Job ID = 2011683 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T17:17:05 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 : 22,877,541 reads read : 45,755,082 reads written : 45,755,082 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: 00:34:10 22877541 reads; of these: 22877541 (100.00%) were paired; of these: 4687953 (20.49%) aligned concordantly 0 times 15023796 (65.67%) aligned concordantly exactly 1 time 3165792 (13.84%) aligned concordantly >1 times ---- 4687953 pairs aligned concordantly 0 times; of these: 2244326 (47.87%) aligned discordantly 1 time ---- 2443627 pairs aligned 0 times concordantly or discordantly; of these: 4887254 mates make up the pairs; of these: 3502476 (71.67%) aligned 0 times 372763 (7.63%) aligned exactly 1 time 1012015 (20.71%) aligned >1 times 92.35% overall alignment rate Time searching: 00:34:10 Overall time: 00:34:10 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 28 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] 808335 / 20288879 = 0.0398 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 03:47:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4560564/SRX4560564.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4560564/SRX4560564.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4560564/SRX4560564.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4560564/SRX4560564.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 03:47:46: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:47:46: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:47:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4560564/SRX4560564.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4560564/SRX4560564.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4560564/SRX4560564.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4560564/SRX4560564.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 03:47:47: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:47:47: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:47:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4560564/SRX4560564.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4560564/SRX4560564.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4560564/SRX4560564.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4560564/SRX4560564.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 03:47:55: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:47:55: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:47:57: 1000000 INFO @ Sat, 06 Jul 2019 03:48:00: 1000000 INFO @ Sat, 06 Jul 2019 03:48:05: 1000000 INFO @ Sat, 06 Jul 2019 03:48:07: 2000000 INFO @ Sat, 06 Jul 2019 03:48:14: 2000000 INFO @ Sat, 06 Jul 2019 03:48:14: 2000000 INFO @ Sat, 06 Jul 2019 03:48:18: 3000000 INFO @ Sat, 06 Jul 2019 03:48:24: 3000000 INFO @ Sat, 06 Jul 2019 03:48:27: 3000000 INFO @ Sat, 06 Jul 2019 03:48:29: 4000000 INFO @ Sat, 06 Jul 2019 03:48:33: 4000000 INFO @ Sat, 06 Jul 2019 03:48:40: 5000000 INFO @ Sat, 06 Jul 2019 03:48:40: 4000000 INFO @ Sat, 06 Jul 2019 03:48:43: 5000000 INFO @ Sat, 06 Jul 2019 03:48:50: 6000000 INFO @ Sat, 06 Jul 2019 03:48:52: 6000000 INFO @ Sat, 06 Jul 2019 03:48:53: 5000000 INFO @ Sat, 06 Jul 2019 03:49:01: 7000000 INFO @ Sat, 06 Jul 2019 03:49:02: 7000000 INFO @ Sat, 06 Jul 2019 03:49:05: 6000000 INFO @ Sat, 06 Jul 2019 03:49:11: 8000000 INFO @ Sat, 06 Jul 2019 03:49:12: 8000000 INFO @ Sat, 06 Jul 2019 03:49:18: 7000000 INFO @ Sat, 06 Jul 2019 03:49:20: 9000000 INFO @ Sat, 06 Jul 2019 03:49:23: 9000000 INFO @ Sat, 06 Jul 2019 03:49:30: 10000000 INFO @ Sat, 06 Jul 2019 03:49:30: 8000000 INFO @ Sat, 06 Jul 2019 03:49:33: 10000000 INFO @ Sat, 06 Jul 2019 03:49:39: 11000000 INFO @ Sat, 06 Jul 2019 03:49:42: 9000000 INFO @ Sat, 06 Jul 2019 03:49:44: 11000000 INFO @ Sat, 06 Jul 2019 03:49:48: 12000000 INFO @ Sat, 06 Jul 2019 03:49:55: 12000000 INFO @ Sat, 06 Jul 2019 03:49:55: 10000000 INFO @ Sat, 06 Jul 2019 03:49:57: 13000000 INFO @ Sat, 06 Jul 2019 03:50:05: 13000000 INFO @ Sat, 06 Jul 2019 03:50:07: 14000000 INFO @ Sat, 06 Jul 2019 03:50:09: 11000000 INFO @ Sat, 06 Jul 2019 03:50:16: 15000000 INFO @ Sat, 06 Jul 2019 03:50:16: 14000000 INFO @ Sat, 06 Jul 2019 03:50:22: 12000000 INFO @ Sat, 06 Jul 2019 03:50:25: 16000000 INFO @ Sat, 06 Jul 2019 03:50:26: 15000000 INFO @ Sat, 06 Jul 2019 03:50:34: 17000000 INFO @ Sat, 06 Jul 2019 03:50:35: 13000000 INFO @ Sat, 06 Jul 2019 03:50:37: 16000000 INFO @ Sat, 06 Jul 2019 03:50:44: 18000000 INFO @ Sat, 06 Jul 2019 03:50:48: 17000000 INFO @ Sat, 06 Jul 2019 03:50:48: 14000000 INFO @ Sat, 06 Jul 2019 03:50:53: 19000000 INFO @ Sat, 06 Jul 2019 03:50:58: 18000000 INFO @ Sat, 06 Jul 2019 03:51:02: 15000000 INFO @ Sat, 06 Jul 2019 03:51:02: 20000000 INFO @ Sat, 06 Jul 2019 03:51:09: 19000000 INFO @ Sat, 06 Jul 2019 03:51:11: 21000000 INFO @ Sat, 06 Jul 2019 03:51:15: 16000000 INFO @ Sat, 06 Jul 2019 03:51:19: 20000000 INFO @ Sat, 06 Jul 2019 03:51:21: 22000000 INFO @ Sat, 06 Jul 2019 03:51:28: 17000000 INFO @ Sat, 06 Jul 2019 03:51:30: 21000000 INFO @ Sat, 06 Jul 2019 03:51:30: 23000000 INFO @ Sat, 06 Jul 2019 03:51:40: 18000000 INFO @ Sat, 06 Jul 2019 03:51:40: 22000000 INFO @ Sat, 06 Jul 2019 03:51:41: 24000000 INFO @ Sat, 06 Jul 2019 03:51:51: 25000000 INFO @ Sat, 06 Jul 2019 03:51:51: 23000000 INFO @ Sat, 06 Jul 2019 03:51:53: 19000000 INFO @ Sat, 06 Jul 2019 03:52:00: 26000000 INFO @ Sat, 06 Jul 2019 03:52:02: 24000000 INFO @ Sat, 06 Jul 2019 03:52:05: 20000000 INFO @ Sat, 06 Jul 2019 03:52:11: 27000000 INFO @ Sat, 06 Jul 2019 03:52:13: 25000000 INFO @ Sat, 06 Jul 2019 03:52:17: 21000000 INFO @ Sat, 06 Jul 2019 03:52:20: 28000000 INFO @ Sat, 06 Jul 2019 03:52:23: 26000000 INFO @ Sat, 06 Jul 2019 03:52:30: 22000000 INFO @ Sat, 06 Jul 2019 03:52:31: 29000000 INFO @ Sat, 06 Jul 2019 03:52:34: 27000000 INFO @ Sat, 06 Jul 2019 03:52:41: 30000000 INFO @ Sat, 06 Jul 2019 03:52:42: 23000000 INFO @ Sat, 06 Jul 2019 03:52:44: 28000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 03:52:51: 31000000 INFO @ Sat, 06 Jul 2019 03:52:54: 24000000 INFO @ Sat, 06 Jul 2019 03:52:55: 29000000 INFO @ Sat, 06 Jul 2019 03:53:01: 32000000 INFO @ Sat, 06 Jul 2019 03:53:06: 30000000 INFO @ Sat, 06 Jul 2019 03:53:07: 25000000 INFO @ Sat, 06 Jul 2019 03:53:10: 33000000 BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 03:53:16: 31000000 INFO @ Sat, 06 Jul 2019 03:53:19: 26000000 INFO @ Sat, 06 Jul 2019 03:53:20: 34000000 INFO @ Sat, 06 Jul 2019 03:53:27: 32000000 INFO @ Sat, 06 Jul 2019 03:53:29: 35000000 INFO @ Sat, 06 Jul 2019 03:53:32: 27000000 INFO @ Sat, 06 Jul 2019 03:53:38: 33000000 INFO @ Sat, 06 Jul 2019 03:53:38: 36000000 INFO @ Sat, 06 Jul 2019 03:53:44: 28000000 INFO @ Sat, 06 Jul 2019 03:53:47: 37000000 INFO @ Sat, 06 Jul 2019 03:53:48: 34000000 INFO @ Sat, 06 Jul 2019 03:53:56: 29000000 INFO @ Sat, 06 Jul 2019 03:53:57: 38000000 INFO @ Sat, 06 Jul 2019 03:53:59: 35000000 INFO @ Sat, 06 Jul 2019 03:54:06: 39000000 INFO @ Sat, 06 Jul 2019 03:54:09: 30000000 INFO @ Sat, 06 Jul 2019 03:54:09: 36000000 INFO @ Sat, 06 Jul 2019 03:54:17: 40000000 INFO @ Sat, 06 Jul 2019 03:54:20: 37000000 INFO @ Sat, 06 Jul 2019 03:54:21: 31000000 INFO @ Sat, 06 Jul 2019 03:54:23: #1 tag size is determined as 126 bps INFO @ Sat, 06 Jul 2019 03:54:23: #1 tag size = 126 INFO @ Sat, 06 Jul 2019 03:54:23: #1 total tags in treatment: 17435681 INFO @ Sat, 06 Jul 2019 03:54:23: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:54:23: #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 03:54:23: #1 tags after filtering in treatment: 11178479 INFO @ Sat, 06 Jul 2019 03:54:23: #1 Redundant rate of treatment: 0.36 INFO @ Sat, 06 Jul 2019 03:54:23: #1 finished! INFO @ Sat, 06 Jul 2019 03:54:23: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:54:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:54:24: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:54:24: 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 03:54:24: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4560564/SRX4560564.20_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/SRX4560564/SRX4560564.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560564/SRX4560564.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560564/SRX4560564.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:54:30: 38000000 INFO @ Sat, 06 Jul 2019 03:54:33: 32000000 INFO @ Sat, 06 Jul 2019 03:54:41: 39000000 INFO @ Sat, 06 Jul 2019 03:54:46: 33000000 INFO @ Sat, 06 Jul 2019 03:54:51: 40000000 INFO @ Sat, 06 Jul 2019 03:54:58: 34000000 INFO @ Sat, 06 Jul 2019 03:54:58: #1 tag size is determined as 126 bps INFO @ Sat, 06 Jul 2019 03:54:58: #1 tag size = 126 INFO @ Sat, 06 Jul 2019 03:54:58: #1 total tags in treatment: 17435681 INFO @ Sat, 06 Jul 2019 03:54:58: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:54:58: #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 03:54:58: #1 tags after filtering in treatment: 11178479 INFO @ Sat, 06 Jul 2019 03:54:58: #1 Redundant rate of treatment: 0.36 INFO @ Sat, 06 Jul 2019 03:54:58: #1 finished! INFO @ Sat, 06 Jul 2019 03:54:58: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:54:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:54:59: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:54:59: 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 03:54:59: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 03:55:10: 35000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX4560564/SRX4560564.05_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/SRX4560564/SRX4560564.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560564/SRX4560564.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560564/SRX4560564.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:55:21: 36000000 INFO @ Sat, 06 Jul 2019 03:55:33: 37000000 INFO @ Sat, 06 Jul 2019 03:55:45: 38000000 INFO @ Sat, 06 Jul 2019 03:55:57: 39000000 INFO @ Sat, 06 Jul 2019 03:56:09: 40000000 INFO @ Sat, 06 Jul 2019 03:56:16: #1 tag size is determined as 126 bps INFO @ Sat, 06 Jul 2019 03:56:16: #1 tag size = 126 INFO @ Sat, 06 Jul 2019 03:56:16: #1 total tags in treatment: 17435681 INFO @ Sat, 06 Jul 2019 03:56:16: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:56:16: #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 03:56:17: #1 tags after filtering in treatment: 11178479 INFO @ Sat, 06 Jul 2019 03:56:17: #1 Redundant rate of treatment: 0.36 INFO @ Sat, 06 Jul 2019 03:56:17: #1 finished! INFO @ Sat, 06 Jul 2019 03:56:17: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:56:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:56:18: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:56:18: 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 03:56:18: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4560564/SRX4560564.10_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/SRX4560564/SRX4560564.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560564/SRX4560564.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560564/SRX4560564.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling