Job ID = 2010296 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T13:03:08 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 ) 2019-07-05T13:03:09 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 ) 2019-07-05T13:03:15 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 ) 2019-07-05T13:04:34 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 ) 2019-07-05T13:06:03 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 45,624,759 reads read : 45,624,759 reads written : 45,624,759 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: 00:04:56 45624759 reads; of these: 45624759 (100.00%) were unpaired; of these: 22915472 (50.23%) aligned 0 times 17823252 (39.06%) aligned exactly 1 time 4886035 (10.71%) aligned >1 times 49.77% overall alignment rate Time searching: 00:04:56 Overall time: 00:04:56 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 8 files... [bam_rmdupse_core] 12172026 / 22709287 = 0.5360 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 @ Fri, 05 Jul 2019 22:34:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX332102/SRX332102.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX332102/SRX332102.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX332102/SRX332102.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX332102/SRX332102.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 @ Fri, 05 Jul 2019 22:34:31: #1 read tag files... INFO @ Fri, 05 Jul 2019 22:34:31: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 22:34:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX332102/SRX332102.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX332102/SRX332102.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX332102/SRX332102.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX332102/SRX332102.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 @ Fri, 05 Jul 2019 22:34:32: #1 read tag files... INFO @ Fri, 05 Jul 2019 22:34:32: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 22:34:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX332102/SRX332102.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX332102/SRX332102.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX332102/SRX332102.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX332102/SRX332102.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 @ Fri, 05 Jul 2019 22:34:33: #1 read tag files... INFO @ Fri, 05 Jul 2019 22:34:33: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 22:34:46: 1000000 INFO @ Fri, 05 Jul 2019 22:34:47: 1000000 INFO @ Fri, 05 Jul 2019 22:34:49: 1000000 INFO @ Fri, 05 Jul 2019 22:35:00: 2000000 INFO @ Fri, 05 Jul 2019 22:35:02: 2000000 INFO @ Fri, 05 Jul 2019 22:35:02: 2000000 INFO @ Fri, 05 Jul 2019 22:35:13: 3000000 INFO @ Fri, 05 Jul 2019 22:35:16: 3000000 INFO @ Fri, 05 Jul 2019 22:35:16: 3000000 INFO @ Fri, 05 Jul 2019 22:35:26: 4000000 INFO @ Fri, 05 Jul 2019 22:35:30: 4000000 INFO @ Fri, 05 Jul 2019 22:35:33: 4000000 INFO @ Fri, 05 Jul 2019 22:35:38: 5000000 INFO @ Fri, 05 Jul 2019 22:35:42: 5000000 INFO @ Fri, 05 Jul 2019 22:35:47: 5000000 INFO @ Fri, 05 Jul 2019 22:35:49: 6000000 INFO @ Fri, 05 Jul 2019 22:35:54: 6000000 INFO @ Fri, 05 Jul 2019 22:36:00: 6000000 INFO @ Fri, 05 Jul 2019 22:36:00: 7000000 INFO @ Fri, 05 Jul 2019 22:36:06: 7000000 INFO @ Fri, 05 Jul 2019 22:36:12: 8000000 INFO @ Fri, 05 Jul 2019 22:36:13: 7000000 INFO @ Fri, 05 Jul 2019 22:36:19: 8000000 INFO @ Fri, 05 Jul 2019 22:36:25: 9000000 INFO @ Fri, 05 Jul 2019 22:36:26: 8000000 INFO @ Fri, 05 Jul 2019 22:36:33: 9000000 INFO @ Fri, 05 Jul 2019 22:36:38: 10000000 INFO @ Fri, 05 Jul 2019 22:36:40: 9000000 INFO @ Fri, 05 Jul 2019 22:36:44: #1 tag size is determined as 40 bps INFO @ Fri, 05 Jul 2019 22:36:44: #1 tag size = 40 INFO @ Fri, 05 Jul 2019 22:36:44: #1 total tags in treatment: 10537261 INFO @ Fri, 05 Jul 2019 22:36:44: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 22:36:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 22:36:45: #1 tags after filtering in treatment: 10537261 INFO @ Fri, 05 Jul 2019 22:36:45: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 22:36:45: #1 finished! INFO @ Fri, 05 Jul 2019 22:36:45: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 22:36:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 22:36:45: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 22:36:45: 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 @ Fri, 05 Jul 2019 22:36:45: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX332102/SRX332102.05_peaks.narrowPeak: No such file or directory INFO @ Fri, 05 Jul 2019 22:36:46: 10000000 pass1 - making usageList (0 chroms): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX332102/SRX332102.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX332102/SRX332102.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX332102/SRX332102.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 22:36:52: #1 tag size is determined as 40 bps INFO @ Fri, 05 Jul 2019 22:36:52: #1 tag size = 40 INFO @ Fri, 05 Jul 2019 22:36:52: #1 total tags in treatment: 10537261 INFO @ Fri, 05 Jul 2019 22:36:52: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 22:36:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 22:36:52: #1 tags after filtering in treatment: 10537261 INFO @ Fri, 05 Jul 2019 22:36:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 22:36:52: #1 finished! INFO @ Fri, 05 Jul 2019 22:36:52: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 22:36:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 22:36:52: 10000000 INFO @ Fri, 05 Jul 2019 22:36:53: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 22:36:53: 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 @ Fri, 05 Jul 2019 22:36:53: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX332102/SRX332102.20_peaks.narrowPeak: No such file or directory INFO @ Fri, 05 Jul 2019 22:36:57: #1 tag size is determined as 40 bps INFO @ Fri, 05 Jul 2019 22:36:57: #1 tag size = 40 INFO @ Fri, 05 Jul 2019 22:36:57: #1 total tags in treatment: 10537261 INFO @ Fri, 05 Jul 2019 22:36:57: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 22:36:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 22:36:58: #1 tags after filtering in treatment: 10537261 INFO @ Fri, 05 Jul 2019 22:36:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 22:36:58: #1 finished! INFO @ Fri, 05 Jul 2019 22:36:58: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 22:36:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 22:36:58: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 22:36:58: 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 @ Fri, 05 Jul 2019 22:36:58: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX332102/SRX332102.10_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX332102/SRX332102.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX332102/SRX332102.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX332102/SRX332102.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX332102/SRX332102.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX332102/SRX332102.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX332102/SRX332102.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling