Job ID = 2010707 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T15:06:44 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 ) 2019-07-05T15:06:44 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 ) 2019-07-05T15:06:44 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 : 9,450,327 reads read : 18,900,654 reads written : 18,900,654 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: 00:08:32 9450327 reads; of these: 9450327 (100.00%) were paired; of these: 1237354 (13.09%) aligned concordantly 0 times 7593792 (80.35%) aligned concordantly exactly 1 time 619181 (6.55%) aligned concordantly >1 times ---- 1237354 pairs aligned concordantly 0 times; of these: 146784 (11.86%) aligned discordantly 1 time ---- 1090570 pairs aligned 0 times concordantly or discordantly; of these: 2181140 mates make up the pairs; of these: 1877947 (86.10%) aligned 0 times 225627 (10.34%) aligned exactly 1 time 77566 (3.56%) aligned >1 times 90.06% overall alignment rate Time searching: 00:08:32 Overall time: 00:08:32 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 8 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] 84736 / 8328178 = 0.0102 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 00:31:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386888/SRX386888.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386888/SRX386888.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386888/SRX386888.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386888/SRX386888.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 00:31:44: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:31:44: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:31:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386888/SRX386888.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386888/SRX386888.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386888/SRX386888.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386888/SRX386888.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 00:31:45: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:31:45: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:31:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386888/SRX386888.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386888/SRX386888.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386888/SRX386888.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386888/SRX386888.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 00:31:46: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:31:46: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:31:53: 1000000 INFO @ Sat, 06 Jul 2019 00:31:54: 1000000 INFO @ Sat, 06 Jul 2019 00:31:56: 1000000 INFO @ Sat, 06 Jul 2019 00:32:02: 2000000 INFO @ Sat, 06 Jul 2019 00:32:03: 2000000 INFO @ Sat, 06 Jul 2019 00:32:06: 2000000 INFO @ Sat, 06 Jul 2019 00:32:10: 3000000 INFO @ Sat, 06 Jul 2019 00:32:11: 3000000 INFO @ Sat, 06 Jul 2019 00:32:17: 3000000 INFO @ Sat, 06 Jul 2019 00:32:18: 4000000 INFO @ Sat, 06 Jul 2019 00:32:20: 4000000 INFO @ Sat, 06 Jul 2019 00:32:27: 4000000 INFO @ Sat, 06 Jul 2019 00:32:27: 5000000 INFO @ Sat, 06 Jul 2019 00:32:28: 5000000 INFO @ Sat, 06 Jul 2019 00:32:35: 6000000 INFO @ Sat, 06 Jul 2019 00:32:37: 5000000 INFO @ Sat, 06 Jul 2019 00:32:37: 6000000 INFO @ Sat, 06 Jul 2019 00:32:43: 7000000 INFO @ Sat, 06 Jul 2019 00:32:45: 7000000 INFO @ Sat, 06 Jul 2019 00:32:47: 6000000 INFO @ Sat, 06 Jul 2019 00:32:51: 8000000 INFO @ Sat, 06 Jul 2019 00:32:54: 8000000 INFO @ Sat, 06 Jul 2019 00:32:57: 7000000 INFO @ Sat, 06 Jul 2019 00:32:59: 9000000 INFO @ Sat, 06 Jul 2019 00:33:04: 9000000 INFO @ Sat, 06 Jul 2019 00:33:06: 10000000 INFO @ Sat, 06 Jul 2019 00:33:08: 8000000 INFO @ Sat, 06 Jul 2019 00:33:14: 11000000 INFO @ Sat, 06 Jul 2019 00:33:16: 10000000 INFO @ Sat, 06 Jul 2019 00:33:18: 9000000 INFO @ Sat, 06 Jul 2019 00:33:21: 12000000 INFO @ Sat, 06 Jul 2019 00:33:26: 11000000 INFO @ Sat, 06 Jul 2019 00:33:28: 10000000 INFO @ Sat, 06 Jul 2019 00:33:29: 13000000 INFO @ Sat, 06 Jul 2019 00:33:37: 12000000 INFO @ Sat, 06 Jul 2019 00:33:37: 14000000 INFO @ Sat, 06 Jul 2019 00:33:39: 11000000 INFO @ Sat, 06 Jul 2019 00:33:45: 15000000 INFO @ Sat, 06 Jul 2019 00:33:47: 13000000 INFO @ Sat, 06 Jul 2019 00:33:49: 12000000 INFO @ Sat, 06 Jul 2019 00:33:52: 16000000 INFO @ Sat, 06 Jul 2019 00:33:57: 14000000 INFO @ Sat, 06 Jul 2019 00:33:59: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 00:33:59: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 00:33:59: #1 total tags in treatment: 8129127 INFO @ Sat, 06 Jul 2019 00:33:59: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:33:59: #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 00:33:59: 13000000 INFO @ Sat, 06 Jul 2019 00:33:59: #1 tags after filtering in treatment: 6249814 INFO @ Sat, 06 Jul 2019 00:33:59: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 06 Jul 2019 00:33:59: #1 finished! INFO @ Sat, 06 Jul 2019 00:33:59: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:33:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:33:59: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:33:59: 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 00:33:59: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX386888/SRX386888.05_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/SRX386888/SRX386888.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386888/SRX386888.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386888/SRX386888.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:34:05: 15000000 INFO @ Sat, 06 Jul 2019 00:34:08: 14000000 INFO @ Sat, 06 Jul 2019 00:34:13: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 00:34:18: 15000000 INFO @ Sat, 06 Jul 2019 00:34:21: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 00:34:21: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 00:34:21: #1 total tags in treatment: 8129127 INFO @ Sat, 06 Jul 2019 00:34:21: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:34:21: #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 00:34:21: #1 tags after filtering in treatment: 6249814 INFO @ Sat, 06 Jul 2019 00:34:21: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 06 Jul 2019 00:34:21: #1 finished! INFO @ Sat, 06 Jul 2019 00:34:21: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:34:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:34:21: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:34:21: 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 00:34:21: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX386888/SRX386888.10_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/SRX386888/SRX386888.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386888/SRX386888.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386888/SRX386888.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:34:28: 16000000 BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 00:34:36: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 00:34:36: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 00:34:36: #1 total tags in treatment: 8129127 INFO @ Sat, 06 Jul 2019 00:34:36: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:34:36: #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 00:34:36: #1 tags after filtering in treatment: 6249814 INFO @ Sat, 06 Jul 2019 00:34:36: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 06 Jul 2019 00:34:36: #1 finished! INFO @ Sat, 06 Jul 2019 00:34:36: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:34:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:34:37: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:34:37: 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 00:34:37: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX386888/SRX386888.20_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/SRX386888/SRX386888.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386888/SRX386888.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386888/SRX386888.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling