Job ID = 2008117 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T08:31:44 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-07-05T08:35:35 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 ) 2019-07-05T08:35:35 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 ) 2019-07-05T08:41:36 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 : 14,952,093 reads read : 29,904,186 reads written : 29,904,186 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: 00:12:09 14952093 reads; of these: 14952093 (100.00%) were paired; of these: 592444 (3.96%) aligned concordantly 0 times 11702780 (78.27%) aligned concordantly exactly 1 time 2656869 (17.77%) aligned concordantly >1 times ---- 592444 pairs aligned concordantly 0 times; of these: 17029 (2.87%) aligned discordantly 1 time ---- 575415 pairs aligned 0 times concordantly or discordantly; of these: 1150830 mates make up the pairs; of these: 1111582 (96.59%) aligned 0 times 22369 (1.94%) aligned exactly 1 time 16879 (1.47%) aligned >1 times 96.28% overall alignment rate Time searching: 00:12:09 Overall time: 00:12:09 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] 837305 / 14362023 = 0.0583 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 @ Fri, 05 Jul 2019 18:09:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX516009/ERX516009.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX516009/ERX516009.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX516009/ERX516009.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX516009/ERX516009.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 @ Fri, 05 Jul 2019 18:09:13: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:09:13: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:09:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX516009/ERX516009.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX516009/ERX516009.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX516009/ERX516009.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX516009/ERX516009.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 @ Fri, 05 Jul 2019 18:09:14: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:09:14: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:09:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX516009/ERX516009.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX516009/ERX516009.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX516009/ERX516009.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX516009/ERX516009.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 @ Fri, 05 Jul 2019 18:09:15: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:09:15: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:09:21: 1000000 INFO @ Fri, 05 Jul 2019 18:09:23: 1000000 INFO @ Fri, 05 Jul 2019 18:09:24: 1000000 INFO @ Fri, 05 Jul 2019 18:09:29: 2000000 INFO @ Fri, 05 Jul 2019 18:09:32: 2000000 INFO @ Fri, 05 Jul 2019 18:09:32: 2000000 INFO @ Fri, 05 Jul 2019 18:09:36: 3000000 INFO @ Fri, 05 Jul 2019 18:09:41: 3000000 INFO @ Fri, 05 Jul 2019 18:09:42: 3000000 INFO @ Fri, 05 Jul 2019 18:09:43: 4000000 INFO @ Fri, 05 Jul 2019 18:09:49: 4000000 INFO @ Fri, 05 Jul 2019 18:09:50: 5000000 INFO @ Fri, 05 Jul 2019 18:09:51: 4000000 INFO @ Fri, 05 Jul 2019 18:09:57: 6000000 INFO @ Fri, 05 Jul 2019 18:09:57: 5000000 INFO @ Fri, 05 Jul 2019 18:10:00: 5000000 INFO @ Fri, 05 Jul 2019 18:10:04: 7000000 INFO @ Fri, 05 Jul 2019 18:10:05: 6000000 INFO @ Fri, 05 Jul 2019 18:10:09: 6000000 INFO @ Fri, 05 Jul 2019 18:10:11: 8000000 INFO @ Fri, 05 Jul 2019 18:10:13: 7000000 INFO @ Fri, 05 Jul 2019 18:10:18: 9000000 INFO @ Fri, 05 Jul 2019 18:10:18: 7000000 INFO @ Fri, 05 Jul 2019 18:10:21: 8000000 INFO @ Fri, 05 Jul 2019 18:10:25: 10000000 INFO @ Fri, 05 Jul 2019 18:10:28: 8000000 INFO @ Fri, 05 Jul 2019 18:10:29: 9000000 INFO @ Fri, 05 Jul 2019 18:10:33: 11000000 INFO @ Fri, 05 Jul 2019 18:10:37: 9000000 INFO @ Fri, 05 Jul 2019 18:10:37: 10000000 INFO @ Fri, 05 Jul 2019 18:10:40: 12000000 INFO @ Fri, 05 Jul 2019 18:10:45: 11000000 INFO @ Fri, 05 Jul 2019 18:10:46: 10000000 INFO @ Fri, 05 Jul 2019 18:10:46: 13000000 INFO @ Fri, 05 Jul 2019 18:10:53: 14000000 INFO @ Fri, 05 Jul 2019 18:10:53: 12000000 INFO @ Fri, 05 Jul 2019 18:10:55: 11000000 INFO @ Fri, 05 Jul 2019 18:11:00: 15000000 INFO @ Fri, 05 Jul 2019 18:11:02: 13000000 INFO @ Fri, 05 Jul 2019 18:11:04: 12000000 INFO @ Fri, 05 Jul 2019 18:11:07: 16000000 INFO @ Fri, 05 Jul 2019 18:11:10: 14000000 INFO @ Fri, 05 Jul 2019 18:11:13: 13000000 INFO @ Fri, 05 Jul 2019 18:11:14: 17000000 INFO @ Fri, 05 Jul 2019 18:11:18: 15000000 INFO @ Fri, 05 Jul 2019 18:11:21: 18000000 INFO @ Fri, 05 Jul 2019 18:11:23: 14000000 INFO @ Fri, 05 Jul 2019 18:11:26: 16000000 INFO @ Fri, 05 Jul 2019 18:11:29: 19000000 INFO @ Fri, 05 Jul 2019 18:11:32: 15000000 INFO @ Fri, 05 Jul 2019 18:11:34: 17000000 INFO @ Fri, 05 Jul 2019 18:11:36: 20000000 INFO @ Fri, 05 Jul 2019 18:11:41: 16000000 INFO @ Fri, 05 Jul 2019 18:11:42: 18000000 INFO @ Fri, 05 Jul 2019 18:11:43: 21000000 INFO @ Fri, 05 Jul 2019 18:11:50: 22000000 INFO @ Fri, 05 Jul 2019 18:11:50: 17000000 INFO @ Fri, 05 Jul 2019 18:11:50: 19000000 INFO @ Fri, 05 Jul 2019 18:11:57: 23000000 INFO @ Fri, 05 Jul 2019 18:11:58: 20000000 INFO @ Fri, 05 Jul 2019 18:11:59: 18000000 INFO @ Fri, 05 Jul 2019 18:12:04: 24000000 INFO @ Fri, 05 Jul 2019 18:12:06: 21000000 INFO @ Fri, 05 Jul 2019 18:12:08: 19000000 INFO @ Fri, 05 Jul 2019 18:12:11: 25000000 INFO @ Fri, 05 Jul 2019 18:12:15: 22000000 INFO @ Fri, 05 Jul 2019 18:12:17: 20000000 INFO @ Fri, 05 Jul 2019 18:12:18: 26000000 INFO @ Fri, 05 Jul 2019 18:12:23: 23000000 INFO @ Fri, 05 Jul 2019 18:12:25: 27000000 INFO @ Fri, 05 Jul 2019 18:12:26: 21000000 INFO @ Fri, 05 Jul 2019 18:12:26: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 18:12:26: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 18:12:26: #1 total tags in treatment: 13522380 INFO @ Fri, 05 Jul 2019 18:12:26: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:12:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 18:12:27: #1 tags after filtering in treatment: 9190181 INFO @ Fri, 05 Jul 2019 18:12:27: #1 Redundant rate of treatment: 0.32 INFO @ Fri, 05 Jul 2019 18:12:27: #1 finished! INFO @ Fri, 05 Jul 2019 18:12:27: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:12:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:12:27: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 18:12:27: 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 @ Fri, 05 Jul 2019 18:12:27: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX516009/ERX516009.10_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/ERX516009/ERX516009.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX516009/ERX516009.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX516009/ERX516009.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 18:12:31: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 18:12:35: 22000000 INFO @ Fri, 05 Jul 2019 18:12:39: 25000000 INFO @ Fri, 05 Jul 2019 18:12:44: 23000000 INFO @ Fri, 05 Jul 2019 18:12:47: 26000000 INFO @ Fri, 05 Jul 2019 18:12:53: 24000000 BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 18:12:55: 27000000 INFO @ Fri, 05 Jul 2019 18:12:56: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 18:12:56: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 18:12:56: #1 total tags in treatment: 13522380 INFO @ Fri, 05 Jul 2019 18:12:56: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:12:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 18:12:56: #1 tags after filtering in treatment: 9190181 INFO @ Fri, 05 Jul 2019 18:12:56: #1 Redundant rate of treatment: 0.32 INFO @ Fri, 05 Jul 2019 18:12:56: #1 finished! INFO @ Fri, 05 Jul 2019 18:12:56: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:12:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:12:57: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 18:12:57: 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 @ Fri, 05 Jul 2019 18:12:57: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX516009/ERX516009.20_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/ERX516009/ERX516009.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX516009/ERX516009.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX516009/ERX516009.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 18:13:01: 25000000 INFO @ Fri, 05 Jul 2019 18:13:10: 26000000 INFO @ Fri, 05 Jul 2019 18:13:18: 27000000 INFO @ Fri, 05 Jul 2019 18:13:19: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 18:13:19: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 18:13:19: #1 total tags in treatment: 13522380 INFO @ Fri, 05 Jul 2019 18:13:19: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:13:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 18:13:19: #1 tags after filtering in treatment: 9190181 INFO @ Fri, 05 Jul 2019 18:13:19: #1 Redundant rate of treatment: 0.32 INFO @ Fri, 05 Jul 2019 18:13:19: #1 finished! INFO @ Fri, 05 Jul 2019 18:13:19: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:13:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:13:20: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 18:13:20: 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 @ Fri, 05 Jul 2019 18:13:20: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX516009/ERX516009.05_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/ERX516009/ERX516009.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX516009/ERX516009.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX516009/ERX516009.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling