Job ID = 2010718 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 ) 2019-07-05T15:04:35 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 ) 2019-07-05T15:04:35 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 ) 2019-07-05T15:06:07 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 ) 2019-07-05T15:11:49 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 ) 2019-07-05T15:13:06 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 : 12,615,137 reads read : 25,230,274 reads written : 25,230,274 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: 00:12:04 12615137 reads; of these: 12615137 (100.00%) were paired; of these: 1860411 (14.75%) aligned concordantly 0 times 9341717 (74.05%) aligned concordantly exactly 1 time 1413009 (11.20%) aligned concordantly >1 times ---- 1860411 pairs aligned concordantly 0 times; of these: 141990 (7.63%) aligned discordantly 1 time ---- 1718421 pairs aligned 0 times concordantly or discordantly; of these: 3436842 mates make up the pairs; of these: 2928958 (85.22%) aligned 0 times 370517 (10.78%) aligned exactly 1 time 137367 (4.00%) aligned >1 times 88.39% overall alignment rate Time searching: 00:12:04 Overall time: 00:12:04 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] 230623 / 10868072 = 0.0212 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 00:47:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386901/SRX386901.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386901/SRX386901.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386901/SRX386901.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386901/SRX386901.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 00:47:17: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:47:17: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:47:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386901/SRX386901.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386901/SRX386901.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386901/SRX386901.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386901/SRX386901.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 00:47:18: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:47:18: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:47:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386901/SRX386901.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386901/SRX386901.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386901/SRX386901.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386901/SRX386901.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 00:47:19: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:47:19: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:47:29: 1000000 INFO @ Sat, 06 Jul 2019 00:47:32: 1000000 INFO @ Sat, 06 Jul 2019 00:47:32: 1000000 INFO @ Sat, 06 Jul 2019 00:47:40: 2000000 INFO @ Sat, 06 Jul 2019 00:47:43: 2000000 INFO @ Sat, 06 Jul 2019 00:47:45: 2000000 INFO @ Sat, 06 Jul 2019 00:47:51: 3000000 INFO @ Sat, 06 Jul 2019 00:47:55: 3000000 INFO @ Sat, 06 Jul 2019 00:47:58: 3000000 INFO @ Sat, 06 Jul 2019 00:48:03: 4000000 INFO @ Sat, 06 Jul 2019 00:48:07: 4000000 INFO @ Sat, 06 Jul 2019 00:48:12: 4000000 INFO @ Sat, 06 Jul 2019 00:48:14: 5000000 INFO @ Sat, 06 Jul 2019 00:48:18: 5000000 INFO @ Sat, 06 Jul 2019 00:48:24: 6000000 INFO @ Sat, 06 Jul 2019 00:48:25: 5000000 INFO @ Sat, 06 Jul 2019 00:48:30: 6000000 INFO @ Sat, 06 Jul 2019 00:48:36: 7000000 INFO @ Sat, 06 Jul 2019 00:48:38: 6000000 INFO @ Sat, 06 Jul 2019 00:48:41: 7000000 INFO @ Sat, 06 Jul 2019 00:48:47: 8000000 INFO @ Sat, 06 Jul 2019 00:48:51: 7000000 INFO @ Sat, 06 Jul 2019 00:48:53: 8000000 INFO @ Sat, 06 Jul 2019 00:49:01: 9000000 INFO @ Sat, 06 Jul 2019 00:49:04: 9000000 INFO @ Sat, 06 Jul 2019 00:49:07: 8000000 INFO @ Sat, 06 Jul 2019 00:49:14: 10000000 INFO @ Sat, 06 Jul 2019 00:49:15: 10000000 INFO @ Sat, 06 Jul 2019 00:49:20: 9000000 INFO @ Sat, 06 Jul 2019 00:49:23: 11000000 INFO @ Sat, 06 Jul 2019 00:49:26: 11000000 INFO @ Sat, 06 Jul 2019 00:49:33: 12000000 INFO @ Sat, 06 Jul 2019 00:49:33: 10000000 INFO @ Sat, 06 Jul 2019 00:49:38: 12000000 INFO @ Sat, 06 Jul 2019 00:49:44: 13000000 INFO @ Sat, 06 Jul 2019 00:49:46: 11000000 INFO @ Sat, 06 Jul 2019 00:49:49: 13000000 INFO @ Sat, 06 Jul 2019 00:49:55: 14000000 INFO @ Sat, 06 Jul 2019 00:49:59: 14000000 INFO @ Sat, 06 Jul 2019 00:50:00: 12000000 INFO @ Sat, 06 Jul 2019 00:50:06: 15000000 INFO @ Sat, 06 Jul 2019 00:50:10: 15000000 INFO @ Sat, 06 Jul 2019 00:50:13: 13000000 INFO @ Sat, 06 Jul 2019 00:50:17: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 00:50:20: 16000000 INFO @ Sat, 06 Jul 2019 00:50:27: 14000000 INFO @ Sat, 06 Jul 2019 00:50:27: 17000000 INFO @ Sat, 06 Jul 2019 00:50:30: 17000000 INFO @ Sat, 06 Jul 2019 00:50:39: 18000000 INFO @ Sat, 06 Jul 2019 00:50:41: 15000000 INFO @ Sat, 06 Jul 2019 00:50:42: 18000000 BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 00:50:50: 19000000 INFO @ Sat, 06 Jul 2019 00:50:53: 19000000 INFO @ Sat, 06 Jul 2019 00:50:54: 16000000 INFO @ Sat, 06 Jul 2019 00:51:01: 20000000 INFO @ Sat, 06 Jul 2019 00:51:04: 20000000 INFO @ Sat, 06 Jul 2019 00:51:07: 17000000 INFO @ Sat, 06 Jul 2019 00:51:12: 21000000 INFO @ Sat, 06 Jul 2019 00:51:15: 21000000 INFO @ Sat, 06 Jul 2019 00:51:21: 18000000 INFO @ Sat, 06 Jul 2019 00:51:22: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 00:51:22: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 00:51:22: #1 total tags in treatment: 10525215 INFO @ Sat, 06 Jul 2019 00:51:22: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:51:22: #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 00:51:22: #1 tags after filtering in treatment: 7808280 INFO @ Sat, 06 Jul 2019 00:51:22: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 06 Jul 2019 00:51:22: #1 finished! INFO @ Sat, 06 Jul 2019 00:51:22: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:51:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:51:22: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:51:22: 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 00:51:22: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX386901/SRX386901.05_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/SRX386901/SRX386901.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386901/SRX386901.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386901/SRX386901.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:51:24: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 00:51:24: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 00:51:24: #1 total tags in treatment: 10525215 INFO @ Sat, 06 Jul 2019 00:51:24: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:51:24: #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 00:51:25: #1 tags after filtering in treatment: 7808280 INFO @ Sat, 06 Jul 2019 00:51:25: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 06 Jul 2019 00:51:25: #1 finished! INFO @ Sat, 06 Jul 2019 00:51:25: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:51:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:51:25: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:51:25: 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 00:51:25: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX386901/SRX386901.20_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/SRX386901/SRX386901.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386901/SRX386901.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386901/SRX386901.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:51:34: 19000000 INFO @ Sat, 06 Jul 2019 00:51:47: 20000000 INFO @ Sat, 06 Jul 2019 00:52:00: 21000000 INFO @ Sat, 06 Jul 2019 00:52:11: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 00:52:11: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 00:52:11: #1 total tags in treatment: 10525215 INFO @ Sat, 06 Jul 2019 00:52:11: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:52:11: #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 00:52:11: #1 tags after filtering in treatment: 7808280 INFO @ Sat, 06 Jul 2019 00:52:11: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 06 Jul 2019 00:52:11: #1 finished! INFO @ Sat, 06 Jul 2019 00:52:11: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:52:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:52:12: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:52:12: 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 00:52:12: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX386901/SRX386901.10_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/SRX386901/SRX386901.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386901/SRX386901.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386901/SRX386901.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling