Job ID = 2010610 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T14:34:29 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 ) 2019-07-05T14:34:29 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 ) 2019-07-05T14:35:41 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 ) 2019-07-05T14:36:01 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 : 10,661,940 reads read : 21,323,880 reads written : 10,661,940 reads 0-length : 10,661,940 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: 00:03:54 10661940 reads; of these: 10661940 (100.00%) were unpaired; of these: 1790254 (16.79%) aligned 0 times 7874197 (73.85%) aligned exactly 1 time 997489 (9.36%) aligned >1 times 83.21% overall alignment rate Time searching: 00:03:54 Overall time: 00:03:54 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_rmdupse_core] 2338476 / 8871686 = 0.2636 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 23:43:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3823261/SRX3823261.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3823261/SRX3823261.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3823261/SRX3823261.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3823261/SRX3823261.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 23:43:31: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:43:31: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:43:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3823261/SRX3823261.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3823261/SRX3823261.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3823261/SRX3823261.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3823261/SRX3823261.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 23:43:32: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:43:32: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:43:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3823261/SRX3823261.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3823261/SRX3823261.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3823261/SRX3823261.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3823261/SRX3823261.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 23:43:33: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:43:33: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:43:38: 1000000 INFO @ Fri, 05 Jul 2019 23:43:42: 1000000 INFO @ Fri, 05 Jul 2019 23:43:43: 1000000 INFO @ Fri, 05 Jul 2019 23:43:46: 2000000 INFO @ Fri, 05 Jul 2019 23:43:53: 3000000 INFO @ Fri, 05 Jul 2019 23:43:53: 2000000 INFO @ Fri, 05 Jul 2019 23:43:54: 2000000 INFO @ Fri, 05 Jul 2019 23:43:59: 4000000 INFO @ Fri, 05 Jul 2019 23:44:03: 3000000 INFO @ Fri, 05 Jul 2019 23:44:04: 3000000 INFO @ Fri, 05 Jul 2019 23:44:06: 5000000 INFO @ Fri, 05 Jul 2019 23:44:12: 4000000 INFO @ Fri, 05 Jul 2019 23:44:13: 6000000 INFO @ Fri, 05 Jul 2019 23:44:14: 4000000 INFO @ Fri, 05 Jul 2019 23:44:17: #1 tag size is determined as 39 bps INFO @ Fri, 05 Jul 2019 23:44:17: #1 tag size = 39 INFO @ Fri, 05 Jul 2019 23:44:17: #1 total tags in treatment: 6533210 INFO @ Fri, 05 Jul 2019 23:44:17: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:44:17: #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 23:44:17: #1 tags after filtering in treatment: 6533210 INFO @ Fri, 05 Jul 2019 23:44:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 23:44:17: #1 finished! INFO @ Fri, 05 Jul 2019 23:44:17: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:44:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:44:17: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 23:44:17: 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 23:44:17: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3823261/SRX3823261.05_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/SRX3823261/SRX3823261.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3823261/SRX3823261.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3823261/SRX3823261.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:44:22: 5000000 INFO @ Fri, 05 Jul 2019 23:44:23: 5000000 INFO @ Fri, 05 Jul 2019 23:44:32: 6000000 INFO @ Fri, 05 Jul 2019 23:44:33: 6000000 INFO @ Fri, 05 Jul 2019 23:44:37: #1 tag size is determined as 39 bps INFO @ Fri, 05 Jul 2019 23:44:37: #1 tag size = 39 INFO @ Fri, 05 Jul 2019 23:44:37: #1 total tags in treatment: 6533210 INFO @ Fri, 05 Jul 2019 23:44:37: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:44:37: #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 23:44:37: #1 tags after filtering in treatment: 6533210 INFO @ Fri, 05 Jul 2019 23:44:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 23:44:37: #1 finished! INFO @ Fri, 05 Jul 2019 23:44:37: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:44:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:44:37: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 23:44:37: 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 23:44:37: Process for pairing-model is terminated! INFO @ Fri, 05 Jul 2019 23:44:38: #1 tag size is determined as 39 bps INFO @ Fri, 05 Jul 2019 23:44:38: #1 tag size = 39 INFO @ Fri, 05 Jul 2019 23:44:38: #1 total tags in treatment: 6533210 INFO @ Fri, 05 Jul 2019 23:44:38: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:44:38: #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 23:44:38: #1 tags after filtering in treatment: 6533210 INFO @ Fri, 05 Jul 2019 23:44:38: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 23:44:38: #1 finished! INFO @ Fri, 05 Jul 2019 23:44:38: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:44:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:44:39: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 23:44:39: 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 23:44:39: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3823261/SRX3823261.10_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/SRX3823261/SRX3823261.20_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/SRX3823261/SRX3823261.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3823261/SRX3823261.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3823261/SRX3823261.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3823261/SRX3823261.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3823261/SRX3823261.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3823261/SRX3823261.20_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。