Job ID = 1293829 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T17:38:45 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 ) 2019-06-02T17:39:38 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 ) 2019-06-02T17:39:38 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 ) 2019-06-02T17:39:39 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 ) 2019-06-02T17:42:17 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 ) 2019-06-02T17:54:54 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 ) 2019-06-02T17:54:54 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 : 38,326,589 reads read : 38,326,589 reads written : 38,326,589 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: 00:11:17 38326589 reads; of these: 38326589 (100.00%) were unpaired; of these: 5342480 (13.94%) aligned 0 times 24159855 (63.04%) aligned exactly 1 time 8824254 (23.02%) aligned >1 times 86.06% overall alignment rate Time searching: 00:11:17 Overall time: 00:11:17 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] 4290365 / 32984109 = 0.1301 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 03:16:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX127436/SRX127436.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX127436/SRX127436.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX127436/SRX127436.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX127436/SRX127436.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 03:16:14: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:16:14: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:16:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX127436/SRX127436.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX127436/SRX127436.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX127436/SRX127436.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX127436/SRX127436.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 03:16:14: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:16:14: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:16:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX127436/SRX127436.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX127436/SRX127436.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX127436/SRX127436.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX127436/SRX127436.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 03:16:14: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:16:14: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:16:21: 1000000 INFO @ Mon, 03 Jun 2019 03:16:21: 1000000 INFO @ Mon, 03 Jun 2019 03:16:23: 1000000 INFO @ Mon, 03 Jun 2019 03:16:28: 2000000 INFO @ Mon, 03 Jun 2019 03:16:28: 2000000 INFO @ Mon, 03 Jun 2019 03:16:31: 2000000 INFO @ Mon, 03 Jun 2019 03:16:34: 3000000 INFO @ Mon, 03 Jun 2019 03:16:35: 3000000 INFO @ Mon, 03 Jun 2019 03:16:39: 3000000 INFO @ Mon, 03 Jun 2019 03:16:41: 4000000 INFO @ Mon, 03 Jun 2019 03:16:41: 4000000 INFO @ Mon, 03 Jun 2019 03:16:47: 4000000 INFO @ Mon, 03 Jun 2019 03:16:47: 5000000 INFO @ Mon, 03 Jun 2019 03:16:48: 5000000 INFO @ Mon, 03 Jun 2019 03:16:54: 6000000 INFO @ Mon, 03 Jun 2019 03:16:54: 5000000 INFO @ Mon, 03 Jun 2019 03:16:55: 6000000 INFO @ Mon, 03 Jun 2019 03:17:00: 7000000 INFO @ Mon, 03 Jun 2019 03:17:01: 7000000 INFO @ Mon, 03 Jun 2019 03:17:02: 6000000 INFO @ Mon, 03 Jun 2019 03:17:07: 8000000 INFO @ Mon, 03 Jun 2019 03:17:08: 8000000 INFO @ Mon, 03 Jun 2019 03:17:10: 7000000 INFO @ Mon, 03 Jun 2019 03:17:13: 9000000 INFO @ Mon, 03 Jun 2019 03:17:14: 9000000 INFO @ Mon, 03 Jun 2019 03:17:17: 8000000 INFO @ Mon, 03 Jun 2019 03:17:20: 10000000 INFO @ Mon, 03 Jun 2019 03:17:21: 10000000 INFO @ Mon, 03 Jun 2019 03:17:25: 9000000 INFO @ Mon, 03 Jun 2019 03:17:26: 11000000 INFO @ Mon, 03 Jun 2019 03:17:28: 11000000 INFO @ Mon, 03 Jun 2019 03:17:33: 12000000 INFO @ Mon, 03 Jun 2019 03:17:33: 10000000 INFO @ Mon, 03 Jun 2019 03:17:34: 12000000 INFO @ Mon, 03 Jun 2019 03:17:39: 13000000 INFO @ Mon, 03 Jun 2019 03:17:41: 11000000 INFO @ Mon, 03 Jun 2019 03:17:41: 13000000 INFO @ Mon, 03 Jun 2019 03:17:46: 14000000 INFO @ Mon, 03 Jun 2019 03:17:47: 14000000 INFO @ Mon, 03 Jun 2019 03:17:48: 12000000 INFO @ Mon, 03 Jun 2019 03:17:52: 15000000 INFO @ Mon, 03 Jun 2019 03:17:54: 15000000 INFO @ Mon, 03 Jun 2019 03:17:56: 13000000 INFO @ Mon, 03 Jun 2019 03:17:59: 16000000 INFO @ Mon, 03 Jun 2019 03:18:01: 16000000 INFO @ Mon, 03 Jun 2019 03:18:04: 14000000 INFO @ Mon, 03 Jun 2019 03:18:05: 17000000 INFO @ Mon, 03 Jun 2019 03:18:07: 17000000 INFO @ Mon, 03 Jun 2019 03:18:11: 15000000 INFO @ Mon, 03 Jun 2019 03:18:12: 18000000 INFO @ Mon, 03 Jun 2019 03:18:14: 18000000 INFO @ Mon, 03 Jun 2019 03:18:18: 19000000 INFO @ Mon, 03 Jun 2019 03:18:19: 16000000 INFO @ Mon, 03 Jun 2019 03:18:20: 19000000 INFO @ Mon, 03 Jun 2019 03:18:25: 20000000 INFO @ Mon, 03 Jun 2019 03:18:27: 17000000 INFO @ Mon, 03 Jun 2019 03:18:27: 20000000 INFO @ Mon, 03 Jun 2019 03:18:31: 21000000 INFO @ Mon, 03 Jun 2019 03:18:33: 21000000 INFO @ Mon, 03 Jun 2019 03:18:34: 18000000 INFO @ Mon, 03 Jun 2019 03:18:37: 22000000 INFO @ Mon, 03 Jun 2019 03:18:40: 22000000 INFO @ Mon, 03 Jun 2019 03:18:42: 19000000 INFO @ Mon, 03 Jun 2019 03:18:44: 23000000 INFO @ Mon, 03 Jun 2019 03:18:46: 23000000 INFO @ Mon, 03 Jun 2019 03:18:50: 20000000 INFO @ Mon, 03 Jun 2019 03:18:50: 24000000 INFO @ Mon, 03 Jun 2019 03:18:53: 24000000 INFO @ Mon, 03 Jun 2019 03:18:56: 25000000 INFO @ Mon, 03 Jun 2019 03:18:57: 21000000 INFO @ Mon, 03 Jun 2019 03:18:59: 25000000 INFO @ Mon, 03 Jun 2019 03:19:03: 26000000 INFO @ Mon, 03 Jun 2019 03:19:05: 22000000 INFO @ Mon, 03 Jun 2019 03:19:06: 26000000 INFO @ Mon, 03 Jun 2019 03:19:09: 27000000 INFO @ Mon, 03 Jun 2019 03:19:12: 23000000 INFO @ Mon, 03 Jun 2019 03:19:14: 27000000 INFO @ Mon, 03 Jun 2019 03:19:16: 28000000 INFO @ Mon, 03 Jun 2019 03:19:20: 24000000 INFO @ Mon, 03 Jun 2019 03:19:21: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 03:19:21: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 03:19:21: #1 total tags in treatment: 28693744 INFO @ Mon, 03 Jun 2019 03:19:21: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:19:21: #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 03:19:21: 28000000 INFO @ Mon, 03 Jun 2019 03:19:21: #1 tags after filtering in treatment: 28693744 INFO @ Mon, 03 Jun 2019 03:19:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:19:21: #1 finished! INFO @ Mon, 03 Jun 2019 03:19:21: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:19:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:19:24: #2 number of paired peaks: 39 WARNING @ Mon, 03 Jun 2019 03:19:24: Too few paired peaks (39) 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 03:19:24: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX127436/SRX127436.05_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/SRX127436/SRX127436.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX127436/SRX127436.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX127436/SRX127436.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:19:26: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 03:19:26: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 03:19:26: #1 total tags in treatment: 28693744 INFO @ Mon, 03 Jun 2019 03:19:26: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:19:26: #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 03:19:27: #1 tags after filtering in treatment: 28693744 INFO @ Mon, 03 Jun 2019 03:19:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:19:27: #1 finished! INFO @ Mon, 03 Jun 2019 03:19:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:19:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:19:27: 25000000 INFO @ Mon, 03 Jun 2019 03:19:29: #2 number of paired peaks: 39 WARNING @ Mon, 03 Jun 2019 03:19:29: Too few paired peaks (39) 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 03:19:29: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX127436/SRX127436.10_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/SRX127436/SRX127436.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX127436/SRX127436.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX127436/SRX127436.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:19:34: 26000000 INFO @ Mon, 03 Jun 2019 03:19:42: 27000000 INFO @ Mon, 03 Jun 2019 03:19:49: 28000000 INFO @ Mon, 03 Jun 2019 03:19:54: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 03:19:54: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 03:19:54: #1 total tags in treatment: 28693744 INFO @ Mon, 03 Jun 2019 03:19:54: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:19:54: #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 03:19:55: #1 tags after filtering in treatment: 28693744 INFO @ Mon, 03 Jun 2019 03:19:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:19:55: #1 finished! INFO @ Mon, 03 Jun 2019 03:19:55: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:19:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:19:57: #2 number of paired peaks: 39 WARNING @ Mon, 03 Jun 2019 03:19:57: Too few paired peaks (39) 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 03:19:57: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX127436/SRX127436.20_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/SRX127436/SRX127436.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX127436/SRX127436.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX127436/SRX127436.20_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。