02:30:19: #1 total tags in treatment: 22584539 INFO @ Mon, 03 Jun 2019 02:30:19: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:30:19: #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 02:30:20: #1 tags after filtering in treatment: 22584539 INFO @ Mon, 03 Jun 2019 02:30:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:30:20: #1 finished! INFO @ Mon, 03 Jun 2019 02:30:20: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:30:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:30:22: #2 number of paired peaks: 26 WARNING @ Mon, 03 Jun 2019 02:30:22: Too few paired peaks (26) 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 02:30:22: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX111785/SRX111785.05_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/SRX111785/SRX111785.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111785/SRX111785.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111785/SRX111785.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:30:23: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 02:30:23: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 02:30:23: #1 total tags in treatment: 22584539 INFO @ Mon, 03 Jun 2019 02:30:23: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:30:23: #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 02:30:24: #1 tags after filtering in treatment: 22584539 INFO @ Mon, 03 Jun 2019 02:30:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:30:24: #1 finished! INFO @ Mon, 03 Jun 2019 02:30:24: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:30:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:30:26: #2 number of paired peaks: 26 WARNING @ Mon, 03 Jun 2019 02:30:26: Too few paired peaks (26) 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 02:30:26: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX111785/SRX111785.10_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/SRX111785/SRX111785.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111785/SRX111785.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111785/SRX111785.10_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。