Job ID = 1293735 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T16:59:45 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 ) 2019-06-02T16:59:45 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 ) 2019-06-02T16:59:45 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 ) 2019-06-02T17:02:19 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 ) 2019-06-02T17:02:19 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 ) 2019-06-02T17:02:19 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 ) 2019-06-02T17:07:54 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 ) 2019-06-02T17:07:54 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 : 22,611,425 reads read : 22,611,425 reads written : 22,611,425 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: 00:08:24 22611425 reads; of these: 22611425 (100.00%) were unpaired; of these: 306256 (1.35%) aligned 0 times 18213737 (80.55%) aligned exactly 1 time 4091432 (18.09%) aligned >1 times 98.65% overall alignment rate Time searching: 00:08:24 Overall time: 00:08:24 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] 4214795 / 22305169 = 0.1890 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 02:29:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX111816/SRX111816.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX111816/SRX111816.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX111816/SRX111816.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX111816/SRX111816.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 02:29:27: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:29:27: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:29:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX111816/SRX111816.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX111816/SRX111816.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX111816/SRX111816.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX111816/SRX111816.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 02:29:27: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:29:27: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:29:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX111816/SRX111816.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX111816/SRX111816.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX111816/SRX111816.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX111816/SRX111816.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 02:29:27: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:29:27: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:29:36: 1000000 INFO @ Mon, 03 Jun 2019 02:29:38: 1000000 INFO @ Mon, 03 Jun 2019 02:29:38: 1000000 INFO @ Mon, 03 Jun 2019 02:29:44: 2000000 INFO @ Mon, 03 Jun 2019 02:29:48: 2000000 INFO @ Mon, 03 Jun 2019 02:29:48: 2000000 INFO @ Mon, 03 Jun 2019 02:29:53: 3000000 INFO @ Mon, 03 Jun 2019 02:29:57: 3000000 INFO @ Mon, 03 Jun 2019 02:29:58: 3000000 INFO @ Mon, 03 Jun 2019 02:30:01: 4000000 INFO @ Mon, 03 Jun 2019 02:30:06: 4000000 INFO @ Mon, 03 Jun 2019 02:30:08: 4000000 INFO @ Mon, 03 Jun 2019 02:30:10: 5000000 INFO @ Mon, 03 Jun 2019 02:30:16: 5000000 INFO @ Mon, 03 Jun 2019 02:30:18: 6000000 INFO @ Mon, 03 Jun 2019 02:30:18: 5000000 INFO @ Mon, 03 Jun 2019 02:30:25: 6000000 INFO @ Mon, 03 Jun 2019 02:30:26: 7000000 INFO @ Mon, 03 Jun 2019 02:30:28: 6000000 INFO @ Mon, 03 Jun 2019 02:30:34: 7000000 INFO @ Mon, 03 Jun 2019 02:30:35: 8000000 INFO @ Mon, 03 Jun 2019 02:30:38: 7000000 INFO @ Mon, 03 Jun 2019 02:30:43: 9000000 INFO @ Mon, 03 Jun 2019 02:30:44: 8000000 INFO @ Mon, 03 Jun 2019 02:30:48: 8000000 INFO @ Mon, 03 Jun 2019 02:30:51: 10000000 INFO @ Mon, 03 Jun 2019 02:30:53: 9000000 INFO @ Mon, 03 Jun 2019 02:30:57: 9000000 INFO @ Mon, 03 Jun 2019 02:30:59: 11000000 INFO @ Mon, 03 Jun 2019 02:31:02: 10000000 INFO @ Mon, 03 Jun 2019 02:31:07: 10000000 INFO @ Mon, 03 Jun 2019 02:31:08: 12000000 INFO @ Mon, 03 Jun 2019 02:31:12: 11000000 INFO @ Mon, 03 Jun 2019 02:31:16: 13000000 INFO @ Mon, 03 Jun 2019 02:31:17: 11000000 INFO @ Mon, 03 Jun 2019 02:31:21: 12000000 INFO @ Mon, 03 Jun 2019 02:31:25: 14000000 INFO @ Mon, 03 Jun 2019 02:31:27: 12000000 INFO @ Mon, 03 Jun 2019 02:31:30: 13000000 INFO @ Mon, 03 Jun 2019 02:31:33: 15000000 INFO @ Mon, 03 Jun 2019 02:31:36: 13000000 INFO @ Mon, 03 Jun 2019 02:31:40: 14000000 INFO @ Mon, 03 Jun 2019 02:31:41: 16000000 INFO @ Mon, 03 Jun 2019 02:31:46: 14000000 INFO @ Mon, 03 Jun 2019 02:31:49: 15000000 INFO @ Mon, 03 Jun 2019 02:31:50: 17000000 INFO @ Mon, 03 Jun 2019 02:31:56: 15000000 INFO @ Mon, 03 Jun 2019 02:31:58: 18000000 INFO @ Mon, 03 Jun 2019 02:31:59: 16000000 INFO @ Mon, 03 Jun 2019 02:31:59: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 02:31:59: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 02:31:59: #1 total tags in treatment: 18090374 INFO @ Mon, 03 Jun 2019 02:31:59: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:31:59: #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 02:32:00: #1 tags after filtering in treatment: 18090374 INFO @ Mon, 03 Jun 2019 02:32:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:32:00: #1 finished! INFO @ Mon, 03 Jun 2019 02:32:00: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:32:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:32:01: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 02:32:01: Too few paired peaks (0) 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 02:32:01: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX111816/SRX111816.20_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/SRX111816/SRX111816.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111816/SRX111816.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111816/SRX111816.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:32:06: 16000000 INFO @ Mon, 03 Jun 2019 02:32:08: 17000000 INFO @ Mon, 03 Jun 2019 02:32:15: 17000000 INFO @ Mon, 03 Jun 2019 02:32:18: 18000000 INFO @ Mon, 03 Jun 2019 02:32:19: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 02:32:19: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 02:32:19: #1 total tags in treatment: 18090374 INFO @ Mon, 03 Jun 2019 02:32:19: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:32:19: #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 02:32:19: #1 tags after filtering in treatment: 18090374 INFO @ Mon, 03 Jun 2019 02:32:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:32:19: #1 finished! INFO @ Mon, 03 Jun 2019 02:32:19: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:32:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:32:21: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 02:32:21: Too few paired peaks (0) 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 02:32:21: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX111816/SRX111816.10_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/SRX111816/SRX111816.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111816/SRX111816.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111816/SRX111816.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:32:25: 18000000 INFO @ Mon, 03 Jun 2019 02:32:26: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 02:32:26: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 02:32:26: #1 total tags in treatment: 18090374 INFO @ Mon, 03 Jun 2019 02:32:26: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:32:26: #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 02:32:26: #1 tags after filtering in treatment: 18090374 INFO @ Mon, 03 Jun 2019 02:32:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:32:26: #1 finished! INFO @ Mon, 03 Jun 2019 02:32:26: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:32:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:32:28: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 02:32:28: Too few paired peaks (0) 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 02:32:28: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX111816/SRX111816.05_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/SRX111816/SRX111816.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111816/SRX111816.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111816/SRX111816.05_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。