Job ID = 2010894 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T16:13:52 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 ) 2019-07-05T16:13:53 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 : 38,221,421 reads read : 76,442,842 reads written : 38,221,421 reads 0-length : 38,221,421 rm: cannot remove ‘[DSE]RR*’: 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: 00:07:15 38221421 reads; of these: 38221421 (100.00%) were unpaired; of these: 1578101 (4.13%) aligned 0 times 31595310 (82.66%) aligned exactly 1 time 5048010 (13.21%) aligned >1 times 95.87% overall alignment rate Time searching: 00:07:15 Overall time: 00:07:15 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 19014618 / 36643320 = 0.5189 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 @ Sat, 06 Jul 2019 01:38:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4225335/SRX4225335.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4225335/SRX4225335.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4225335/SRX4225335.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4225335/SRX4225335.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Sat, 06 Jul 2019 01:38:05: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:38:05: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:38:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4225335/SRX4225335.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4225335/SRX4225335.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4225335/SRX4225335.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4225335/SRX4225335.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Sat, 06 Jul 2019 01:38:06: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:38:06: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:38:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4225335/SRX4225335.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4225335/SRX4225335.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4225335/SRX4225335.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4225335/SRX4225335.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Sat, 06 Jul 2019 01:38:06: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:38:06: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:38:14: 1000000 INFO @ Sat, 06 Jul 2019 01:38:15: 1000000 INFO @ Sat, 06 Jul 2019 01:38:16: 1000000 INFO @ Sat, 06 Jul 2019 01:38:22: 2000000 INFO @ Sat, 06 Jul 2019 01:38:23: 2000000 INFO @ Sat, 06 Jul 2019 01:38:25: 2000000 INFO @ Sat, 06 Jul 2019 01:38:31: 3000000 INFO @ Sat, 06 Jul 2019 01:38:32: 3000000 INFO @ Sat, 06 Jul 2019 01:38:34: 3000000 INFO @ Sat, 06 Jul 2019 01:38:39: 4000000 INFO @ Sat, 06 Jul 2019 01:38:40: 4000000 INFO @ Sat, 06 Jul 2019 01:38:42: 4000000 INFO @ Sat, 06 Jul 2019 01:38:48: 5000000 INFO @ Sat, 06 Jul 2019 01:38:49: 5000000 INFO @ Sat, 06 Jul 2019 01:38:51: 5000000 INFO @ Sat, 06 Jul 2019 01:38:56: 6000000 INFO @ Sat, 06 Jul 2019 01:38:57: 6000000 INFO @ Sat, 06 Jul 2019 01:39:00: 6000000 INFO @ Sat, 06 Jul 2019 01:39:05: 7000000 INFO @ Sat, 06 Jul 2019 01:39:06: 7000000 INFO @ Sat, 06 Jul 2019 01:39:09: 7000000 INFO @ Sat, 06 Jul 2019 01:39:13: 8000000 INFO @ Sat, 06 Jul 2019 01:39:15: 8000000 INFO @ Sat, 06 Jul 2019 01:39:18: 8000000 INFO @ Sat, 06 Jul 2019 01:39:21: 9000000 INFO @ Sat, 06 Jul 2019 01:39:22: 9000000 INFO @ Sat, 06 Jul 2019 01:39:27: 9000000 INFO @ Sat, 06 Jul 2019 01:39:29: 10000000 INFO @ Sat, 06 Jul 2019 01:39:29: 10000000 INFO @ Sat, 06 Jul 2019 01:39:36: 10000000 INFO @ Sat, 06 Jul 2019 01:39:37: 11000000 INFO @ Sat, 06 Jul 2019 01:39:38: 11000000 INFO @ Sat, 06 Jul 2019 01:39:45: 12000000 INFO @ Sat, 06 Jul 2019 01:39:46: 12000000 INFO @ Sat, 06 Jul 2019 01:39:46: 11000000 INFO @ Sat, 06 Jul 2019 01:39:52: 13000000 INFO @ Sat, 06 Jul 2019 01:39:53: 13000000 INFO @ Sat, 06 Jul 2019 01:39:55: 12000000 INFO @ Sat, 06 Jul 2019 01:40:00: 14000000 INFO @ Sat, 06 Jul 2019 01:40:01: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 01:40:04: 13000000 INFO @ Sat, 06 Jul 2019 01:40:07: 15000000 INFO @ Sat, 06 Jul 2019 01:40:09: 15000000 INFO @ Sat, 06 Jul 2019 01:40:14: 14000000 INFO @ Sat, 06 Jul 2019 01:40:14: 16000000 INFO @ Sat, 06 Jul 2019 01:40:17: 16000000 BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 01:40:23: 17000000 INFO @ Sat, 06 Jul 2019 01:40:23: 15000000 INFO @ Sat, 06 Jul 2019 01:40:25: 17000000 INFO @ Sat, 06 Jul 2019 01:40:28: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 01:40:28: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 01:40:28: #1 total tags in treatment: 17628702 INFO @ Sat, 06 Jul 2019 01:40:28: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:40:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 01:40:28: #1 tags after filtering in treatment: 17628702 INFO @ Sat, 06 Jul 2019 01:40:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 01:40:28: #1 finished! INFO @ Sat, 06 Jul 2019 01:40:28: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:40:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:40:30: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 01:40:30: 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 @ Sat, 06 Jul 2019 01:40:30: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 01:40:31: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 01:40:31: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 01:40:31: #1 total tags in treatment: 17628702 INFO @ Sat, 06 Jul 2019 01:40:31: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:40:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 01:40:32: #1 tags after filtering in treatment: 17628702 INFO @ Sat, 06 Jul 2019 01:40:32: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 01:40:32: #1 finished! INFO @ Sat, 06 Jul 2019 01:40:32: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:40:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:40:32: 16000000 INFO @ Sat, 06 Jul 2019 01:40:33: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 01:40:33: 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 @ Sat, 06 Jul 2019 01:40:33: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 01:40:42: 17000000 INFO @ Sat, 06 Jul 2019 01:40:48: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 01:40:48: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 01:40:48: #1 total tags in treatment: 17628702 INFO @ Sat, 06 Jul 2019 01:40:48: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:40:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 01:40:48: #1 tags after filtering in treatment: 17628702 INFO @ Sat, 06 Jul 2019 01:40:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 01:40:48: #1 finished! INFO @ Sat, 06 Jul 2019 01:40:48: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:40:48: #2 looking for paired plus/minus strand peaks... cut: /home/okishinya/chipatlas/results/sacCer3/SRX4225335/SRX4225335.10_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/SRX4225335/SRX4225335.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4225335/SRX4225335.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4225335/SRX4225335.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4225335/SRX4225335.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4225335/SRX4225335.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4225335/SRX4225335.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4225335/SRX4225335.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 01:40:49: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 01:40:49: 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 @ Sat, 06 Jul 2019 01:40:49: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4225335/SRX4225335.20_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/sacCer3/SRX4225335/SRX4225335.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4225335/SRX4225335.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4225335/SRX4225335.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling