Job ID = 2010632 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T14:41:21 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 ) 2019-07-05T14:41:22 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 ) 2019-07-05T14:46:23 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 ) 2019-07-05T14:46:23 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 : 14,821,421 reads read : 29,642,842 reads written : 29,642,842 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: 00:08:10 14821421 reads; of these: 14821421 (100.00%) were paired; of these: 9035816 (60.96%) aligned concordantly 0 times 2414464 (16.29%) aligned concordantly exactly 1 time 3371141 (22.75%) aligned concordantly >1 times ---- 9035816 pairs aligned concordantly 0 times; of these: 11040 (0.12%) aligned discordantly 1 time ---- 9024776 pairs aligned 0 times concordantly or discordantly; of these: 18049552 mates make up the pairs; of these: 17347945 (96.11%) aligned 0 times 111797 (0.62%) aligned exactly 1 time 589810 (3.27%) aligned >1 times 41.48% overall alignment rate Time searching: 00:08:10 Overall time: 00:08:10 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] 2257286 / 5792498 = 0.3897 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 00:08:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3829148/SRX3829148.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3829148/SRX3829148.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3829148/SRX3829148.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3829148/SRX3829148.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 00:08:32: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:08:32: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:08:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3829148/SRX3829148.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3829148/SRX3829148.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3829148/SRX3829148.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3829148/SRX3829148.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 00:08:33: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:08:33: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:08:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3829148/SRX3829148.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3829148/SRX3829148.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3829148/SRX3829148.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3829148/SRX3829148.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 00:08:34: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:08:34: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:08:41: 1000000 INFO @ Sat, 06 Jul 2019 00:08:42: 1000000 INFO @ Sat, 06 Jul 2019 00:08:43: 1000000 INFO @ Sat, 06 Jul 2019 00:08:51: 2000000 INFO @ Sat, 06 Jul 2019 00:08:51: 2000000 INFO @ Sat, 06 Jul 2019 00:08:52: 2000000 INFO @ Sat, 06 Jul 2019 00:08:59: 3000000 INFO @ Sat, 06 Jul 2019 00:09:01: 3000000 INFO @ Sat, 06 Jul 2019 00:09:02: 3000000 INFO @ Sat, 06 Jul 2019 00:09:07: 4000000 INFO @ Sat, 06 Jul 2019 00:09:10: 4000000 INFO @ Sat, 06 Jul 2019 00:09:12: 4000000 INFO @ Sat, 06 Jul 2019 00:09:16: 5000000 INFO @ Sat, 06 Jul 2019 00:09:19: 5000000 INFO @ Sat, 06 Jul 2019 00:09:22: 5000000 INFO @ Sat, 06 Jul 2019 00:09:24: 6000000 INFO @ Sat, 06 Jul 2019 00:09:29: 6000000 INFO @ Sat, 06 Jul 2019 00:09:32: 6000000 INFO @ Sat, 06 Jul 2019 00:09:33: 7000000 INFO @ Sat, 06 Jul 2019 00:09:38: 7000000 INFO @ Sat, 06 Jul 2019 00:09:39: #1 tag size is determined as 76 bps INFO @ Sat, 06 Jul 2019 00:09:39: #1 tag size = 76 INFO @ Sat, 06 Jul 2019 00:09:39: #1 total tags in treatment: 3530307 INFO @ Sat, 06 Jul 2019 00:09:39: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:09:39: #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 00:09:39: #1 tags after filtering in treatment: 1662577 INFO @ Sat, 06 Jul 2019 00:09:39: #1 Redundant rate of treatment: 0.53 INFO @ Sat, 06 Jul 2019 00:09:39: #1 finished! INFO @ Sat, 06 Jul 2019 00:09:39: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:09:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:09:39: #2 number of paired peaks: 49 WARNING @ Sat, 06 Jul 2019 00:09:39: Too few paired peaks (49) 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 00:09:39: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 00:09:42: 7000000 BedGraph に変換しました。 INFO @ Sat, 06 Jul 2019 00:09:46: #1 tag size is determined as 76 bps INFO @ Sat, 06 Jul 2019 00:09:46: #1 tag size = 76 INFO @ Sat, 06 Jul 2019 00:09:46: #1 total tags in treatment: 3530307 INFO @ Sat, 06 Jul 2019 00:09:46: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:09:46: #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 00:09:46: #1 tags after filtering in treatment: 1662577 INFO @ Sat, 06 Jul 2019 00:09:46: #1 Redundant rate of treatment: 0.53 INFO @ Sat, 06 Jul 2019 00:09:46: #1 finished! INFO @ Sat, 06 Jul 2019 00:09:46: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:09:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:09:46: #2 number of paired peaks: 49 WARNING @ Sat, 06 Jul 2019 00:09:46: Too few paired peaks (49) 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 00:09:46: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3829148/SRX3829148.20_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/SRX3829148/SRX3829148.05_peaks.narrowPeak BigWig に変換中... : No such file or directory pass1 - making usageList (0 chroms): 1 millis pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3829148/SRX3829148.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3829148/SRX3829148.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3829148/SRX3829148.20_peaks.narrowPeak’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3829148/SRX3829148.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3829148/SRX3829148.05_*.xls’: No such file or directory CompletedMACS2peakCalling rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3829148/SRX3829148.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:09:50: #1 tag size is determined as 76 bps INFO @ Sat, 06 Jul 2019 00:09:50: #1 tag size = 76 INFO @ Sat, 06 Jul 2019 00:09:50: #1 total tags in treatment: 3530307 INFO @ Sat, 06 Jul 2019 00:09:50: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:09:50: #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 00:09:50: #1 tags after filtering in treatment: 1662577 INFO @ Sat, 06 Jul 2019 00:09:50: #1 Redundant rate of treatment: 0.53 INFO @ Sat, 06 Jul 2019 00:09:50: #1 finished! INFO @ Sat, 06 Jul 2019 00:09:50: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:09:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:09:50: #2 number of paired peaks: 49 WARNING @ Sat, 06 Jul 2019 00:09:50: Too few paired peaks (49) 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 00:09:50: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3829148/SRX3829148.10_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/SRX3829148/SRX3829148.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3829148/SRX3829148.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3829148/SRX3829148.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。