Job ID = 1295321 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T04:09:55 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 ) 2019-06-03T04:09:55 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 ) 2019-06-03T04:21:42 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 ) 2019-06-03T04:22:28 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 ) 2019-06-03T04:22:28 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 ) 2019-06-03T04:22:28 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 : 47,571,085 reads read : 47,571,085 reads written : 47,571,085 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: 00:12:25 47571085 reads; of these: 47571085 (100.00%) were unpaired; of these: 2413562 (5.07%) aligned 0 times 40196249 (84.50%) aligned exactly 1 time 4961274 (10.43%) aligned >1 times 94.93% overall alignment rate Time searching: 00:12:25 Overall time: 00:12:25 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] 16385710 / 45157523 = 0.3629 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 13:59:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX335489/SRX335489.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX335489/SRX335489.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX335489/SRX335489.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX335489/SRX335489.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 13:59:14: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:59:14: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:59:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX335489/SRX335489.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX335489/SRX335489.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX335489/SRX335489.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX335489/SRX335489.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 13:59:14: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:59:14: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:59:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX335489/SRX335489.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX335489/SRX335489.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX335489/SRX335489.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX335489/SRX335489.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 13:59:14: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:59:14: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:59:24: 1000000 INFO @ Mon, 03 Jun 2019 13:59:27: 1000000 INFO @ Mon, 03 Jun 2019 13:59:27: 1000000 INFO @ Mon, 03 Jun 2019 13:59:34: 2000000 INFO @ Mon, 03 Jun 2019 13:59:39: 2000000 INFO @ Mon, 03 Jun 2019 13:59:39: 2000000 INFO @ Mon, 03 Jun 2019 13:59:43: 3000000 INFO @ Mon, 03 Jun 2019 13:59:51: 3000000 INFO @ Mon, 03 Jun 2019 13:59:51: 3000000 INFO @ Mon, 03 Jun 2019 13:59:52: 4000000 INFO @ Mon, 03 Jun 2019 14:00:01: 5000000 INFO @ Mon, 03 Jun 2019 14:00:02: 4000000 INFO @ Mon, 03 Jun 2019 14:00:02: 4000000 INFO @ Mon, 03 Jun 2019 14:00:10: 6000000 INFO @ Mon, 03 Jun 2019 14:00:14: 5000000 INFO @ Mon, 03 Jun 2019 14:00:14: 5000000 INFO @ Mon, 03 Jun 2019 14:00:19: 7000000 INFO @ Mon, 03 Jun 2019 14:00:25: 6000000 INFO @ Mon, 03 Jun 2019 14:00:25: 6000000 INFO @ Mon, 03 Jun 2019 14:00:28: 8000000 INFO @ Mon, 03 Jun 2019 14:00:36: 7000000 INFO @ Mon, 03 Jun 2019 14:00:36: 7000000 INFO @ Mon, 03 Jun 2019 14:00:38: 9000000 INFO @ Mon, 03 Jun 2019 14:00:46: 10000000 INFO @ Mon, 03 Jun 2019 14:00:47: 8000000 INFO @ Mon, 03 Jun 2019 14:00:47: 8000000 INFO @ Mon, 03 Jun 2019 14:00:55: 11000000 INFO @ Mon, 03 Jun 2019 14:00:58: 9000000 INFO @ Mon, 03 Jun 2019 14:00:58: 9000000 INFO @ Mon, 03 Jun 2019 14:01:04: 12000000 INFO @ Mon, 03 Jun 2019 14:01:08: 10000000 INFO @ Mon, 03 Jun 2019 14:01:09: 10000000 INFO @ Mon, 03 Jun 2019 14:01:12: 13000000 INFO @ Mon, 03 Jun 2019 14:01:19: 11000000 INFO @ Mon, 03 Jun 2019 14:01:19: 11000000 INFO @ Mon, 03 Jun 2019 14:01:21: 14000000 INFO @ Mon, 03 Jun 2019 14:01:30: 15000000 INFO @ Mon, 03 Jun 2019 14:01:30: 12000000 INFO @ Mon, 03 Jun 2019 14:01:30: 12000000 INFO @ Mon, 03 Jun 2019 14:01:41: 16000000 INFO @ Mon, 03 Jun 2019 14:01:41: 13000000 INFO @ Mon, 03 Jun 2019 14:01:41: 13000000 INFO @ Mon, 03 Jun 2019 14:01:50: 17000000 INFO @ Mon, 03 Jun 2019 14:01:51: 14000000 INFO @ Mon, 03 Jun 2019 14:01:52: 14000000 INFO @ Mon, 03 Jun 2019 14:01:58: 18000000 INFO @ Mon, 03 Jun 2019 14:02:02: 15000000 INFO @ Mon, 03 Jun 2019 14:02:02: 15000000 INFO @ Mon, 03 Jun 2019 14:02:08: 19000000 INFO @ Mon, 03 Jun 2019 14:02:12: 16000000 INFO @ Mon, 03 Jun 2019 14:02:13: 16000000 INFO @ Mon, 03 Jun 2019 14:02:16: 20000000 INFO @ Mon, 03 Jun 2019 14:02:23: 17000000 INFO @ Mon, 03 Jun 2019 14:02:23: 17000000 INFO @ Mon, 03 Jun 2019 14:02:24: 21000000 INFO @ Mon, 03 Jun 2019 14:02:33: 22000000 INFO @ Mon, 03 Jun 2019 14:02:34: 18000000 INFO @ Mon, 03 Jun 2019 14:02:34: 18000000 INFO @ Mon, 03 Jun 2019 14:02:42: 23000000 INFO @ Mon, 03 Jun 2019 14:02:44: 19000000 INFO @ Mon, 03 Jun 2019 14:02:45: 19000000 INFO @ Mon, 03 Jun 2019 14:02:51: 24000000 INFO @ Mon, 03 Jun 2019 14:02:55: 20000000 INFO @ Mon, 03 Jun 2019 14:02:55: 20000000 INFO @ Mon, 03 Jun 2019 14:03:01: 25000000 INFO @ Mon, 03 Jun 2019 14:03:06: 21000000 INFO @ Mon, 03 Jun 2019 14:03:06: 21000000 INFO @ Mon, 03 Jun 2019 14:03:10: 26000000 INFO @ Mon, 03 Jun 2019 14:03:16: 22000000 INFO @ Mon, 03 Jun 2019 14:03:17: 22000000 INFO @ Mon, 03 Jun 2019 14:03:20: 27000000 INFO @ Mon, 03 Jun 2019 14:03:27: 23000000 INFO @ Mon, 03 Jun 2019 14:03:27: 23000000 INFO @ Mon, 03 Jun 2019 14:03:30: 28000000 INFO @ Mon, 03 Jun 2019 14:03:38: 24000000 INFO @ Mon, 03 Jun 2019 14:03:38: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 14:03:38: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 14:03:38: #1 total tags in treatment: 28771813 INFO @ Mon, 03 Jun 2019 14:03:38: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:03:38: #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 14:03:38: 24000000 INFO @ Mon, 03 Jun 2019 14:03:39: #1 tags after filtering in treatment: 28771813 INFO @ Mon, 03 Jun 2019 14:03:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:03:39: #1 finished! INFO @ Mon, 03 Jun 2019 14:03:39: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:03:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:03:41: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 14:03:41: 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 14:03:41: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX335489/SRX335489.20_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/SRX335489/SRX335489.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX335489/SRX335489.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX335489/SRX335489.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 14:03:50: 25000000 INFO @ Mon, 03 Jun 2019 14:03:50: 25000000 INFO @ Mon, 03 Jun 2019 14:04:01: 26000000 INFO @ Mon, 03 Jun 2019 14:04:01: 26000000 INFO @ Mon, 03 Jun 2019 14:04:12: 27000000 INFO @ Mon, 03 Jun 2019 14:04:12: 27000000 INFO @ Mon, 03 Jun 2019 14:04:22: 28000000 INFO @ Mon, 03 Jun 2019 14:04:22: 28000000 INFO @ Mon, 03 Jun 2019 14:04:30: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 14:04:30: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 14:04:30: #1 total tags in treatment: 28771813 INFO @ Mon, 03 Jun 2019 14:04:30: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:04:30: #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 14:04:31: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 14:04:31: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 14:04:31: #1 total tags in treatment: 28771813 INFO @ Mon, 03 Jun 2019 14:04:31: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:04:31: #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 14:04:31: #1 tags after filtering in treatment: 28771813 INFO @ Mon, 03 Jun 2019 14:04:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:04:31: #1 finished! INFO @ Mon, 03 Jun 2019 14:04:31: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:04:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:04:31: #1 tags after filtering in treatment: 28771813 INFO @ Mon, 03 Jun 2019 14:04:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:04:31: #1 finished! INFO @ Mon, 03 Jun 2019 14:04:31: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:04:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:04:33: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 14:04:33: 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 14:04:33: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX335489/SRX335489.10_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/SRX335489/SRX335489.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX335489/SRX335489.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX335489/SRX335489.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 14:04:34: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 14:04:34: 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 14:04:34: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX335489/SRX335489.05_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/SRX335489/SRX335489.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX335489/SRX335489.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX335489/SRX335489.05_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。