Job ID = 2011860 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 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 ) 2019-07-05T17:55:12 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 ) 2019-07-05T17:55:12 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 ) 2019-07-05T17:55:12 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 ) spots read : 26,185,258 reads read : 52,370,516 reads written : 52,370,516 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: 00:20:08 26185258 reads; of these: 26185258 (100.00%) were paired; of these: 2308134 (8.81%) aligned concordantly 0 times 19696469 (75.22%) aligned concordantly exactly 1 time 4180655 (15.97%) aligned concordantly >1 times ---- 2308134 pairs aligned concordantly 0 times; of these: 898168 (38.91%) aligned discordantly 1 time ---- 1409966 pairs aligned 0 times concordantly or discordantly; of these: 2819932 mates make up the pairs; of these: 1431386 (50.76%) aligned 0 times 793148 (28.13%) aligned exactly 1 time 595398 (21.11%) aligned >1 times 97.27% overall alignment rate Time searching: 00:20:08 Overall time: 00:20:08 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] 1480794 / 23973077 = 0.0618 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 03:43:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5170657/SRX5170657.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5170657/SRX5170657.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5170657/SRX5170657.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5170657/SRX5170657.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 03:43:05: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:43:05: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:43:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5170657/SRX5170657.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5170657/SRX5170657.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5170657/SRX5170657.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5170657/SRX5170657.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 03:43:06: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:43:06: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:43:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5170657/SRX5170657.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5170657/SRX5170657.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5170657/SRX5170657.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5170657/SRX5170657.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 03:43:06: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:43:06: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:43:13: 1000000 INFO @ Sat, 06 Jul 2019 03:43:15: 1000000 INFO @ Sat, 06 Jul 2019 03:43:17: 1000000 INFO @ Sat, 06 Jul 2019 03:43:20: 2000000 INFO @ Sat, 06 Jul 2019 03:43:25: 2000000 INFO @ Sat, 06 Jul 2019 03:43:27: 2000000 INFO @ Sat, 06 Jul 2019 03:43:28: 3000000 INFO @ Sat, 06 Jul 2019 03:43:35: 4000000 INFO @ Sat, 06 Jul 2019 03:43:36: 3000000 INFO @ Sat, 06 Jul 2019 03:43:38: 3000000 INFO @ Sat, 06 Jul 2019 03:43:42: 5000000 INFO @ Sat, 06 Jul 2019 03:43:46: 4000000 INFO @ Sat, 06 Jul 2019 03:43:48: 4000000 INFO @ Sat, 06 Jul 2019 03:43:49: 6000000 INFO @ Sat, 06 Jul 2019 03:43:56: 5000000 INFO @ Sat, 06 Jul 2019 03:43:57: 7000000 INFO @ Sat, 06 Jul 2019 03:43:58: 5000000 INFO @ Sat, 06 Jul 2019 03:44:04: 8000000 INFO @ Sat, 06 Jul 2019 03:44:06: 6000000 INFO @ Sat, 06 Jul 2019 03:44:08: 6000000 INFO @ Sat, 06 Jul 2019 03:44:11: 9000000 INFO @ Sat, 06 Jul 2019 03:44:16: 7000000 INFO @ Sat, 06 Jul 2019 03:44:18: 10000000 INFO @ Sat, 06 Jul 2019 03:44:18: 7000000 INFO @ Sat, 06 Jul 2019 03:44:26: 8000000 INFO @ Sat, 06 Jul 2019 03:44:26: 11000000 INFO @ Sat, 06 Jul 2019 03:44:29: 8000000 INFO @ Sat, 06 Jul 2019 03:44:34: 12000000 INFO @ Sat, 06 Jul 2019 03:44:36: 9000000 INFO @ Sat, 06 Jul 2019 03:44:39: 9000000 INFO @ Sat, 06 Jul 2019 03:44:42: 13000000 INFO @ Sat, 06 Jul 2019 03:44:45: 10000000 INFO @ Sat, 06 Jul 2019 03:44:49: 10000000 INFO @ Sat, 06 Jul 2019 03:44:50: 14000000 INFO @ Sat, 06 Jul 2019 03:44:54: 11000000 INFO @ Sat, 06 Jul 2019 03:44:57: 15000000 INFO @ Sat, 06 Jul 2019 03:44:59: 11000000 INFO @ Sat, 06 Jul 2019 03:45:01: 12000000 INFO @ Sat, 06 Jul 2019 03:45:05: 16000000 INFO @ Sat, 06 Jul 2019 03:45:08: 13000000 INFO @ Sat, 06 Jul 2019 03:45:09: 12000000 INFO @ Sat, 06 Jul 2019 03:45:12: 17000000 INFO @ Sat, 06 Jul 2019 03:45:16: 14000000 INFO @ Sat, 06 Jul 2019 03:45:19: 18000000 INFO @ Sat, 06 Jul 2019 03:45:20: 13000000 INFO @ Sat, 06 Jul 2019 03:45:25: 15000000 INFO @ Sat, 06 Jul 2019 03:45:26: 19000000 INFO @ Sat, 06 Jul 2019 03:45:30: 14000000 INFO @ Sat, 06 Jul 2019 03:45:33: 16000000 INFO @ Sat, 06 Jul 2019 03:45:33: 20000000 INFO @ Sat, 06 Jul 2019 03:45:40: 15000000 INFO @ Sat, 06 Jul 2019 03:45:40: 21000000 INFO @ Sat, 06 Jul 2019 03:45:41: 17000000 INFO @ Sat, 06 Jul 2019 03:45:47: 22000000 INFO @ Sat, 06 Jul 2019 03:45:49: 18000000 INFO @ Sat, 06 Jul 2019 03:45:50: 16000000 INFO @ Sat, 06 Jul 2019 03:45:55: 23000000 INFO @ Sat, 06 Jul 2019 03:45:57: 19000000 INFO @ Sat, 06 Jul 2019 03:46:00: 17000000 INFO @ Sat, 06 Jul 2019 03:46:02: 24000000 INFO @ Sat, 06 Jul 2019 03:46:05: 20000000 INFO @ Sat, 06 Jul 2019 03:46:09: 25000000 INFO @ Sat, 06 Jul 2019 03:46:10: 18000000 INFO @ Sat, 06 Jul 2019 03:46:14: 21000000 INFO @ Sat, 06 Jul 2019 03:46:16: 26000000 INFO @ Sat, 06 Jul 2019 03:46:20: 19000000 INFO @ Sat, 06 Jul 2019 03:46:22: 22000000 INFO @ Sat, 06 Jul 2019 03:46:23: 27000000 INFO @ Sat, 06 Jul 2019 03:46:30: 23000000 INFO @ Sat, 06 Jul 2019 03:46:30: 28000000 INFO @ Sat, 06 Jul 2019 03:46:30: 20000000 INFO @ Sat, 06 Jul 2019 03:46:37: 29000000 INFO @ Sat, 06 Jul 2019 03:46:38: 24000000 INFO @ Sat, 06 Jul 2019 03:46:41: 21000000 INFO @ Sat, 06 Jul 2019 03:46:44: 30000000 INFO @ Sat, 06 Jul 2019 03:46:46: 25000000 INFO @ Sat, 06 Jul 2019 03:46:51: 22000000 INFO @ Sat, 06 Jul 2019 03:46:52: 31000000 INFO @ Sat, 06 Jul 2019 03:46:54: 26000000 INFO @ Sat, 06 Jul 2019 03:46:59: 32000000 INFO @ Sat, 06 Jul 2019 03:47:01: 23000000 INFO @ Sat, 06 Jul 2019 03:47:02: 27000000 INFO @ Sat, 06 Jul 2019 03:47:06: 33000000 INFO @ Sat, 06 Jul 2019 03:47:11: 28000000 INFO @ Sat, 06 Jul 2019 03:47:11: 24000000 INFO @ Sat, 06 Jul 2019 03:47:13: 34000000 INFO @ Sat, 06 Jul 2019 03:47:19: 29000000 INFO @ Sat, 06 Jul 2019 03:47:20: 35000000 INFO @ Sat, 06 Jul 2019 03:47:21: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 03:47:27: 36000000 INFO @ Sat, 06 Jul 2019 03:47:27: 30000000 INFO @ Sat, 06 Jul 2019 03:47:31: 26000000 INFO @ Sat, 06 Jul 2019 03:47:34: 37000000 INFO @ Sat, 06 Jul 2019 03:47:35: 31000000 INFO @ Sat, 06 Jul 2019 03:47:41: 27000000 INFO @ Sat, 06 Jul 2019 03:47:41: 38000000 INFO @ Sat, 06 Jul 2019 03:47:43: 32000000 INFO @ Sat, 06 Jul 2019 03:47:48: 39000000 INFO @ Sat, 06 Jul 2019 03:47:51: 33000000 INFO @ Sat, 06 Jul 2019 03:47:51: 28000000 INFO @ Sat, 06 Jul 2019 03:47:55: 40000000 INFO @ Sat, 06 Jul 2019 03:47:59: 34000000 INFO @ Sat, 06 Jul 2019 03:48:02: 29000000 INFO @ Sat, 06 Jul 2019 03:48:03: 41000000 INFO @ Sat, 06 Jul 2019 03:48:07: 35000000 INFO @ Sat, 06 Jul 2019 03:48:10: 42000000 INFO @ Sat, 06 Jul 2019 03:48:12: 30000000 BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 03:48:16: 36000000 INFO @ Sat, 06 Jul 2019 03:48:17: 43000000 INFO @ Sat, 06 Jul 2019 03:48:22: 31000000 INFO @ Sat, 06 Jul 2019 03:48:24: 37000000 INFO @ Sat, 06 Jul 2019 03:48:24: 44000000 INFO @ Sat, 06 Jul 2019 03:48:31: 45000000 INFO @ Sat, 06 Jul 2019 03:48:32: 38000000 INFO @ Sat, 06 Jul 2019 03:48:33: 32000000 INFO @ Sat, 06 Jul 2019 03:48:38: 46000000 INFO @ Sat, 06 Jul 2019 03:48:40: 39000000 INFO @ Sat, 06 Jul 2019 03:48:43: 33000000 INFO @ Sat, 06 Jul 2019 03:48:46: 47000000 INFO @ Sat, 06 Jul 2019 03:48:48: 40000000 INFO @ Sat, 06 Jul 2019 03:48:53: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 03:48:53: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 03:48:53: #1 total tags in treatment: 22397654 INFO @ Sat, 06 Jul 2019 03:48:53: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:48:53: #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 03:48:53: 34000000 INFO @ Sat, 06 Jul 2019 03:48:53: #1 tags after filtering in treatment: 12998838 INFO @ Sat, 06 Jul 2019 03:48:53: #1 Redundant rate of treatment: 0.42 INFO @ Sat, 06 Jul 2019 03:48:53: #1 finished! INFO @ Sat, 06 Jul 2019 03:48:53: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:48:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:48:54: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:48:54: 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 03:48:54: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 03:48:57: 41000000 INFO @ Sat, 06 Jul 2019 03:49:03: 35000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX5170657/SRX5170657.10_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/SRX5170657/SRX5170657.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5170657/SRX5170657.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5170657/SRX5170657.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:49:05: 42000000 INFO @ Sat, 06 Jul 2019 03:49:13: 43000000 INFO @ Sat, 06 Jul 2019 03:49:13: 36000000 INFO @ Sat, 06 Jul 2019 03:49:21: 44000000 INFO @ Sat, 06 Jul 2019 03:49:23: 37000000 INFO @ Sat, 06 Jul 2019 03:49:29: 45000000 INFO @ Sat, 06 Jul 2019 03:49:33: 38000000 INFO @ Sat, 06 Jul 2019 03:49:37: 46000000 INFO @ Sat, 06 Jul 2019 03:49:44: 39000000 INFO @ Sat, 06 Jul 2019 03:49:45: 47000000 INFO @ Sat, 06 Jul 2019 03:49:54: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 03:49:54: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 03:49:54: #1 total tags in treatment: 22397654 INFO @ Sat, 06 Jul 2019 03:49:54: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:49:54: #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 03:49:54: 40000000 INFO @ Sat, 06 Jul 2019 03:49:54: #1 tags after filtering in treatment: 12998838 INFO @ Sat, 06 Jul 2019 03:49:54: #1 Redundant rate of treatment: 0.42 INFO @ Sat, 06 Jul 2019 03:49:54: #1 finished! INFO @ Sat, 06 Jul 2019 03:49:54: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:49:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:49:55: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:49:55: 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 03:49:55: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 03:50:03: 41000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX5170657/SRX5170657.05_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/SRX5170657/SRX5170657.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5170657/SRX5170657.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5170657/SRX5170657.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:50:12: 42000000 INFO @ Sat, 06 Jul 2019 03:50:22: 43000000 INFO @ Sat, 06 Jul 2019 03:50:32: 44000000 INFO @ Sat, 06 Jul 2019 03:50:41: 45000000 INFO @ Sat, 06 Jul 2019 03:50:51: 46000000 INFO @ Sat, 06 Jul 2019 03:51:00: 47000000 INFO @ Sat, 06 Jul 2019 03:51:10: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 03:51:10: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 03:51:10: #1 total tags in treatment: 22397654 INFO @ Sat, 06 Jul 2019 03:51:10: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:51:10: #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 03:51:10: #1 tags after filtering in treatment: 12998838 INFO @ Sat, 06 Jul 2019 03:51:10: #1 Redundant rate of treatment: 0.42 INFO @ Sat, 06 Jul 2019 03:51:10: #1 finished! INFO @ Sat, 06 Jul 2019 03:51:10: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:51:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:51:11: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:51:11: 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 03:51:11: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5170657/SRX5170657.20_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/SRX5170657/SRX5170657.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5170657/SRX5170657.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5170657/SRX5170657.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling