Job ID = 2011829 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T17:50:10 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 ) 2019-07-05T17:50:10 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 ) 2019-07-05T17:53:37 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 ) 2019-07-05T17:55:12 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 ) 2019-07-05T17:56:07 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 : 11,704,841 reads read : 23,409,682 reads written : 23,409,682 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: 00:11:37 11704841 reads; of these: 11704841 (100.00%) were paired; of these: 542936 (4.64%) aligned concordantly 0 times 6989616 (59.72%) aligned concordantly exactly 1 time 4172289 (35.65%) aligned concordantly >1 times ---- 542936 pairs aligned concordantly 0 times; of these: 5405 (1.00%) aligned discordantly 1 time ---- 537531 pairs aligned 0 times concordantly or discordantly; of these: 1075062 mates make up the pairs; of these: 859440 (79.94%) aligned 0 times 127407 (11.85%) aligned exactly 1 time 88215 (8.21%) aligned >1 times 96.33% overall alignment rate Time searching: 00:11:37 Overall time: 00:11:37 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 12 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] 3429124 / 11164496 = 0.3071 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 03:17:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5126587/SRX5126587.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5126587/SRX5126587.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5126587/SRX5126587.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5126587/SRX5126587.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 03:17:36: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:17:36: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:17:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5126587/SRX5126587.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5126587/SRX5126587.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5126587/SRX5126587.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5126587/SRX5126587.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 03:17:37: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:17:37: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:17:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5126587/SRX5126587.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5126587/SRX5126587.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5126587/SRX5126587.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5126587/SRX5126587.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 03:17:38: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:17:38: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:17:44: 1000000 INFO @ Sat, 06 Jul 2019 03:17:45: 1000000 INFO @ Sat, 06 Jul 2019 03:17:47: 1000000 INFO @ Sat, 06 Jul 2019 03:17:50: 2000000 INFO @ Sat, 06 Jul 2019 03:17:54: 2000000 INFO @ Sat, 06 Jul 2019 03:17:56: 2000000 INFO @ Sat, 06 Jul 2019 03:17:57: 3000000 INFO @ Sat, 06 Jul 2019 03:18:03: 3000000 INFO @ Sat, 06 Jul 2019 03:18:04: 4000000 INFO @ Sat, 06 Jul 2019 03:18:04: 3000000 INFO @ Sat, 06 Jul 2019 03:18:11: 5000000 INFO @ Sat, 06 Jul 2019 03:18:11: 4000000 INFO @ Sat, 06 Jul 2019 03:18:12: 4000000 INFO @ Sat, 06 Jul 2019 03:18:18: 6000000 INFO @ Sat, 06 Jul 2019 03:18:21: 5000000 INFO @ Sat, 06 Jul 2019 03:18:21: 5000000 INFO @ Sat, 06 Jul 2019 03:18:24: 7000000 INFO @ Sat, 06 Jul 2019 03:18:29: 6000000 INFO @ Sat, 06 Jul 2019 03:18:30: 6000000 INFO @ Sat, 06 Jul 2019 03:18:31: 8000000 INFO @ Sat, 06 Jul 2019 03:18:36: 7000000 INFO @ Sat, 06 Jul 2019 03:18:37: 9000000 INFO @ Sat, 06 Jul 2019 03:18:39: 7000000 INFO @ Sat, 06 Jul 2019 03:18:44: 10000000 INFO @ Sat, 06 Jul 2019 03:18:44: 8000000 INFO @ Sat, 06 Jul 2019 03:18:48: 8000000 INFO @ Sat, 06 Jul 2019 03:18:50: 11000000 INFO @ Sat, 06 Jul 2019 03:18:52: 9000000 INFO @ Sat, 06 Jul 2019 03:18:56: 9000000 INFO @ Sat, 06 Jul 2019 03:18:56: 12000000 INFO @ Sat, 06 Jul 2019 03:18:59: 10000000 INFO @ Sat, 06 Jul 2019 03:19:03: 13000000 INFO @ Sat, 06 Jul 2019 03:19:05: 10000000 INFO @ Sat, 06 Jul 2019 03:19:07: 11000000 INFO @ Sat, 06 Jul 2019 03:19:09: 14000000 INFO @ Sat, 06 Jul 2019 03:19:13: 11000000 INFO @ Sat, 06 Jul 2019 03:19:14: 12000000 INFO @ Sat, 06 Jul 2019 03:19:16: 15000000 INFO @ Sat, 06 Jul 2019 03:19:20: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 03:19:20: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 03:19:20: #1 total tags in treatment: 7733271 INFO @ Sat, 06 Jul 2019 03:19:20: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:19:20: #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 03:19:20: #1 tags after filtering in treatment: 4985066 INFO @ Sat, 06 Jul 2019 03:19:20: #1 Redundant rate of treatment: 0.36 INFO @ Sat, 06 Jul 2019 03:19:20: #1 finished! INFO @ Sat, 06 Jul 2019 03:19:20: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:19:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:19:21: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:19:21: 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 03:19:21: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5126587/SRX5126587.10_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/SRX5126587/SRX5126587.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126587/SRX5126587.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126587/SRX5126587.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:19:21: 13000000 INFO @ Sat, 06 Jul 2019 03:19:22: 12000000 INFO @ Sat, 06 Jul 2019 03:19:29: 14000000 INFO @ Sat, 06 Jul 2019 03:19:30: 13000000 INFO @ Sat, 06 Jul 2019 03:19:36: 15000000 INFO @ Sat, 06 Jul 2019 03:19:39: 14000000 INFO @ Sat, 06 Jul 2019 03:19:42: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 03:19:42: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 03:19:42: #1 total tags in treatment: 7733271 INFO @ Sat, 06 Jul 2019 03:19:42: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:19:42: #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 03:19:42: #1 tags after filtering in treatment: 4985066 INFO @ Sat, 06 Jul 2019 03:19:42: #1 Redundant rate of treatment: 0.36 INFO @ Sat, 06 Jul 2019 03:19:42: #1 finished! INFO @ Sat, 06 Jul 2019 03:19:42: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:19:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:19:42: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:19:42: 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 03:19:42: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5126587/SRX5126587.20_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/SRX5126587/SRX5126587.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126587/SRX5126587.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126587/SRX5126587.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:19:47: 15000000 INFO @ Sat, 06 Jul 2019 03:19:53: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 03:19:53: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 03:19:53: #1 total tags in treatment: 7733271 INFO @ Sat, 06 Jul 2019 03:19:53: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:19:53: #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 03:19:53: #1 tags after filtering in treatment: 4985066 INFO @ Sat, 06 Jul 2019 03:19:53: #1 Redundant rate of treatment: 0.36 INFO @ Sat, 06 Jul 2019 03:19:53: #1 finished! INFO @ Sat, 06 Jul 2019 03:19:53: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:19:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:19:53: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:19:53: 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 @ Sat, 06 Jul 2019 03:19:53: Process for pairing-model is terminated! BedGraph に変換しました。 cut: /home/okishinya/chipatlas/results/sacCer3/SRX5126587/SRX5126587.05_peaks.narrowPeak: No such file or directory BigWig に変換中... pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126587/SRX5126587.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126587/SRX5126587.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126587/SRX5126587.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。