Job ID = 2011685 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T17:12:49 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 ) 2019-07-05T17:23:13 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 ) 2019-07-05T17:23:57 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 : 21,480,355 reads read : 42,960,710 reads written : 42,960,710 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: 00:37:07 21480355 reads; of these: 21480355 (100.00%) were paired; of these: 4135097 (19.25%) aligned concordantly 0 times 14718308 (68.52%) aligned concordantly exactly 1 time 2626950 (12.23%) aligned concordantly >1 times ---- 4135097 pairs aligned concordantly 0 times; of these: 2026056 (49.00%) aligned discordantly 1 time ---- 2109041 pairs aligned 0 times concordantly or discordantly; of these: 4218082 mates make up the pairs; of these: 3090228 (73.26%) aligned 0 times 337915 (8.01%) aligned exactly 1 time 789939 (18.73%) aligned >1 times 92.81% overall alignment rate Time searching: 00:37:07 Overall time: 00:37:07 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] 534827 / 19247209 = 0.0278 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 03:45:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4560566/SRX4560566.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4560566/SRX4560566.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4560566/SRX4560566.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4560566/SRX4560566.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 03:45:16: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:45:16: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:45:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4560566/SRX4560566.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4560566/SRX4560566.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4560566/SRX4560566.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4560566/SRX4560566.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 03:45:17: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:45:17: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:45:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4560566/SRX4560566.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4560566/SRX4560566.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4560566/SRX4560566.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4560566/SRX4560566.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 03:45:18: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:45:18: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:45:30: 1000000 INFO @ Sat, 06 Jul 2019 03:45:34: 1000000 INFO @ Sat, 06 Jul 2019 03:45:35: 1000000 INFO @ Sat, 06 Jul 2019 03:45:44: 2000000 INFO @ Sat, 06 Jul 2019 03:45:51: 2000000 INFO @ Sat, 06 Jul 2019 03:45:52: 2000000 INFO @ Sat, 06 Jul 2019 03:45:57: 3000000 INFO @ Sat, 06 Jul 2019 03:46:09: 3000000 INFO @ Sat, 06 Jul 2019 03:46:09: 3000000 INFO @ Sat, 06 Jul 2019 03:46:10: 4000000 INFO @ Sat, 06 Jul 2019 03:46:24: 5000000 INFO @ Sat, 06 Jul 2019 03:46:26: 4000000 INFO @ Sat, 06 Jul 2019 03:46:26: 4000000 INFO @ Sat, 06 Jul 2019 03:46:37: 6000000 INFO @ Sat, 06 Jul 2019 03:46:43: 5000000 INFO @ Sat, 06 Jul 2019 03:46:44: 5000000 INFO @ Sat, 06 Jul 2019 03:46:51: 7000000 INFO @ Sat, 06 Jul 2019 03:47:00: 6000000 INFO @ Sat, 06 Jul 2019 03:47:01: 6000000 INFO @ Sat, 06 Jul 2019 03:47:04: 8000000 INFO @ Sat, 06 Jul 2019 03:47:17: 9000000 INFO @ Sat, 06 Jul 2019 03:47:17: 7000000 INFO @ Sat, 06 Jul 2019 03:47:18: 7000000 INFO @ Sat, 06 Jul 2019 03:47:31: 10000000 INFO @ Sat, 06 Jul 2019 03:47:35: 8000000 INFO @ Sat, 06 Jul 2019 03:47:35: 8000000 INFO @ Sat, 06 Jul 2019 03:47:44: 11000000 INFO @ Sat, 06 Jul 2019 03:47:52: 9000000 INFO @ Sat, 06 Jul 2019 03:47:52: 9000000 INFO @ Sat, 06 Jul 2019 03:47:58: 12000000 INFO @ Sat, 06 Jul 2019 03:48:09: 10000000 INFO @ Sat, 06 Jul 2019 03:48:09: 10000000 INFO @ Sat, 06 Jul 2019 03:48:11: 13000000 INFO @ Sat, 06 Jul 2019 03:48:25: 14000000 INFO @ Sat, 06 Jul 2019 03:48:27: 11000000 INFO @ Sat, 06 Jul 2019 03:48:27: 11000000 INFO @ Sat, 06 Jul 2019 03:48:39: 15000000 INFO @ Sat, 06 Jul 2019 03:48:44: 12000000 INFO @ Sat, 06 Jul 2019 03:48:44: 12000000 INFO @ Sat, 06 Jul 2019 03:48:52: 16000000 INFO @ Sat, 06 Jul 2019 03:49:02: 13000000 INFO @ Sat, 06 Jul 2019 03:49:02: 13000000 INFO @ Sat, 06 Jul 2019 03:49:05: 17000000 INFO @ Sat, 06 Jul 2019 03:49:18: 18000000 INFO @ Sat, 06 Jul 2019 03:49:20: 14000000 INFO @ Sat, 06 Jul 2019 03:49:20: 14000000 INFO @ Sat, 06 Jul 2019 03:49:32: 19000000 INFO @ Sat, 06 Jul 2019 03:49:38: 15000000 INFO @ Sat, 06 Jul 2019 03:49:38: 15000000 INFO @ Sat, 06 Jul 2019 03:49:45: 20000000 INFO @ Sat, 06 Jul 2019 03:49:55: 16000000 INFO @ Sat, 06 Jul 2019 03:49:55: 16000000 INFO @ Sat, 06 Jul 2019 03:49:58: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 03:50:11: 22000000 INFO @ Sat, 06 Jul 2019 03:50:13: 17000000 INFO @ Sat, 06 Jul 2019 03:50:13: 17000000 INFO @ Sat, 06 Jul 2019 03:50:24: 23000000 INFO @ Sat, 06 Jul 2019 03:50:29: 18000000 BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 03:50:29: 18000000 INFO @ Sat, 06 Jul 2019 03:50:37: 24000000 INFO @ Sat, 06 Jul 2019 03:50:45: 19000000 INFO @ Sat, 06 Jul 2019 03:50:45: 19000000 INFO @ Sat, 06 Jul 2019 03:50:50: 25000000 INFO @ Sat, 06 Jul 2019 03:51:02: 20000000 INFO @ Sat, 06 Jul 2019 03:51:02: 20000000 INFO @ Sat, 06 Jul 2019 03:51:03: 26000000 INFO @ Sat, 06 Jul 2019 03:51:16: 27000000 INFO @ Sat, 06 Jul 2019 03:51:18: 21000000 INFO @ Sat, 06 Jul 2019 03:51:18: 21000000 INFO @ Sat, 06 Jul 2019 03:51:29: 28000000 INFO @ Sat, 06 Jul 2019 03:51:35: 22000000 INFO @ Sat, 06 Jul 2019 03:51:35: 22000000 INFO @ Sat, 06 Jul 2019 03:51:43: 29000000 INFO @ Sat, 06 Jul 2019 03:51:51: 23000000 INFO @ Sat, 06 Jul 2019 03:51:51: 23000000 INFO @ Sat, 06 Jul 2019 03:51:56: 30000000 INFO @ Sat, 06 Jul 2019 03:52:08: 24000000 INFO @ Sat, 06 Jul 2019 03:52:08: 24000000 INFO @ Sat, 06 Jul 2019 03:52:10: 31000000 INFO @ Sat, 06 Jul 2019 03:52:23: 32000000 INFO @ Sat, 06 Jul 2019 03:52:25: 25000000 INFO @ Sat, 06 Jul 2019 03:52:25: 25000000 INFO @ Sat, 06 Jul 2019 03:52:37: 33000000 INFO @ Sat, 06 Jul 2019 03:52:42: 26000000 INFO @ Sat, 06 Jul 2019 03:52:42: 26000000 INFO @ Sat, 06 Jul 2019 03:52:50: 34000000 INFO @ Sat, 06 Jul 2019 03:52:58: 27000000 INFO @ Sat, 06 Jul 2019 03:52:59: 27000000 INFO @ Sat, 06 Jul 2019 03:53:04: 35000000 INFO @ Sat, 06 Jul 2019 03:53:15: 28000000 INFO @ Sat, 06 Jul 2019 03:53:17: 28000000 INFO @ Sat, 06 Jul 2019 03:53:17: 36000000 INFO @ Sat, 06 Jul 2019 03:53:31: 37000000 INFO @ Sat, 06 Jul 2019 03:53:33: 29000000 INFO @ Sat, 06 Jul 2019 03:53:38: 29000000 INFO @ Sat, 06 Jul 2019 03:53:45: 38000000 INFO @ Sat, 06 Jul 2019 03:53:50: 30000000 INFO @ Sat, 06 Jul 2019 03:53:56: #1 tag size is determined as 126 bps INFO @ Sat, 06 Jul 2019 03:53:56: #1 tag size = 126 INFO @ Sat, 06 Jul 2019 03:53:56: #1 total tags in treatment: 16850177 INFO @ Sat, 06 Jul 2019 03:53:56: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:53:56: #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 03:53:56: #1 tags after filtering in treatment: 10941303 INFO @ Sat, 06 Jul 2019 03:53:56: #1 Redundant rate of treatment: 0.35 INFO @ Sat, 06 Jul 2019 03:53:56: #1 finished! INFO @ Sat, 06 Jul 2019 03:53:56: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:53:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:53:57: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:53:57: 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 03:53:57: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4560566/SRX4560566.05_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/SRX4560566/SRX4560566.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560566/SRX4560566.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560566/SRX4560566.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:53:58: 30000000 INFO @ Sat, 06 Jul 2019 03:54:07: 31000000 INFO @ Sat, 06 Jul 2019 03:54:18: 31000000 INFO @ Sat, 06 Jul 2019 03:54:24: 32000000 INFO @ Sat, 06 Jul 2019 03:54:38: 32000000 INFO @ Sat, 06 Jul 2019 03:54:41: 33000000 INFO @ Sat, 06 Jul 2019 03:54:58: 33000000 INFO @ Sat, 06 Jul 2019 03:54:58: 34000000 INFO @ Sat, 06 Jul 2019 03:55:15: 35000000 INFO @ Sat, 06 Jul 2019 03:55:18: 34000000 INFO @ Sat, 06 Jul 2019 03:55:32: 36000000 INFO @ Sat, 06 Jul 2019 03:55:38: 35000000 INFO @ Sat, 06 Jul 2019 03:55:49: 37000000 INFO @ Sat, 06 Jul 2019 03:55:58: 36000000 INFO @ Sat, 06 Jul 2019 03:56:05: 38000000 INFO @ Sat, 06 Jul 2019 03:56:18: 37000000 INFO @ Sat, 06 Jul 2019 03:56:18: #1 tag size is determined as 126 bps INFO @ Sat, 06 Jul 2019 03:56:18: #1 tag size = 126 INFO @ Sat, 06 Jul 2019 03:56:18: #1 total tags in treatment: 16850177 INFO @ Sat, 06 Jul 2019 03:56:18: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:56:18: #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 03:56:19: #1 tags after filtering in treatment: 10941303 INFO @ Sat, 06 Jul 2019 03:56:19: #1 Redundant rate of treatment: 0.35 INFO @ Sat, 06 Jul 2019 03:56:19: #1 finished! INFO @ Sat, 06 Jul 2019 03:56:19: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:56:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:56:20: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:56:20: 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 03:56:20: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4560566/SRX4560566.20_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/SRX4560566/SRX4560566.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560566/SRX4560566.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560566/SRX4560566.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:56:37: 38000000 INFO @ Sat, 06 Jul 2019 03:56:52: #1 tag size is determined as 126 bps INFO @ Sat, 06 Jul 2019 03:56:52: #1 tag size = 126 INFO @ Sat, 06 Jul 2019 03:56:52: #1 total tags in treatment: 16850177 INFO @ Sat, 06 Jul 2019 03:56:52: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:56:52: #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 03:56:53: #1 tags after filtering in treatment: 10941303 INFO @ Sat, 06 Jul 2019 03:56:53: #1 Redundant rate of treatment: 0.35 INFO @ Sat, 06 Jul 2019 03:56:53: #1 finished! INFO @ Sat, 06 Jul 2019 03:56:53: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:56:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:56:54: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:56:54: 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 03:56:54: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4560566/SRX4560566.10_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/SRX4560566/SRX4560566.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560566/SRX4560566.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560566/SRX4560566.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling