Job ID = 1293816 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 ) 2019-06-02T17:38:45 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 ) 2019-06-02T17:38:45 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 ) 2019-06-02T17:40:24 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 ) 2019-06-02T17:40:24 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 ) 2019-06-02T17:45:38 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 ) 2019-06-02T17:48:44 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 ) 2019-06-02T17:48:44 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 ) 2019-06-02T17:48:44 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 : 56,553,726 reads read : 56,553,726 reads written : 56,553,726 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: 00:17:43 56553726 reads; of these: 56553726 (100.00%) were unpaired; of these: 11246013 (19.89%) aligned 0 times 33911828 (59.96%) aligned exactly 1 time 11395885 (20.15%) aligned >1 times 80.11% overall alignment rate Time searching: 00:17:43 Overall time: 00:17:43 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] 5283369 / 45307713 = 0.1166 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 03:29:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1167422/SRX1167422.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1167422/SRX1167422.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1167422/SRX1167422.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1167422/SRX1167422.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 03:29:44: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:29:44: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:29:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1167422/SRX1167422.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1167422/SRX1167422.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1167422/SRX1167422.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1167422/SRX1167422.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 03:29:44: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:29:44: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:29:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1167422/SRX1167422.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1167422/SRX1167422.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1167422/SRX1167422.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1167422/SRX1167422.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 03:29:44: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:29:44: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:29:53: 1000000 INFO @ Mon, 03 Jun 2019 03:29:54: 1000000 INFO @ Mon, 03 Jun 2019 03:29:54: 1000000 INFO @ Mon, 03 Jun 2019 03:30:02: 2000000 INFO @ Mon, 03 Jun 2019 03:30:03: 2000000 INFO @ Mon, 03 Jun 2019 03:30:05: 2000000 INFO @ Mon, 03 Jun 2019 03:30:12: 3000000 INFO @ Mon, 03 Jun 2019 03:30:13: 3000000 INFO @ Mon, 03 Jun 2019 03:30:15: 3000000 INFO @ Mon, 03 Jun 2019 03:30:21: 4000000 INFO @ Mon, 03 Jun 2019 03:30:22: 4000000 INFO @ Mon, 03 Jun 2019 03:30:25: 4000000 INFO @ Mon, 03 Jun 2019 03:30:31: 5000000 INFO @ Mon, 03 Jun 2019 03:30:32: 5000000 INFO @ Mon, 03 Jun 2019 03:30:35: 5000000 INFO @ Mon, 03 Jun 2019 03:30:39: 6000000 INFO @ Mon, 03 Jun 2019 03:30:41: 6000000 INFO @ Mon, 03 Jun 2019 03:30:44: 6000000 INFO @ Mon, 03 Jun 2019 03:30:47: 7000000 INFO @ Mon, 03 Jun 2019 03:30:50: 7000000 INFO @ Mon, 03 Jun 2019 03:30:53: 7000000 INFO @ Mon, 03 Jun 2019 03:30:55: 8000000 INFO @ Mon, 03 Jun 2019 03:30:59: 8000000 INFO @ Mon, 03 Jun 2019 03:31:02: 8000000 INFO @ Mon, 03 Jun 2019 03:31:02: 9000000 INFO @ Mon, 03 Jun 2019 03:31:09: 9000000 INFO @ Mon, 03 Jun 2019 03:31:10: 10000000 INFO @ Mon, 03 Jun 2019 03:31:11: 9000000 INFO @ Mon, 03 Jun 2019 03:31:18: 11000000 INFO @ Mon, 03 Jun 2019 03:31:18: 10000000 INFO @ Mon, 03 Jun 2019 03:31:20: 10000000 INFO @ Mon, 03 Jun 2019 03:31:26: 12000000 INFO @ Mon, 03 Jun 2019 03:31:28: 11000000 INFO @ Mon, 03 Jun 2019 03:31:29: 11000000 INFO @ Mon, 03 Jun 2019 03:31:34: 13000000 INFO @ Mon, 03 Jun 2019 03:31:37: 12000000 INFO @ Mon, 03 Jun 2019 03:31:39: 12000000 INFO @ Mon, 03 Jun 2019 03:31:41: 14000000 INFO @ Mon, 03 Jun 2019 03:31:47: 13000000 INFO @ Mon, 03 Jun 2019 03:31:48: 13000000 INFO @ Mon, 03 Jun 2019 03:31:49: 15000000 INFO @ Mon, 03 Jun 2019 03:31:56: 16000000 INFO @ Mon, 03 Jun 2019 03:31:57: 14000000 INFO @ Mon, 03 Jun 2019 03:31:57: 14000000 INFO @ Mon, 03 Jun 2019 03:32:04: 17000000 INFO @ Mon, 03 Jun 2019 03:32:06: 15000000 INFO @ Mon, 03 Jun 2019 03:32:07: 15000000 INFO @ Mon, 03 Jun 2019 03:32:11: 18000000 INFO @ Mon, 03 Jun 2019 03:32:15: 16000000 INFO @ Mon, 03 Jun 2019 03:32:16: 16000000 INFO @ Mon, 03 Jun 2019 03:32:18: 19000000 INFO @ Mon, 03 Jun 2019 03:32:25: 17000000 INFO @ Mon, 03 Jun 2019 03:32:25: 17000000 INFO @ Mon, 03 Jun 2019 03:32:26: 20000000 INFO @ Mon, 03 Jun 2019 03:32:34: 21000000 INFO @ Mon, 03 Jun 2019 03:32:34: 18000000 INFO @ Mon, 03 Jun 2019 03:32:34: 18000000 INFO @ Mon, 03 Jun 2019 03:32:41: 22000000 INFO @ Mon, 03 Jun 2019 03:32:43: 19000000 INFO @ Mon, 03 Jun 2019 03:32:43: 19000000 INFO @ Mon, 03 Jun 2019 03:32:49: 23000000 INFO @ Mon, 03 Jun 2019 03:32:52: 20000000 INFO @ Mon, 03 Jun 2019 03:32:53: 20000000 INFO @ Mon, 03 Jun 2019 03:32:56: 24000000 INFO @ Mon, 03 Jun 2019 03:33:01: 21000000 INFO @ Mon, 03 Jun 2019 03:33:02: 21000000 INFO @ Mon, 03 Jun 2019 03:33:06: 25000000 INFO @ Mon, 03 Jun 2019 03:33:10: 22000000 INFO @ Mon, 03 Jun 2019 03:33:12: 22000000 INFO @ Mon, 03 Jun 2019 03:33:14: 26000000 INFO @ Mon, 03 Jun 2019 03:33:19: 23000000 INFO @ Mon, 03 Jun 2019 03:33:21: 27000000 INFO @ Mon, 03 Jun 2019 03:33:21: 23000000 INFO @ Mon, 03 Jun 2019 03:33:28: 28000000 INFO @ Mon, 03 Jun 2019 03:33:28: 24000000 INFO @ Mon, 03 Jun 2019 03:33:30: 24000000 INFO @ Mon, 03 Jun 2019 03:33:35: 29000000 INFO @ Mon, 03 Jun 2019 03:33:38: 25000000 INFO @ Mon, 03 Jun 2019 03:33:38: 25000000 INFO @ Mon, 03 Jun 2019 03:33:43: 30000000 INFO @ Mon, 03 Jun 2019 03:33:47: 26000000 INFO @ Mon, 03 Jun 2019 03:33:47: 26000000 INFO @ Mon, 03 Jun 2019 03:33:50: 31000000 INFO @ Mon, 03 Jun 2019 03:33:55: 27000000 INFO @ Mon, 03 Jun 2019 03:33:56: 27000000 INFO @ Mon, 03 Jun 2019 03:33:57: 32000000 INFO @ Mon, 03 Jun 2019 03:34:04: 28000000 INFO @ Mon, 03 Jun 2019 03:34:05: 28000000 INFO @ Mon, 03 Jun 2019 03:34:05: 33000000 INFO @ Mon, 03 Jun 2019 03:34:12: 34000000 INFO @ Mon, 03 Jun 2019 03:34:13: 29000000 INFO @ Mon, 03 Jun 2019 03:34:14: 29000000 INFO @ Mon, 03 Jun 2019 03:34:19: 35000000 INFO @ Mon, 03 Jun 2019 03:34:22: 30000000 INFO @ Mon, 03 Jun 2019 03:34:24: 30000000 INFO @ Mon, 03 Jun 2019 03:34:26: 36000000 INFO @ Mon, 03 Jun 2019 03:34:31: 31000000 INFO @ Mon, 03 Jun 2019 03:34:33: 31000000 INFO @ Mon, 03 Jun 2019 03:34:33: 37000000 INFO @ Mon, 03 Jun 2019 03:34:40: 32000000 INFO @ Mon, 03 Jun 2019 03:34:41: 38000000 INFO @ Mon, 03 Jun 2019 03:34:43: 32000000 INFO @ Mon, 03 Jun 2019 03:34:49: 39000000 INFO @ Mon, 03 Jun 2019 03:34:49: 33000000 INFO @ Mon, 03 Jun 2019 03:34:53: 33000000 INFO @ Mon, 03 Jun 2019 03:34:56: 40000000 INFO @ Mon, 03 Jun 2019 03:34:57: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 03:34:57: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 03:34:57: #1 total tags in treatment: 40024344 INFO @ Mon, 03 Jun 2019 03:34:57: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:34:57: #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 03:34:58: #1 tags after filtering in treatment: 40024344 INFO @ Mon, 03 Jun 2019 03:34:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:34:58: #1 finished! INFO @ Mon, 03 Jun 2019 03:34:58: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:34:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:34:58: 34000000 INFO @ Mon, 03 Jun 2019 03:35:01: #2 number of paired peaks: 42 WARNING @ Mon, 03 Jun 2019 03:35:01: Too few paired peaks (42) 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 03:35:01: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX1167422/SRX1167422.10_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/SRX1167422/SRX1167422.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1167422/SRX1167422.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1167422/SRX1167422.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:35:03: 34000000 INFO @ Mon, 03 Jun 2019 03:35:07: 35000000 INFO @ Mon, 03 Jun 2019 03:35:12: 35000000 INFO @ Mon, 03 Jun 2019 03:35:15: 36000000 INFO @ Mon, 03 Jun 2019 03:35:22: 36000000 INFO @ Mon, 03 Jun 2019 03:35:23: 37000000 INFO @ Mon, 03 Jun 2019 03:35:31: 37000000 INFO @ Mon, 03 Jun 2019 03:35:31: 38000000 INFO @ Mon, 03 Jun 2019 03:35:40: 39000000 INFO @ Mon, 03 Jun 2019 03:35:41: 38000000 INFO @ Mon, 03 Jun 2019 03:35:49: 40000000 INFO @ Mon, 03 Jun 2019 03:35:49: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 03:35:49: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 03:35:49: #1 total tags in treatment: 40024344 INFO @ Mon, 03 Jun 2019 03:35:49: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:35:49: #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 03:35:50: #1 tags after filtering in treatment: 40024344 INFO @ Mon, 03 Jun 2019 03:35:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:35:50: #1 finished! INFO @ Mon, 03 Jun 2019 03:35:50: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:35:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:35:50: 39000000 INFO @ Mon, 03 Jun 2019 03:35:54: #2 number of paired peaks: 42 WARNING @ Mon, 03 Jun 2019 03:35:54: Too few paired peaks (42) 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 03:35:54: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX1167422/SRX1167422.20_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/SRX1167422/SRX1167422.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1167422/SRX1167422.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1167422/SRX1167422.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:36:00: 40000000 INFO @ Mon, 03 Jun 2019 03:36:00: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 03:36:00: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 03:36:00: #1 total tags in treatment: 40024344 INFO @ Mon, 03 Jun 2019 03:36:00: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:36:00: #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 03:36:01: #1 tags after filtering in treatment: 40024344 INFO @ Mon, 03 Jun 2019 03:36:01: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:36:01: #1 finished! INFO @ Mon, 03 Jun 2019 03:36:01: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:36:01: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:36:04: #2 number of paired peaks: 42 WARNING @ Mon, 03 Jun 2019 03:36:04: Too few paired peaks (42) 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 03:36:04: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX1167422/SRX1167422.05_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/SRX1167422/SRX1167422.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1167422/SRX1167422.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1167422/SRX1167422.05_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。