Job ID = 1298350 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T08:20:33 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 ) 2019-06-03T08:20:48 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 ) 2019-06-03T08:20:48 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 ) 2019-06-03T08:22:01 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 ) 2019-06-03T08:22:01 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 ) 2019-06-03T08:24:04 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 ) 2019-06-03T08:24:04 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 ) 2019-06-03T08:24:04 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 ) 2019-06-03T08:37:41 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 : 48,787,082 reads read : 48,787,082 reads written : 48,787,082 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: 00:17:00 48787082 reads; of these: 48787082 (100.00%) were unpaired; of these: 2537253 (5.20%) aligned 0 times 37963153 (77.81%) aligned exactly 1 time 8286676 (16.99%) aligned >1 times 94.80% overall alignment rate Time searching: 00:17:00 Overall time: 00:17:00 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 20 files... [bam_rmdupse_core] 13253636 / 46249829 = 0.2866 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 18:10:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467024/SRX467024.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467024/SRX467024.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467024/SRX467024.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467024/SRX467024.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 18:10:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467024/SRX467024.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467024/SRX467024.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467024/SRX467024.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467024/SRX467024.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 18:10:34: #1 read tag files... INFO @ Mon, 03 Jun 2019 18:10:34: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 18:10:34: #1 read tag files... INFO @ Mon, 03 Jun 2019 18:10:34: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 18:10:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467024/SRX467024.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467024/SRX467024.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467024/SRX467024.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467024/SRX467024.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 18:10:35: #1 read tag files... INFO @ Mon, 03 Jun 2019 18:10:35: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 18:10:43: 1000000 INFO @ Mon, 03 Jun 2019 18:10:43: 1000000 INFO @ Mon, 03 Jun 2019 18:10:46: 1000000 INFO @ Mon, 03 Jun 2019 18:10:50: 2000000 INFO @ Mon, 03 Jun 2019 18:10:51: 2000000 INFO @ Mon, 03 Jun 2019 18:10:58: 2000000 INFO @ Mon, 03 Jun 2019 18:10:58: 3000000 INFO @ Mon, 03 Jun 2019 18:10:59: 3000000 INFO @ Mon, 03 Jun 2019 18:11:06: 4000000 INFO @ Mon, 03 Jun 2019 18:11:07: 4000000 INFO @ Mon, 03 Jun 2019 18:11:09: 3000000 INFO @ Mon, 03 Jun 2019 18:11:14: 5000000 INFO @ Mon, 03 Jun 2019 18:11:15: 5000000 INFO @ Mon, 03 Jun 2019 18:11:21: 4000000 INFO @ Mon, 03 Jun 2019 18:11:22: 6000000 INFO @ Mon, 03 Jun 2019 18:11:23: 6000000 INFO @ Mon, 03 Jun 2019 18:11:30: 7000000 INFO @ Mon, 03 Jun 2019 18:11:30: 7000000 INFO @ Mon, 03 Jun 2019 18:11:32: 5000000 INFO @ Mon, 03 Jun 2019 18:11:38: 8000000 INFO @ Mon, 03 Jun 2019 18:11:38: 8000000 INFO @ Mon, 03 Jun 2019 18:11:43: 6000000 INFO @ Mon, 03 Jun 2019 18:11:45: 9000000 INFO @ Mon, 03 Jun 2019 18:11:46: 9000000 INFO @ Mon, 03 Jun 2019 18:11:54: 7000000 INFO @ Mon, 03 Jun 2019 18:11:54: 10000000 INFO @ Mon, 03 Jun 2019 18:11:54: 10000000 INFO @ Mon, 03 Jun 2019 18:12:03: 11000000 INFO @ Mon, 03 Jun 2019 18:12:03: 11000000 INFO @ Mon, 03 Jun 2019 18:12:05: 8000000 INFO @ Mon, 03 Jun 2019 18:12:11: 12000000 INFO @ Mon, 03 Jun 2019 18:12:12: 12000000 INFO @ Mon, 03 Jun 2019 18:12:17: 9000000 INFO @ Mon, 03 Jun 2019 18:12:19: 13000000 INFO @ Mon, 03 Jun 2019 18:12:21: 13000000 INFO @ Mon, 03 Jun 2019 18:12:27: 14000000 INFO @ Mon, 03 Jun 2019 18:12:29: 10000000 INFO @ Mon, 03 Jun 2019 18:12:30: 14000000 INFO @ Mon, 03 Jun 2019 18:12:35: 15000000 INFO @ Mon, 03 Jun 2019 18:12:39: 15000000 INFO @ Mon, 03 Jun 2019 18:12:40: 11000000 INFO @ Mon, 03 Jun 2019 18:12:43: 16000000 INFO @ Mon, 03 Jun 2019 18:12:47: 16000000 INFO @ Mon, 03 Jun 2019 18:12:51: 17000000 INFO @ Mon, 03 Jun 2019 18:12:52: 12000000 INFO @ Mon, 03 Jun 2019 18:12:56: 17000000 INFO @ Mon, 03 Jun 2019 18:12:59: 18000000 INFO @ Mon, 03 Jun 2019 18:13:03: 13000000 INFO @ Mon, 03 Jun 2019 18:13:05: 18000000 INFO @ Mon, 03 Jun 2019 18:13:07: 19000000 INFO @ Mon, 03 Jun 2019 18:13:13: 19000000 INFO @ Mon, 03 Jun 2019 18:13:13: 14000000 INFO @ Mon, 03 Jun 2019 18:13:15: 20000000 INFO @ Mon, 03 Jun 2019 18:13:22: 20000000 INFO @ Mon, 03 Jun 2019 18:13:23: 21000000 INFO @ Mon, 03 Jun 2019 18:13:24: 15000000 INFO @ Mon, 03 Jun 2019 18:13:30: 21000000 INFO @ Mon, 03 Jun 2019 18:13:31: 22000000 INFO @ Mon, 03 Jun 2019 18:13:36: 16000000 INFO @ Mon, 03 Jun 2019 18:13:39: 23000000 INFO @ Mon, 03 Jun 2019 18:13:39: 22000000 INFO @ Mon, 03 Jun 2019 18:13:46: 17000000 INFO @ Mon, 03 Jun 2019 18:13:47: 24000000 INFO @ Mon, 03 Jun 2019 18:13:48: 23000000 INFO @ Mon, 03 Jun 2019 18:13:55: 25000000 INFO @ Mon, 03 Jun 2019 18:13:57: 18000000 INFO @ Mon, 03 Jun 2019 18:13:57: 24000000 INFO @ Mon, 03 Jun 2019 18:14:04: 26000000 INFO @ Mon, 03 Jun 2019 18:14:07: 25000000 INFO @ Mon, 03 Jun 2019 18:14:08: 19000000 INFO @ Mon, 03 Jun 2019 18:14:12: 27000000 INFO @ Mon, 03 Jun 2019 18:14:16: 26000000 INFO @ Mon, 03 Jun 2019 18:14:19: 20000000 INFO @ Mon, 03 Jun 2019 18:14:21: 28000000 INFO @ Mon, 03 Jun 2019 18:14:25: 27000000 INFO @ Mon, 03 Jun 2019 18:14:30: 29000000 INFO @ Mon, 03 Jun 2019 18:14:30: 21000000 INFO @ Mon, 03 Jun 2019 18:14:34: 28000000 INFO @ Mon, 03 Jun 2019 18:14:38: 30000000 INFO @ Mon, 03 Jun 2019 18:14:41: 22000000 INFO @ Mon, 03 Jun 2019 18:14:43: 29000000 INFO @ Mon, 03 Jun 2019 18:14:46: 31000000 INFO @ Mon, 03 Jun 2019 18:14:52: 30000000 INFO @ Mon, 03 Jun 2019 18:14:52: 23000000 INFO @ Mon, 03 Jun 2019 18:14:54: 32000000 INFO @ Mon, 03 Jun 2019 18:15:01: 31000000 INFO @ Mon, 03 Jun 2019 18:15:02: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 18:15:02: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 18:15:02: #1 total tags in treatment: 32996193 INFO @ Mon, 03 Jun 2019 18:15:02: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:15:02: #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 18:15:03: #1 tags after filtering in treatment: 32996193 INFO @ Mon, 03 Jun 2019 18:15:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 18:15:03: #1 finished! INFO @ Mon, 03 Jun 2019 18:15:03: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:15:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:15:05: 24000000 INFO @ Mon, 03 Jun 2019 18:15:07: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 18:15:07: 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 18:15:07: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX467024/SRX467024.05_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/SRX467024/SRX467024.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467024/SRX467024.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467024/SRX467024.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 18:15:10: 32000000 INFO @ Mon, 03 Jun 2019 18:15:17: 25000000 INFO @ Mon, 03 Jun 2019 18:15:19: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 18:15:19: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 18:15:19: #1 total tags in treatment: 32996193 INFO @ Mon, 03 Jun 2019 18:15:19: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:15:19: #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 18:15:20: #1 tags after filtering in treatment: 32996193 INFO @ Mon, 03 Jun 2019 18:15:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 18:15:20: #1 finished! INFO @ Mon, 03 Jun 2019 18:15:20: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:15:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:15:23: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 18:15:23: 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 18:15:23: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX467024/SRX467024.20_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/SRX467024/SRX467024.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467024/SRX467024.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467024/SRX467024.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 18:15:28: 26000000 INFO @ Mon, 03 Jun 2019 18:15:39: 27000000 INFO @ Mon, 03 Jun 2019 18:15:50: 28000000 INFO @ Mon, 03 Jun 2019 18:16:01: 29000000 INFO @ Mon, 03 Jun 2019 18:16:12: 30000000 INFO @ Mon, 03 Jun 2019 18:16:23: 31000000 INFO @ Mon, 03 Jun 2019 18:16:34: 32000000 INFO @ Mon, 03 Jun 2019 18:16:45: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 18:16:45: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 18:16:45: #1 total tags in treatment: 32996193 INFO @ Mon, 03 Jun 2019 18:16:45: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:16:45: #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 18:16:46: #1 tags after filtering in treatment: 32996193 INFO @ Mon, 03 Jun 2019 18:16:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 18:16:46: #1 finished! INFO @ Mon, 03 Jun 2019 18:16:46: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:16:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:16:50: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 18:16:50: 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 18:16:50: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX467024/SRX467024.10_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/SRX467024/SRX467024.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467024/SRX467024.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467024/SRX467024.10_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。