Job ID = 1305919 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T12:24:39 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 ) 2019-06-03T12:28:11 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 ) 2019-06-03T12:30:42 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 ) 2019-06-03T12:30:42 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 ) 2019-06-03T12:32:01 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 ) 2019-06-03T12:33:18 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 ) 2019-06-03T12:33:18 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 ) 2019-06-03T12:33:18 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 : 55,261,147 reads read : 55,261,147 reads written : 55,261,147 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: 00:16:56 55261147 reads; of these: 55261147 (100.00%) were unpaired; of these: 1066896 (1.93%) aligned 0 times 45427154 (82.20%) aligned exactly 1 time 8767097 (15.86%) aligned >1 times 98.07% overall alignment rate Time searching: 00:16:56 Overall time: 00:16:56 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 24 files... [bam_rmdupse_core] 16999498 / 54194251 = 0.3137 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 22:24:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495310/SRX495310.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495310/SRX495310.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495310/SRX495310.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495310/SRX495310.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 22:24:25: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:24:25: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:24:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495310/SRX495310.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495310/SRX495310.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495310/SRX495310.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495310/SRX495310.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 22:24:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495310/SRX495310.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495310/SRX495310.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495310/SRX495310.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495310/SRX495310.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 22:24:25: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:24:25: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:24:25: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:24:25: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:24:35: 1000000 INFO @ Mon, 03 Jun 2019 22:24:36: 1000000 INFO @ Mon, 03 Jun 2019 22:24:36: 1000000 INFO @ Mon, 03 Jun 2019 22:24:45: 2000000 INFO @ Mon, 03 Jun 2019 22:24:46: 2000000 INFO @ Mon, 03 Jun 2019 22:24:46: 2000000 INFO @ Mon, 03 Jun 2019 22:24:54: 3000000 INFO @ Mon, 03 Jun 2019 22:24:56: 3000000 INFO @ Mon, 03 Jun 2019 22:24:56: 3000000 INFO @ Mon, 03 Jun 2019 22:25:04: 4000000 INFO @ Mon, 03 Jun 2019 22:25:06: 4000000 INFO @ Mon, 03 Jun 2019 22:25:06: 4000000 INFO @ Mon, 03 Jun 2019 22:25:13: 5000000 INFO @ Mon, 03 Jun 2019 22:25:16: 5000000 INFO @ Mon, 03 Jun 2019 22:25:16: 5000000 INFO @ Mon, 03 Jun 2019 22:25:23: 6000000 INFO @ Mon, 03 Jun 2019 22:25:26: 6000000 INFO @ Mon, 03 Jun 2019 22:25:26: 6000000 INFO @ Mon, 03 Jun 2019 22:25:32: 7000000 INFO @ Mon, 03 Jun 2019 22:25:36: 7000000 INFO @ Mon, 03 Jun 2019 22:25:36: 7000000 INFO @ Mon, 03 Jun 2019 22:25:41: 8000000 INFO @ Mon, 03 Jun 2019 22:25:46: 8000000 INFO @ Mon, 03 Jun 2019 22:25:46: 8000000 INFO @ Mon, 03 Jun 2019 22:25:51: 9000000 INFO @ Mon, 03 Jun 2019 22:25:56: 9000000 INFO @ Mon, 03 Jun 2019 22:25:56: 9000000 INFO @ Mon, 03 Jun 2019 22:26:00: 10000000 INFO @ Mon, 03 Jun 2019 22:26:06: 10000000 INFO @ Mon, 03 Jun 2019 22:26:06: 10000000 INFO @ Mon, 03 Jun 2019 22:26:10: 11000000 INFO @ Mon, 03 Jun 2019 22:26:16: 11000000 INFO @ Mon, 03 Jun 2019 22:26:16: 11000000 INFO @ Mon, 03 Jun 2019 22:26:19: 12000000 INFO @ Mon, 03 Jun 2019 22:26:26: 12000000 INFO @ Mon, 03 Jun 2019 22:26:26: 12000000 INFO @ Mon, 03 Jun 2019 22:26:28: 13000000 INFO @ Mon, 03 Jun 2019 22:26:35: 13000000 INFO @ Mon, 03 Jun 2019 22:26:36: 13000000 INFO @ Mon, 03 Jun 2019 22:26:37: 14000000 INFO @ Mon, 03 Jun 2019 22:26:45: 14000000 INFO @ Mon, 03 Jun 2019 22:26:45: 14000000 INFO @ Mon, 03 Jun 2019 22:26:46: 15000000 INFO @ Mon, 03 Jun 2019 22:26:54: 16000000 INFO @ Mon, 03 Jun 2019 22:26:54: 15000000 INFO @ Mon, 03 Jun 2019 22:26:54: 15000000 INFO @ Mon, 03 Jun 2019 22:27:03: 17000000 INFO @ Mon, 03 Jun 2019 22:27:04: 16000000 INFO @ Mon, 03 Jun 2019 22:27:04: 16000000 INFO @ Mon, 03 Jun 2019 22:27:12: 18000000 INFO @ Mon, 03 Jun 2019 22:27:13: 17000000 INFO @ Mon, 03 Jun 2019 22:27:14: 17000000 INFO @ Mon, 03 Jun 2019 22:27:21: 19000000 INFO @ Mon, 03 Jun 2019 22:27:23: 18000000 INFO @ Mon, 03 Jun 2019 22:27:23: 18000000 INFO @ Mon, 03 Jun 2019 22:27:30: 20000000 INFO @ Mon, 03 Jun 2019 22:27:33: 19000000 INFO @ Mon, 03 Jun 2019 22:27:33: 19000000 INFO @ Mon, 03 Jun 2019 22:27:39: 21000000 INFO @ Mon, 03 Jun 2019 22:27:43: 20000000 INFO @ Mon, 03 Jun 2019 22:27:43: 20000000 INFO @ Mon, 03 Jun 2019 22:27:48: 22000000 INFO @ Mon, 03 Jun 2019 22:27:52: 21000000 INFO @ Mon, 03 Jun 2019 22:27:53: 21000000 INFO @ Mon, 03 Jun 2019 22:27:57: 23000000 INFO @ Mon, 03 Jun 2019 22:28:02: 22000000 INFO @ Mon, 03 Jun 2019 22:28:02: 22000000 INFO @ Mon, 03 Jun 2019 22:28:06: 24000000 INFO @ Mon, 03 Jun 2019 22:28:12: 23000000 INFO @ Mon, 03 Jun 2019 22:28:12: 23000000 INFO @ Mon, 03 Jun 2019 22:28:15: 25000000 INFO @ Mon, 03 Jun 2019 22:28:22: 24000000 INFO @ Mon, 03 Jun 2019 22:28:22: 24000000 INFO @ Mon, 03 Jun 2019 22:28:24: 26000000 INFO @ Mon, 03 Jun 2019 22:28:31: 25000000 INFO @ Mon, 03 Jun 2019 22:28:31: 25000000 INFO @ Mon, 03 Jun 2019 22:28:33: 27000000 INFO @ Mon, 03 Jun 2019 22:28:41: 26000000 INFO @ Mon, 03 Jun 2019 22:28:41: 26000000 INFO @ Mon, 03 Jun 2019 22:28:42: 28000000 INFO @ Mon, 03 Jun 2019 22:28:51: 27000000 INFO @ Mon, 03 Jun 2019 22:28:51: 27000000 INFO @ Mon, 03 Jun 2019 22:28:51: 29000000 INFO @ Mon, 03 Jun 2019 22:29:00: 30000000 INFO @ Mon, 03 Jun 2019 22:29:00: 28000000 INFO @ Mon, 03 Jun 2019 22:29:01: 28000000 INFO @ Mon, 03 Jun 2019 22:29:10: 31000000 INFO @ Mon, 03 Jun 2019 22:29:10: 29000000 INFO @ Mon, 03 Jun 2019 22:29:11: 29000000 INFO @ Mon, 03 Jun 2019 22:29:19: 32000000 INFO @ Mon, 03 Jun 2019 22:29:20: 30000000 INFO @ Mon, 03 Jun 2019 22:29:20: 30000000 INFO @ Mon, 03 Jun 2019 22:29:28: 33000000 INFO @ Mon, 03 Jun 2019 22:29:30: 31000000 INFO @ Mon, 03 Jun 2019 22:29:30: 31000000 INFO @ Mon, 03 Jun 2019 22:29:37: 34000000 INFO @ Mon, 03 Jun 2019 22:29:40: 32000000 INFO @ Mon, 03 Jun 2019 22:29:40: 32000000 INFO @ Mon, 03 Jun 2019 22:29:46: 35000000 INFO @ Mon, 03 Jun 2019 22:29:50: 33000000 INFO @ Mon, 03 Jun 2019 22:29:50: 33000000 INFO @ Mon, 03 Jun 2019 22:29:55: 36000000 INFO @ Mon, 03 Jun 2019 22:29:59: 34000000 INFO @ Mon, 03 Jun 2019 22:29:59: 34000000 INFO @ Mon, 03 Jun 2019 22:30:04: 37000000 INFO @ Mon, 03 Jun 2019 22:30:06: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 22:30:06: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 22:30:06: #1 total tags in treatment: 37194753 INFO @ Mon, 03 Jun 2019 22:30:06: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:30:06: #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 22:30:06: #1 tags after filtering in treatment: 37194753 INFO @ Mon, 03 Jun 2019 22:30:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:30:06: #1 finished! INFO @ Mon, 03 Jun 2019 22:30:06: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:30:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:30:09: 35000000 INFO @ Mon, 03 Jun 2019 22:30:09: 35000000 INFO @ Mon, 03 Jun 2019 22:30:09: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 22:30:09: 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 22:30:09: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX495310/SRX495310.20_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/SRX495310/SRX495310.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495310/SRX495310.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495310/SRX495310.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:30:18: 36000000 INFO @ Mon, 03 Jun 2019 22:30:18: 36000000 INFO @ Mon, 03 Jun 2019 22:30:26: 37000000 INFO @ Mon, 03 Jun 2019 22:30:26: 37000000 INFO @ Mon, 03 Jun 2019 22:30:29: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 22:30:29: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 22:30:29: #1 total tags in treatment: 37194753 INFO @ Mon, 03 Jun 2019 22:30:29: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:30:29: #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 22:30:29: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 22:30:29: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 22:30:29: #1 total tags in treatment: 37194753 INFO @ Mon, 03 Jun 2019 22:30:29: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:30:29: #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 22:30:29: #1 tags after filtering in treatment: 37194753 INFO @ Mon, 03 Jun 2019 22:30:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:30:29: #1 finished! INFO @ Mon, 03 Jun 2019 22:30:29: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:30:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:30:29: #1 tags after filtering in treatment: 37194753 INFO @ Mon, 03 Jun 2019 22:30:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:30:29: #1 finished! INFO @ Mon, 03 Jun 2019 22:30:29: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:30:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:30:32: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 22:30:32: 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 22:30:32: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX495310/SRX495310.05_peaks.narrowPeak: No such file or directory INFO @ Mon, 03 Jun 2019 22:30:32: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 22:30:32: 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 22:30:32: Process for pairing-model is terminated! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495310/SRX495310.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495310/SRX495310.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495310/SRX495310.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling cut: /home/okishinya/chipatlas/results/dm3/SRX495310/SRX495310.10_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/SRX495310/SRX495310.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495310/SRX495310.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495310/SRX495310.10_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。