Job ID = 2010719 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T15:04:35 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 ) 2019-07-05T15:10:43 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 ) 2019-07-05T15:10:43 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 ) 2019-07-05T15:13:06 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 : 11,174,860 reads read : 22,349,720 reads written : 22,349,720 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: 00:10:31 11174860 reads; of these: 11174860 (100.00%) were paired; of these: 1628706 (14.57%) aligned concordantly 0 times 8273434 (74.04%) aligned concordantly exactly 1 time 1272720 (11.39%) aligned concordantly >1 times ---- 1628706 pairs aligned concordantly 0 times; of these: 124472 (7.64%) aligned discordantly 1 time ---- 1504234 pairs aligned 0 times concordantly or discordantly; of these: 3008468 mates make up the pairs; of these: 2559885 (85.09%) aligned 0 times 323645 (10.76%) aligned exactly 1 time 124938 (4.15%) aligned >1 times 88.55% overall alignment rate Time searching: 00:10:31 Overall time: 00:10:31 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] 188719 / 9645079 = 0.0196 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 00:46:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386902/SRX386902.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386902/SRX386902.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386902/SRX386902.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386902/SRX386902.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 00:46:27: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:46:27: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:46:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386902/SRX386902.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386902/SRX386902.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386902/SRX386902.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386902/SRX386902.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 00:46:28: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:46:28: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:46:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386902/SRX386902.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386902/SRX386902.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386902/SRX386902.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386902/SRX386902.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 00:46:29: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:46:29: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:46:37: 1000000 INFO @ Sat, 06 Jul 2019 00:46:38: 1000000 INFO @ Sat, 06 Jul 2019 00:46:39: 1000000 INFO @ Sat, 06 Jul 2019 00:46:46: 2000000 INFO @ Sat, 06 Jul 2019 00:46:47: 2000000 INFO @ Sat, 06 Jul 2019 00:46:50: 2000000 INFO @ Sat, 06 Jul 2019 00:46:55: 3000000 INFO @ Sat, 06 Jul 2019 00:46:57: 3000000 INFO @ Sat, 06 Jul 2019 00:47:00: 3000000 INFO @ Sat, 06 Jul 2019 00:47:03: 4000000 INFO @ Sat, 06 Jul 2019 00:47:07: 4000000 INFO @ Sat, 06 Jul 2019 00:47:11: 4000000 INFO @ Sat, 06 Jul 2019 00:47:11: 5000000 INFO @ Sat, 06 Jul 2019 00:47:16: 5000000 INFO @ Sat, 06 Jul 2019 00:47:20: 6000000 INFO @ Sat, 06 Jul 2019 00:47:22: 5000000 INFO @ Sat, 06 Jul 2019 00:47:26: 6000000 INFO @ Sat, 06 Jul 2019 00:47:28: 7000000 INFO @ Sat, 06 Jul 2019 00:47:33: 6000000 INFO @ Sat, 06 Jul 2019 00:47:35: 7000000 INFO @ Sat, 06 Jul 2019 00:47:37: 8000000 INFO @ Sat, 06 Jul 2019 00:47:44: 7000000 INFO @ Sat, 06 Jul 2019 00:47:45: 9000000 INFO @ Sat, 06 Jul 2019 00:47:45: 8000000 INFO @ Sat, 06 Jul 2019 00:47:53: 10000000 INFO @ Sat, 06 Jul 2019 00:47:55: 8000000 INFO @ Sat, 06 Jul 2019 00:47:56: 9000000 INFO @ Sat, 06 Jul 2019 00:48:01: 11000000 INFO @ Sat, 06 Jul 2019 00:48:06: 10000000 INFO @ Sat, 06 Jul 2019 00:48:06: 9000000 INFO @ Sat, 06 Jul 2019 00:48:09: 12000000 INFO @ Sat, 06 Jul 2019 00:48:17: 11000000 INFO @ Sat, 06 Jul 2019 00:48:17: 10000000 INFO @ Sat, 06 Jul 2019 00:48:17: 13000000 INFO @ Sat, 06 Jul 2019 00:48:26: 14000000 INFO @ Sat, 06 Jul 2019 00:48:27: 12000000 INFO @ Sat, 06 Jul 2019 00:48:28: 11000000 INFO @ Sat, 06 Jul 2019 00:48:34: 15000000 INFO @ Sat, 06 Jul 2019 00:48:38: 13000000 INFO @ Sat, 06 Jul 2019 00:48:39: 12000000 INFO @ Sat, 06 Jul 2019 00:48:42: 16000000 INFO @ Sat, 06 Jul 2019 00:48:48: 14000000 INFO @ Sat, 06 Jul 2019 00:48:50: 17000000 INFO @ Sat, 06 Jul 2019 00:48:51: 13000000 INFO @ Sat, 06 Jul 2019 00:48:59: 18000000 INFO @ Sat, 06 Jul 2019 00:48:59: 15000000 INFO @ Sat, 06 Jul 2019 00:49:01: 14000000 INFO @ Sat, 06 Jul 2019 00:49:07: 19000000 INFO @ Sat, 06 Jul 2019 00:49:09: 16000000 INFO @ Sat, 06 Jul 2019 00:49:10: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 00:49:10: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 00:49:10: #1 total tags in treatment: 9358290 INFO @ Sat, 06 Jul 2019 00:49:10: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:49:10: #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 00:49:10: #1 tags after filtering in treatment: 7103778 INFO @ Sat, 06 Jul 2019 00:49:10: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 06 Jul 2019 00:49:10: #1 finished! INFO @ Sat, 06 Jul 2019 00:49:10: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:49:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:49:11: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:49:11: 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 00:49:11: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 00:49:12: 15000000 INFO @ Sat, 06 Jul 2019 00:49:19: 17000000 INFO @ Sat, 06 Jul 2019 00:49:22: 16000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX386902/SRX386902.20_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/SRX386902/SRX386902.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386902/SRX386902.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386902/SRX386902.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 00:49:30: 18000000 INFO @ Sat, 06 Jul 2019 00:49:32: 17000000 INFO @ Sat, 06 Jul 2019 00:49:40: 19000000 INFO @ Sat, 06 Jul 2019 00:49:42: 18000000 INFO @ Sat, 06 Jul 2019 00:49:44: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 00:49:44: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 00:49:44: #1 total tags in treatment: 9358290 INFO @ Sat, 06 Jul 2019 00:49:44: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:49:44: #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 00:49:44: #1 tags after filtering in treatment: 7103778 INFO @ Sat, 06 Jul 2019 00:49:44: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 06 Jul 2019 00:49:44: #1 finished! INFO @ Sat, 06 Jul 2019 00:49:44: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:49:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:49:45: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:49:45: 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 @ Sat, 06 Jul 2019 00:49:45: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX386902/SRX386902.05_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/SRX386902/SRX386902.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386902/SRX386902.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386902/SRX386902.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 00:49:52: 19000000 INFO @ Sat, 06 Jul 2019 00:49:56: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 00:49:56: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 00:49:56: #1 total tags in treatment: 9358290 INFO @ Sat, 06 Jul 2019 00:49:56: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:49:56: #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 00:49:57: #1 tags after filtering in treatment: 7103778 INFO @ Sat, 06 Jul 2019 00:49:57: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 06 Jul 2019 00:49:57: #1 finished! INFO @ Sat, 06 Jul 2019 00:49:57: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:49:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:49:57: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:49:57: 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 00:49:57: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX386902/SRX386902.10_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/SRX386902/SRX386902.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386902/SRX386902.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386902/SRX386902.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling