Job ID = 2011728 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T17:14:20 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 ) 2019-07-05T17:14:20 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 ) 2019-07-05T17:14:20 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 ) 2019-07-05T17:27:22 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 : 30,834,426 reads read : 30,834,426 reads written : 30,834,426 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: 00:05:14 30834426 reads; of these: 30834426 (100.00%) were unpaired; of these: 1170572 (3.80%) aligned 0 times 24579891 (79.72%) aligned exactly 1 time 5083963 (16.49%) aligned >1 times 96.20% overall alignment rate Time searching: 00:05:14 Overall time: 00:05:14 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] 15105956 / 29663854 = 0.5092 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 02:41:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4726627/SRX4726627.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4726627/SRX4726627.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4726627/SRX4726627.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4726627/SRX4726627.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 02:41:01: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:41:01: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:41:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4726627/SRX4726627.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4726627/SRX4726627.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4726627/SRX4726627.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4726627/SRX4726627.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 02:41:02: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:41:02: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:41:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4726627/SRX4726627.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4726627/SRX4726627.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4726627/SRX4726627.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4726627/SRX4726627.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 02:41:03: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:41:03: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:41:11: 1000000 INFO @ Sat, 06 Jul 2019 02:41:11: 1000000 INFO @ Sat, 06 Jul 2019 02:41:14: 1000000 INFO @ Sat, 06 Jul 2019 02:41:21: 2000000 INFO @ Sat, 06 Jul 2019 02:41:21: 2000000 INFO @ Sat, 06 Jul 2019 02:41:25: 2000000 INFO @ Sat, 06 Jul 2019 02:41:30: 3000000 INFO @ Sat, 06 Jul 2019 02:41:30: 3000000 INFO @ Sat, 06 Jul 2019 02:41:36: 3000000 INFO @ Sat, 06 Jul 2019 02:41:39: 4000000 INFO @ Sat, 06 Jul 2019 02:41:39: 4000000 INFO @ Sat, 06 Jul 2019 02:41:46: 4000000 INFO @ Sat, 06 Jul 2019 02:41:48: 5000000 INFO @ Sat, 06 Jul 2019 02:41:49: 5000000 INFO @ Sat, 06 Jul 2019 02:41:56: 6000000 INFO @ Sat, 06 Jul 2019 02:41:57: 5000000 INFO @ Sat, 06 Jul 2019 02:41:58: 6000000 INFO @ Sat, 06 Jul 2019 02:42:05: 7000000 INFO @ Sat, 06 Jul 2019 02:42:07: 7000000 INFO @ Sat, 06 Jul 2019 02:42:08: 6000000 INFO @ Sat, 06 Jul 2019 02:42:14: 8000000 INFO @ Sat, 06 Jul 2019 02:42:17: 8000000 INFO @ Sat, 06 Jul 2019 02:42:18: 7000000 INFO @ Sat, 06 Jul 2019 02:42:23: 9000000 INFO @ Sat, 06 Jul 2019 02:42:26: 9000000 INFO @ Sat, 06 Jul 2019 02:42:27: 8000000 INFO @ Sat, 06 Jul 2019 02:42:32: 10000000 INFO @ Sat, 06 Jul 2019 02:42:36: 10000000 INFO @ Sat, 06 Jul 2019 02:42:37: 9000000 INFO @ Sat, 06 Jul 2019 02:42:41: 11000000 INFO @ Sat, 06 Jul 2019 02:42:46: 11000000 INFO @ Sat, 06 Jul 2019 02:42:48: 10000000 INFO @ Sat, 06 Jul 2019 02:42:51: 12000000 INFO @ Sat, 06 Jul 2019 02:42:57: 12000000 INFO @ Sat, 06 Jul 2019 02:42:58: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 02:43:00: 13000000 INFO @ Sat, 06 Jul 2019 02:43:08: 13000000 INFO @ Sat, 06 Jul 2019 02:43:09: 12000000 INFO @ Sat, 06 Jul 2019 02:43:09: 14000000 INFO @ Sat, 06 Jul 2019 02:43:13: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 02:43:13: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 02:43:13: #1 total tags in treatment: 14557898 INFO @ Sat, 06 Jul 2019 02:43:13: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:43:13: #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 02:43:14: #1 tags after filtering in treatment: 14557898 INFO @ Sat, 06 Jul 2019 02:43:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 02:43:14: #1 finished! INFO @ Sat, 06 Jul 2019 02:43:14: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:43:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:43:15: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 02:43:15: 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 02:43:15: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4726627/SRX4726627.10_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/sacCer3/SRX4726627/SRX4726627.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4726627/SRX4726627.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4726627/SRX4726627.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 02:43:18: 14000000 INFO @ Sat, 06 Jul 2019 02:43:19: 13000000 INFO @ Sat, 06 Jul 2019 02:43:24: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 02:43:24: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 02:43:24: #1 total tags in treatment: 14557898 INFO @ Sat, 06 Jul 2019 02:43:24: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:43:24: #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 02:43:24: #1 tags after filtering in treatment: 14557898 INFO @ Sat, 06 Jul 2019 02:43:24: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 02:43:24: #1 finished! INFO @ Sat, 06 Jul 2019 02:43:24: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:43:24: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 02:43:25: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 02:43:25: 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 02:43:25: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4726627/SRX4726627.05_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/SRX4726627/SRX4726627.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4726627/SRX4726627.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4726627/SRX4726627.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 02:43:28: 14000000 INFO @ Sat, 06 Jul 2019 02:43:33: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 02:43:33: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 02:43:33: #1 total tags in treatment: 14557898 INFO @ Sat, 06 Jul 2019 02:43:33: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:43:33: #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 02:43:34: #1 tags after filtering in treatment: 14557898 INFO @ Sat, 06 Jul 2019 02:43:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 02:43:34: #1 finished! INFO @ Sat, 06 Jul 2019 02:43:34: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:43:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:43:35: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 02:43:35: 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 02:43:35: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4726627/SRX4726627.20_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/SRX4726627/SRX4726627.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4726627/SRX4726627.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4726627/SRX4726627.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling