Job ID = 2011727 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T17:19:15 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 ) 2019-07-05T17:19:15 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 ) 2019-07-05T17:21:47 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 ) 2019-07-05T17:23:13 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 ) 2019-07-05T17:23:57 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 : 24,239,678 reads read : 24,239,678 reads written : 24,239,678 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: 00:04:13 24239678 reads; of these: 24239678 (100.00%) were unpaired; of these: 1034888 (4.27%) aligned 0 times 18864877 (77.83%) aligned exactly 1 time 4339913 (17.90%) aligned >1 times 95.73% overall alignment rate Time searching: 00:04:13 Overall time: 00:04:13 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 12 files... [bam_rmdupse_core] 10336782 / 23204790 = 0.4455 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 02:37:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4726626/SRX4726626.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4726626/SRX4726626.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4726626/SRX4726626.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4726626/SRX4726626.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 02:37:09: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:37:09: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:37:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4726626/SRX4726626.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4726626/SRX4726626.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4726626/SRX4726626.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4726626/SRX4726626.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 02:37:10: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:37:10: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:37:17: 1000000 INFO @ Sat, 06 Jul 2019 02:37:19: 1000000 INFO @ Sat, 06 Jul 2019 02:37:26: 2000000 INFO @ Sat, 06 Jul 2019 02:37:27: 2000000 INFO @ Sat, 06 Jul 2019 02:37:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4726626/SRX4726626.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4726626/SRX4726626.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4726626/SRX4726626.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4726626/SRX4726626.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 02:37:29: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:37:29: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:37:34: 3000000 INFO @ Sat, 06 Jul 2019 02:37:35: 3000000 INFO @ Sat, 06 Jul 2019 02:37:40: 1000000 INFO @ Sat, 06 Jul 2019 02:37:42: 4000000 INFO @ Sat, 06 Jul 2019 02:37:43: 4000000 INFO @ Sat, 06 Jul 2019 02:37:50: 5000000 INFO @ Sat, 06 Jul 2019 02:37:51: 5000000 INFO @ Sat, 06 Jul 2019 02:37:51: 2000000 INFO @ Sat, 06 Jul 2019 02:37:58: 6000000 INFO @ Sat, 06 Jul 2019 02:37:59: 6000000 INFO @ Sat, 06 Jul 2019 02:38:02: 3000000 INFO @ Sat, 06 Jul 2019 02:38:06: 7000000 INFO @ Sat, 06 Jul 2019 02:38:07: 7000000 INFO @ Sat, 06 Jul 2019 02:38:13: 4000000 INFO @ Sat, 06 Jul 2019 02:38:15: 8000000 INFO @ Sat, 06 Jul 2019 02:38:16: 8000000 INFO @ Sat, 06 Jul 2019 02:38:23: 5000000 INFO @ Sat, 06 Jul 2019 02:38:23: 9000000 INFO @ Sat, 06 Jul 2019 02:38:24: 9000000 INFO @ Sat, 06 Jul 2019 02:38:32: 10000000 INFO @ Sat, 06 Jul 2019 02:38:33: 10000000 INFO @ Sat, 06 Jul 2019 02:38:34: 6000000 INFO @ Sat, 06 Jul 2019 02:38:41: 11000000 INFO @ Sat, 06 Jul 2019 02:38:42: 11000000 INFO @ Sat, 06 Jul 2019 02:38:44: 7000000 INFO @ Sat, 06 Jul 2019 02:38:50: 12000000 INFO @ Sat, 06 Jul 2019 02:38:51: 12000000 INFO @ Sat, 06 Jul 2019 02:38:54: 8000000 INFO @ Sat, 06 Jul 2019 02:38:57: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 02:38:57: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 02:38:57: #1 total tags in treatment: 12868008 INFO @ Sat, 06 Jul 2019 02:38:57: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:38:57: #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 02:38:57: #1 tags after filtering in treatment: 12868008 INFO @ Sat, 06 Jul 2019 02:38:57: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 02:38:57: #1 finished! INFO @ Sat, 06 Jul 2019 02:38:57: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:38:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:38:58: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 02:38:58: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 02:38:58: #1 total tags in treatment: 12868008 INFO @ Sat, 06 Jul 2019 02:38:58: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:38:58: #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 02:38:58: #1 tags after filtering in treatment: 12868008 INFO @ Sat, 06 Jul 2019 02:38:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 02:38:58: #1 finished! INFO @ Sat, 06 Jul 2019 02:38:58: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:38:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:38:58: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 02:38:58: 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 02:38:58: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4726626/SRX4726626.05_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/sacCer3/SRX4726626/SRX4726626.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4726626/SRX4726626.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4726626/SRX4726626.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 02:38:59: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 02:38:59: 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 02:38:59: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4726626/SRX4726626.10_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/sacCer3/SRX4726626/SRX4726626.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4726626/SRX4726626.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4726626/SRX4726626.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 02:39:06: 9000000 INFO @ Sat, 06 Jul 2019 02:39:17: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 02:39:28: 11000000 BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 02:39:39: 12000000 INFO @ Sat, 06 Jul 2019 02:39:48: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 02:39:48: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 02:39:48: #1 total tags in treatment: 12868008 INFO @ Sat, 06 Jul 2019 02:39:48: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:39:48: #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 02:39:48: #1 tags after filtering in treatment: 12868008 INFO @ Sat, 06 Jul 2019 02:39:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 02:39:48: #1 finished! INFO @ Sat, 06 Jul 2019 02:39:48: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:39:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:39:49: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 02:39:49: 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 02:39:49: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4726626/SRX4726626.20_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/sacCer3/SRX4726626/SRX4726626.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4726626/SRX4726626.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4726626/SRX4726626.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling