Job ID = 1298918 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T08:41:58 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 ) 2019-06-03T08:41:58 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 ) 2019-06-03T08:41:58 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 : 29,206,592 reads read : 29,206,592 reads written : 29,206,592 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: 00:10:43 29206592 reads; of these: 29206592 (100.00%) were unpaired; of these: 909644 (3.11%) aligned 0 times 22185916 (75.96%) aligned exactly 1 time 6111032 (20.92%) aligned >1 times 96.89% overall alignment rate Time searching: 00:10:43 Overall time: 00:10:43 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 12 files... [bam_rmdupse_core] 6072995 / 28296948 = 0.2146 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 18:11:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467059/SRX467059.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467059/SRX467059.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467059/SRX467059.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467059/SRX467059.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 18:11:50: #1 read tag files... INFO @ Mon, 03 Jun 2019 18:11:50: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 18:11:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467059/SRX467059.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467059/SRX467059.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467059/SRX467059.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467059/SRX467059.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 18:11:50: #1 read tag files... INFO @ Mon, 03 Jun 2019 18:11:50: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 18:11:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467059/SRX467059.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467059/SRX467059.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467059/SRX467059.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467059/SRX467059.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 18:11:50: #1 read tag files... INFO @ Mon, 03 Jun 2019 18:11:50: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 18:11:59: 1000000 INFO @ Mon, 03 Jun 2019 18:11:59: 1000000 INFO @ Mon, 03 Jun 2019 18:12:01: 1000000 INFO @ Mon, 03 Jun 2019 18:12:07: 2000000 INFO @ Mon, 03 Jun 2019 18:12:08: 2000000 INFO @ Mon, 03 Jun 2019 18:12:12: 2000000 INFO @ Mon, 03 Jun 2019 18:12:16: 3000000 INFO @ Mon, 03 Jun 2019 18:12:17: 3000000 INFO @ Mon, 03 Jun 2019 18:12:22: 3000000 INFO @ Mon, 03 Jun 2019 18:12:25: 4000000 INFO @ Mon, 03 Jun 2019 18:12:26: 4000000 INFO @ Mon, 03 Jun 2019 18:12:33: 4000000 INFO @ Mon, 03 Jun 2019 18:12:35: 5000000 INFO @ Mon, 03 Jun 2019 18:12:35: 5000000 INFO @ Mon, 03 Jun 2019 18:12:43: 5000000 INFO @ Mon, 03 Jun 2019 18:12:44: 6000000 INFO @ Mon, 03 Jun 2019 18:12:45: 6000000 INFO @ Mon, 03 Jun 2019 18:12:53: 6000000 INFO @ Mon, 03 Jun 2019 18:12:54: 7000000 INFO @ Mon, 03 Jun 2019 18:12:54: 7000000 INFO @ Mon, 03 Jun 2019 18:13:03: 8000000 INFO @ Mon, 03 Jun 2019 18:13:04: 7000000 INFO @ Mon, 03 Jun 2019 18:13:04: 8000000 INFO @ Mon, 03 Jun 2019 18:13:13: 9000000 INFO @ Mon, 03 Jun 2019 18:13:13: 9000000 INFO @ Mon, 03 Jun 2019 18:13:14: 8000000 INFO @ Mon, 03 Jun 2019 18:13:22: 10000000 INFO @ Mon, 03 Jun 2019 18:13:23: 10000000 INFO @ Mon, 03 Jun 2019 18:13:24: 9000000 INFO @ Mon, 03 Jun 2019 18:13:31: 11000000 INFO @ Mon, 03 Jun 2019 18:13:32: 11000000 INFO @ Mon, 03 Jun 2019 18:13:35: 10000000 INFO @ Mon, 03 Jun 2019 18:13:40: 12000000 INFO @ Mon, 03 Jun 2019 18:13:41: 12000000 INFO @ Mon, 03 Jun 2019 18:13:45: 11000000 INFO @ Mon, 03 Jun 2019 18:13:48: 13000000 INFO @ Mon, 03 Jun 2019 18:13:49: 13000000 INFO @ Mon, 03 Jun 2019 18:13:56: 12000000 INFO @ Mon, 03 Jun 2019 18:13:57: 14000000 INFO @ Mon, 03 Jun 2019 18:13:58: 14000000 INFO @ Mon, 03 Jun 2019 18:14:06: 15000000 INFO @ Mon, 03 Jun 2019 18:14:06: 13000000 INFO @ Mon, 03 Jun 2019 18:14:07: 15000000 INFO @ Mon, 03 Jun 2019 18:14:15: 16000000 INFO @ Mon, 03 Jun 2019 18:14:16: 16000000 INFO @ Mon, 03 Jun 2019 18:14:17: 14000000 INFO @ Mon, 03 Jun 2019 18:14:24: 17000000 INFO @ Mon, 03 Jun 2019 18:14:25: 17000000 INFO @ Mon, 03 Jun 2019 18:14:27: 15000000 INFO @ Mon, 03 Jun 2019 18:14:33: 18000000 INFO @ Mon, 03 Jun 2019 18:14:34: 18000000 INFO @ Mon, 03 Jun 2019 18:14:37: 16000000 INFO @ Mon, 03 Jun 2019 18:14:41: 19000000 INFO @ Mon, 03 Jun 2019 18:14:42: 19000000 INFO @ Mon, 03 Jun 2019 18:14:48: 17000000 INFO @ Mon, 03 Jun 2019 18:14:50: 20000000 INFO @ Mon, 03 Jun 2019 18:14:51: 20000000 INFO @ Mon, 03 Jun 2019 18:14:59: 18000000 INFO @ Mon, 03 Jun 2019 18:14:59: 21000000 INFO @ Mon, 03 Jun 2019 18:15:00: 21000000 INFO @ Mon, 03 Jun 2019 18:15:08: 22000000 INFO @ Mon, 03 Jun 2019 18:15:09: 19000000 INFO @ Mon, 03 Jun 2019 18:15:09: 22000000 INFO @ Mon, 03 Jun 2019 18:15:10: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 18:15:10: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 18:15:10: #1 total tags in treatment: 22223953 INFO @ Mon, 03 Jun 2019 18:15:10: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:15:10: #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 18:15:11: #1 tags after filtering in treatment: 22223953 INFO @ Mon, 03 Jun 2019 18:15:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 18:15:11: #1 finished! INFO @ Mon, 03 Jun 2019 18:15:11: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:15:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:15:11: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 18:15:11: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 18:15:11: #1 total tags in treatment: 22223953 INFO @ Mon, 03 Jun 2019 18:15:11: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:15:11: #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 18:15:12: #1 tags after filtering in treatment: 22223953 INFO @ Mon, 03 Jun 2019 18:15:12: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 18:15:12: #1 finished! INFO @ Mon, 03 Jun 2019 18:15:12: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:15:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:15:13: #2 number of paired peaks: 24 WARNING @ Mon, 03 Jun 2019 18:15:13: Too few paired peaks (24) 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 18:15:13: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX467059/SRX467059.10_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/SRX467059/SRX467059.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467059/SRX467059.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467059/SRX467059.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 18:15:14: #2 number of paired peaks: 24 WARNING @ Mon, 03 Jun 2019 18:15:14: Too few paired peaks (24) 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 18:15:14: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX467059/SRX467059.20_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/SRX467059/SRX467059.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467059/SRX467059.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467059/SRX467059.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 18:15:20: 20000000 INFO @ Mon, 03 Jun 2019 18:15:29: 21000000 INFO @ Mon, 03 Jun 2019 18:15:38: 22000000 INFO @ Mon, 03 Jun 2019 18:15:40: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 18:15:40: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 18:15:40: #1 total tags in treatment: 22223953 INFO @ Mon, 03 Jun 2019 18:15:40: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:15:40: #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 18:15:41: #1 tags after filtering in treatment: 22223953 INFO @ Mon, 03 Jun 2019 18:15:41: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 18:15:41: #1 finished! INFO @ Mon, 03 Jun 2019 18:15:41: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:15:41: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:15:43: #2 number of paired peaks: 24 WARNING @ Mon, 03 Jun 2019 18:15:43: Too few paired peaks (24) 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 18:15:43: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX467059/SRX467059.05_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/SRX467059/SRX467059.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467059/SRX467059.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467059/SRX467059.05_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。