Job ID = 2010540 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T14:02:36 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 ) 2019-07-05T14:05:02 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 ) 2019-07-05T14:05:02 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 : 14,194,359 reads read : 28,388,718 reads written : 28,388,718 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: 00:07:10 14194359 reads; of these: 14194359 (100.00%) were paired; of these: 8446353 (59.50%) aligned concordantly 0 times 3955500 (27.87%) aligned concordantly exactly 1 time 1792506 (12.63%) aligned concordantly >1 times ---- 8446353 pairs aligned concordantly 0 times; of these: 382159 (4.52%) aligned discordantly 1 time ---- 8064194 pairs aligned 0 times concordantly or discordantly; of these: 16128388 mates make up the pairs; of these: 15730346 (97.53%) aligned 0 times 118702 (0.74%) aligned exactly 1 time 279340 (1.73%) aligned >1 times 44.59% overall alignment rate Time searching: 00:07:10 Overall time: 00:07:10 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_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 531982 / 6122221 = 0.0869 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 23:18:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381242/SRX381242.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381242/SRX381242.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381242/SRX381242.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381242/SRX381242.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 23:18:10: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:18:10: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:18:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381242/SRX381242.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381242/SRX381242.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381242/SRX381242.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381242/SRX381242.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 23:18:12: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:18:12: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:18:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381242/SRX381242.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381242/SRX381242.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381242/SRX381242.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381242/SRX381242.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 23:18:17: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:18:17: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:18:20: 1000000 INFO @ Fri, 05 Jul 2019 23:18:21: 1000000 INFO @ Fri, 05 Jul 2019 23:18:27: 1000000 INFO @ Fri, 05 Jul 2019 23:18:30: 2000000 INFO @ Fri, 05 Jul 2019 23:18:31: 2000000 INFO @ Fri, 05 Jul 2019 23:18:37: 2000000 INFO @ Fri, 05 Jul 2019 23:18:39: 3000000 INFO @ Fri, 05 Jul 2019 23:18:41: 3000000 INFO @ Fri, 05 Jul 2019 23:18:48: 3000000 INFO @ Fri, 05 Jul 2019 23:18:49: 4000000 INFO @ Fri, 05 Jul 2019 23:18:51: 4000000 INFO @ Fri, 05 Jul 2019 23:18:58: 4000000 INFO @ Fri, 05 Jul 2019 23:18:59: 5000000 INFO @ Fri, 05 Jul 2019 23:19:01: 5000000 INFO @ Fri, 05 Jul 2019 23:19:08: 5000000 INFO @ Fri, 05 Jul 2019 23:19:09: 6000000 INFO @ Fri, 05 Jul 2019 23:19:11: 6000000 INFO @ Fri, 05 Jul 2019 23:19:18: 7000000 INFO @ Fri, 05 Jul 2019 23:19:18: 6000000 INFO @ Fri, 05 Jul 2019 23:19:21: 7000000 INFO @ Fri, 05 Jul 2019 23:19:28: 8000000 INFO @ Fri, 05 Jul 2019 23:19:28: 7000000 INFO @ Fri, 05 Jul 2019 23:19:31: 8000000 INFO @ Fri, 05 Jul 2019 23:19:37: 9000000 INFO @ Fri, 05 Jul 2019 23:19:38: 8000000 INFO @ Fri, 05 Jul 2019 23:19:41: 9000000 INFO @ Fri, 05 Jul 2019 23:19:45: 10000000 INFO @ Fri, 05 Jul 2019 23:19:48: 9000000 INFO @ Fri, 05 Jul 2019 23:19:51: 10000000 INFO @ Fri, 05 Jul 2019 23:19:54: 11000000 INFO @ Fri, 05 Jul 2019 23:19:58: 10000000 INFO @ Fri, 05 Jul 2019 23:19:59: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:19:59: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:19:59: #1 total tags in treatment: 5248333 INFO @ Fri, 05 Jul 2019 23:19:59: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:19:59: #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 23:19:59: #1 tags after filtering in treatment: 3285342 INFO @ Fri, 05 Jul 2019 23:19:59: #1 Redundant rate of treatment: 0.37 INFO @ Fri, 05 Jul 2019 23:19:59: #1 finished! INFO @ Fri, 05 Jul 2019 23:19:59: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:19:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:19:59: #2 number of paired peaks: 61 WARNING @ Fri, 05 Jul 2019 23:19:59: Too few paired peaks (61) 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 23:19:59: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX381242/SRX381242.10_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/SRX381242/SRX381242.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381242/SRX381242.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381242/SRX381242.10_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 23:20:02: 11000000 INFO @ Fri, 05 Jul 2019 23:20:07: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:20:07: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:20:07: #1 total tags in treatment: 5248333 INFO @ Fri, 05 Jul 2019 23:20:07: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:20:07: #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 23:20:07: #1 tags after filtering in treatment: 3285342 INFO @ Fri, 05 Jul 2019 23:20:07: #1 Redundant rate of treatment: 0.37 INFO @ Fri, 05 Jul 2019 23:20:07: #1 finished! INFO @ Fri, 05 Jul 2019 23:20:07: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:20:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:20:08: #2 number of paired peaks: 61 WARNING @ Fri, 05 Jul 2019 23:20:08: Too few paired peaks (61) 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 23:20:08: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX381242/SRX381242.05_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/SRX381242/SRX381242.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381242/SRX381242.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381242/SRX381242.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:20:08: 11000000 INFO @ Fri, 05 Jul 2019 23:20:13: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:20:13: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:20:13: #1 total tags in treatment: 5248333 INFO @ Fri, 05 Jul 2019 23:20:13: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:20:13: #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 23:20:14: #1 tags after filtering in treatment: 3285342 INFO @ Fri, 05 Jul 2019 23:20:14: #1 Redundant rate of treatment: 0.37 INFO @ Fri, 05 Jul 2019 23:20:14: #1 finished! INFO @ Fri, 05 Jul 2019 23:20:14: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:20:14: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 23:20:14: #2 number of paired peaks: 61 WARNING @ Fri, 05 Jul 2019 23:20:14: Too few paired peaks (61) 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 23:20:14: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX381242/SRX381242.20_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/SRX381242/SRX381242.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381242/SRX381242.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381242/SRX381242.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling