Job ID = 2011686 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T17:31:56 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 ) 2019-07-05T17:32:05 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 : 19,043,234 reads read : 38,086,468 reads written : 38,086,468 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: 00:30:22 19043234 reads; of these: 19043234 (100.00%) were paired; of these: 3734782 (19.61%) aligned concordantly 0 times 12529927 (65.80%) aligned concordantly exactly 1 time 2778525 (14.59%) aligned concordantly >1 times ---- 3734782 pairs aligned concordantly 0 times; of these: 1898462 (50.83%) aligned discordantly 1 time ---- 1836320 pairs aligned 0 times concordantly or discordantly; of these: 3672640 mates make up the pairs; of these: 2484000 (67.64%) aligned 0 times 284332 (7.74%) aligned exactly 1 time 904308 (24.62%) aligned >1 times 93.48% overall alignment rate Time searching: 00:30:22 Overall time: 00:30:22 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 24 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] 617009 / 17088094 = 0.0361 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 03:29:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4560567/SRX4560567.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4560567/SRX4560567.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4560567/SRX4560567.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4560567/SRX4560567.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 03:29:04: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:29:04: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:29:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4560567/SRX4560567.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4560567/SRX4560567.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4560567/SRX4560567.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4560567/SRX4560567.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 03:29:05: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:29:05: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:29:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4560567/SRX4560567.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4560567/SRX4560567.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4560567/SRX4560567.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4560567/SRX4560567.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 03:29:06: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:29:06: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:29:13: 1000000 INFO @ Sat, 06 Jul 2019 03:29:14: 1000000 INFO @ Sat, 06 Jul 2019 03:29:16: 1000000 INFO @ Sat, 06 Jul 2019 03:29:22: 2000000 INFO @ Sat, 06 Jul 2019 03:29:24: 2000000 INFO @ Sat, 06 Jul 2019 03:29:26: 2000000 INFO @ Sat, 06 Jul 2019 03:29:32: 3000000 INFO @ Sat, 06 Jul 2019 03:29:33: 3000000 INFO @ Sat, 06 Jul 2019 03:29:35: 3000000 INFO @ Sat, 06 Jul 2019 03:29:41: 4000000 INFO @ Sat, 06 Jul 2019 03:29:42: 4000000 INFO @ Sat, 06 Jul 2019 03:29:45: 4000000 INFO @ Sat, 06 Jul 2019 03:29:50: 5000000 INFO @ Sat, 06 Jul 2019 03:29:51: 5000000 INFO @ Sat, 06 Jul 2019 03:29:54: 5000000 INFO @ Sat, 06 Jul 2019 03:29:59: 6000000 INFO @ Sat, 06 Jul 2019 03:30:01: 6000000 INFO @ Sat, 06 Jul 2019 03:30:03: 6000000 INFO @ Sat, 06 Jul 2019 03:30:09: 7000000 INFO @ Sat, 06 Jul 2019 03:30:10: 7000000 INFO @ Sat, 06 Jul 2019 03:30:13: 7000000 INFO @ Sat, 06 Jul 2019 03:30:18: 8000000 INFO @ Sat, 06 Jul 2019 03:30:19: 8000000 INFO @ Sat, 06 Jul 2019 03:30:22: 8000000 INFO @ Sat, 06 Jul 2019 03:30:27: 9000000 INFO @ Sat, 06 Jul 2019 03:30:29: 9000000 INFO @ Sat, 06 Jul 2019 03:30:31: 9000000 INFO @ Sat, 06 Jul 2019 03:30:36: 10000000 INFO @ Sat, 06 Jul 2019 03:30:38: 10000000 INFO @ Sat, 06 Jul 2019 03:30:41: 10000000 INFO @ Sat, 06 Jul 2019 03:30:46: 11000000 INFO @ Sat, 06 Jul 2019 03:30:47: 11000000 INFO @ Sat, 06 Jul 2019 03:30:50: 11000000 INFO @ Sat, 06 Jul 2019 03:30:55: 12000000 INFO @ Sat, 06 Jul 2019 03:30:56: 12000000 INFO @ Sat, 06 Jul 2019 03:30:59: 12000000 INFO @ Sat, 06 Jul 2019 03:31:04: 13000000 INFO @ Sat, 06 Jul 2019 03:31:06: 13000000 INFO @ Sat, 06 Jul 2019 03:31:08: 13000000 INFO @ Sat, 06 Jul 2019 03:31:13: 14000000 INFO @ Sat, 06 Jul 2019 03:31:15: 14000000 INFO @ Sat, 06 Jul 2019 03:31:18: 14000000 INFO @ Sat, 06 Jul 2019 03:31:23: 15000000 INFO @ Sat, 06 Jul 2019 03:31:24: 15000000 INFO @ Sat, 06 Jul 2019 03:31:27: 15000000 INFO @ Sat, 06 Jul 2019 03:31:32: 16000000 INFO @ Sat, 06 Jul 2019 03:31:33: 16000000 INFO @ Sat, 06 Jul 2019 03:31:37: 16000000 INFO @ Sat, 06 Jul 2019 03:31:41: 17000000 INFO @ Sat, 06 Jul 2019 03:31:43: 17000000 INFO @ Sat, 06 Jul 2019 03:31:46: 17000000 INFO @ Sat, 06 Jul 2019 03:31:50: 18000000 INFO @ Sat, 06 Jul 2019 03:31:52: 18000000 INFO @ Sat, 06 Jul 2019 03:31:55: 18000000 INFO @ Sat, 06 Jul 2019 03:31:59: 19000000 INFO @ Sat, 06 Jul 2019 03:32:01: 19000000 INFO @ Sat, 06 Jul 2019 03:32:05: 19000000 INFO @ Sat, 06 Jul 2019 03:32:09: 20000000 INFO @ Sat, 06 Jul 2019 03:32:10: 20000000 INFO @ Sat, 06 Jul 2019 03:32:14: 20000000 INFO @ Sat, 06 Jul 2019 03:32:18: 21000000 INFO @ Sat, 06 Jul 2019 03:32:19: 21000000 INFO @ Sat, 06 Jul 2019 03:32:23: 21000000 INFO @ Sat, 06 Jul 2019 03:32:27: 22000000 INFO @ Sat, 06 Jul 2019 03:32:29: 22000000 INFO @ Sat, 06 Jul 2019 03:32:32: 22000000 INFO @ Sat, 06 Jul 2019 03:32:36: 23000000 INFO @ Sat, 06 Jul 2019 03:32:38: 23000000 INFO @ Sat, 06 Jul 2019 03:32:42: 23000000 INFO @ Sat, 06 Jul 2019 03:32:45: 24000000 INFO @ Sat, 06 Jul 2019 03:32:47: 24000000 INFO @ Sat, 06 Jul 2019 03:32:51: 24000000 INFO @ Sat, 06 Jul 2019 03:32:54: 25000000 INFO @ Sat, 06 Jul 2019 03:32:56: 25000000 INFO @ Sat, 06 Jul 2019 03:33:00: 25000000 INFO @ Sat, 06 Jul 2019 03:33:04: 26000000 INFO @ Sat, 06 Jul 2019 03:33:05: 26000000 INFO @ Sat, 06 Jul 2019 03:33:10: 26000000 INFO @ Sat, 06 Jul 2019 03:33:13: 27000000 INFO @ Sat, 06 Jul 2019 03:33:15: 27000000 INFO @ Sat, 06 Jul 2019 03:33:19: 27000000 INFO @ Sat, 06 Jul 2019 03:33:22: 28000000 INFO @ Sat, 06 Jul 2019 03:33:24: 28000000 INFO @ Sat, 06 Jul 2019 03:33:28: 28000000 INFO @ Sat, 06 Jul 2019 03:33:31: 29000000 INFO @ Sat, 06 Jul 2019 03:33:33: 29000000 INFO @ Sat, 06 Jul 2019 03:33:37: 29000000 INFO @ Sat, 06 Jul 2019 03:33:40: 30000000 INFO @ Sat, 06 Jul 2019 03:33:42: 30000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 03:33:47: 30000000 INFO @ Sat, 06 Jul 2019 03:33:49: 31000000 INFO @ Sat, 06 Jul 2019 03:33:51: 31000000 INFO @ Sat, 06 Jul 2019 03:33:56: 31000000 INFO @ Sat, 06 Jul 2019 03:33:58: 32000000 INFO @ Sat, 06 Jul 2019 03:34:01: 32000000 INFO @ Sat, 06 Jul 2019 03:34:05: 32000000 INFO @ Sat, 06 Jul 2019 03:34:07: 33000000 BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 03:34:10: 33000000 INFO @ Sat, 06 Jul 2019 03:34:14: 33000000 INFO @ Sat, 06 Jul 2019 03:34:17: 34000000 INFO @ Sat, 06 Jul 2019 03:34:19: 34000000 INFO @ Sat, 06 Jul 2019 03:34:20: #1 tag size is determined as 126 bps INFO @ Sat, 06 Jul 2019 03:34:20: #1 tag size = 126 INFO @ Sat, 06 Jul 2019 03:34:20: #1 total tags in treatment: 14726559 INFO @ Sat, 06 Jul 2019 03:34:20: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:34:20: #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 03:34:20: #1 tags after filtering in treatment: 9917667 INFO @ Sat, 06 Jul 2019 03:34:20: #1 Redundant rate of treatment: 0.33 INFO @ Sat, 06 Jul 2019 03:34:20: #1 finished! INFO @ Sat, 06 Jul 2019 03:34:20: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:34:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:34:21: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:34:21: 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 03:34:21: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4560567/SRX4560567.05_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/SRX4560567/SRX4560567.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560567/SRX4560567.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560567/SRX4560567.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:34:22: #1 tag size is determined as 126 bps INFO @ Sat, 06 Jul 2019 03:34:22: #1 tag size = 126 INFO @ Sat, 06 Jul 2019 03:34:22: #1 total tags in treatment: 14726559 INFO @ Sat, 06 Jul 2019 03:34:22: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:34:22: #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 03:34:23: #1 tags after filtering in treatment: 9917667 INFO @ Sat, 06 Jul 2019 03:34:23: #1 Redundant rate of treatment: 0.33 INFO @ Sat, 06 Jul 2019 03:34:23: #1 finished! INFO @ Sat, 06 Jul 2019 03:34:23: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:34:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:34:23: 34000000 INFO @ Sat, 06 Jul 2019 03:34:24: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:34:24: 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 03:34:24: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4560567/SRX4560567.10_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/SRX4560567/SRX4560567.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560567/SRX4560567.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560567/SRX4560567.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:34:27: #1 tag size is determined as 126 bps INFO @ Sat, 06 Jul 2019 03:34:27: #1 tag size = 126 INFO @ Sat, 06 Jul 2019 03:34:27: #1 total tags in treatment: 14726559 INFO @ Sat, 06 Jul 2019 03:34:27: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:34:27: #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 03:34:27: #1 tags after filtering in treatment: 9917667 INFO @ Sat, 06 Jul 2019 03:34:27: #1 Redundant rate of treatment: 0.33 INFO @ Sat, 06 Jul 2019 03:34:27: #1 finished! INFO @ Sat, 06 Jul 2019 03:34:27: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:34:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:34:28: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:34:28: 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 03:34:28: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4560567/SRX4560567.20_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/SRX4560567/SRX4560567.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560567/SRX4560567.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560567/SRX4560567.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling