Job ID = 2010584 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T14:22:53 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 ) 2019-07-05T14:24:30 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 ) 2019-07-05T14:24:30 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 ) 2019-07-05T14:26:05 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 ) 2019-07-05T14:26:05 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 ) 2019-07-05T14:27:57 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 ) 2019-07-05T14:30:21 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 ) 2019-07-05T14:32:27 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 ) 2019-07-05T14:38:32 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 : 17,972,910 reads read : 35,945,820 reads written : 35,945,820 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: 00:15:16 17972910 reads; of these: 17972910 (100.00%) were paired; of these: 1921050 (10.69%) aligned concordantly 0 times 13250883 (73.73%) aligned concordantly exactly 1 time 2800977 (15.58%) aligned concordantly >1 times ---- 1921050 pairs aligned concordantly 0 times; of these: 234274 (12.20%) aligned discordantly 1 time ---- 1686776 pairs aligned 0 times concordantly or discordantly; of these: 3373552 mates make up the pairs; of these: 3104451 (92.02%) aligned 0 times 120074 (3.56%) aligned exactly 1 time 149027 (4.42%) aligned >1 times 91.36% overall alignment rate Time searching: 00:15:16 Overall time: 00:15:16 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 16 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] 2874099 / 16269555 = 0.1767 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 00:08:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381285/SRX381285.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381285/SRX381285.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381285/SRX381285.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381285/SRX381285.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 00:08:08: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:08:08: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:08:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381285/SRX381285.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381285/SRX381285.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381285/SRX381285.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381285/SRX381285.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 00:08:09: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:08:09: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:08:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381285/SRX381285.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381285/SRX381285.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381285/SRX381285.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381285/SRX381285.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 00:08:10: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:08:10: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:08:16: 1000000 INFO @ Sat, 06 Jul 2019 00:08:17: 1000000 INFO @ Sat, 06 Jul 2019 00:08:17: 1000000 INFO @ Sat, 06 Jul 2019 00:08:24: 2000000 INFO @ Sat, 06 Jul 2019 00:08:25: 2000000 INFO @ Sat, 06 Jul 2019 00:08:26: 2000000 INFO @ Sat, 06 Jul 2019 00:08:32: 3000000 INFO @ Sat, 06 Jul 2019 00:08:33: 3000000 INFO @ Sat, 06 Jul 2019 00:08:34: 3000000 INFO @ Sat, 06 Jul 2019 00:08:39: 4000000 INFO @ Sat, 06 Jul 2019 00:08:41: 4000000 INFO @ Sat, 06 Jul 2019 00:08:42: 4000000 INFO @ Sat, 06 Jul 2019 00:08:46: 5000000 INFO @ Sat, 06 Jul 2019 00:08:49: 5000000 INFO @ Sat, 06 Jul 2019 00:08:50: 5000000 INFO @ Sat, 06 Jul 2019 00:08:53: 6000000 INFO @ Sat, 06 Jul 2019 00:08:57: 6000000 INFO @ Sat, 06 Jul 2019 00:08:59: 6000000 INFO @ Sat, 06 Jul 2019 00:09:01: 7000000 INFO @ Sat, 06 Jul 2019 00:09:05: 7000000 INFO @ Sat, 06 Jul 2019 00:09:07: 7000000 INFO @ Sat, 06 Jul 2019 00:09:08: 8000000 INFO @ Sat, 06 Jul 2019 00:09:14: 8000000 INFO @ Sat, 06 Jul 2019 00:09:15: 9000000 INFO @ Sat, 06 Jul 2019 00:09:15: 8000000 INFO @ Sat, 06 Jul 2019 00:09:22: 9000000 INFO @ Sat, 06 Jul 2019 00:09:22: 10000000 INFO @ Sat, 06 Jul 2019 00:09:23: 9000000 INFO @ Sat, 06 Jul 2019 00:09:29: 11000000 INFO @ Sat, 06 Jul 2019 00:09:30: 10000000 INFO @ Sat, 06 Jul 2019 00:09:31: 10000000 INFO @ Sat, 06 Jul 2019 00:09:36: 12000000 INFO @ Sat, 06 Jul 2019 00:09:38: 11000000 INFO @ Sat, 06 Jul 2019 00:09:39: 11000000 INFO @ Sat, 06 Jul 2019 00:09:43: 13000000 INFO @ Sat, 06 Jul 2019 00:09:46: 12000000 INFO @ Sat, 06 Jul 2019 00:09:47: 12000000 INFO @ Sat, 06 Jul 2019 00:09:50: 14000000 INFO @ Sat, 06 Jul 2019 00:09:54: 13000000 INFO @ Sat, 06 Jul 2019 00:09:55: 13000000 INFO @ Sat, 06 Jul 2019 00:09:57: 15000000 INFO @ Sat, 06 Jul 2019 00:10:02: 14000000 INFO @ Sat, 06 Jul 2019 00:10:04: 14000000 INFO @ Sat, 06 Jul 2019 00:10:04: 16000000 INFO @ Sat, 06 Jul 2019 00:10:10: 15000000 INFO @ Sat, 06 Jul 2019 00:10:11: 17000000 INFO @ Sat, 06 Jul 2019 00:10:12: 15000000 INFO @ Sat, 06 Jul 2019 00:10:18: 18000000 INFO @ Sat, 06 Jul 2019 00:10:19: 16000000 INFO @ Sat, 06 Jul 2019 00:10:20: 16000000 INFO @ Sat, 06 Jul 2019 00:10:25: 19000000 INFO @ Sat, 06 Jul 2019 00:10:27: 17000000 INFO @ Sat, 06 Jul 2019 00:10:28: 17000000 INFO @ Sat, 06 Jul 2019 00:10:32: 20000000 INFO @ Sat, 06 Jul 2019 00:10:35: 18000000 INFO @ Sat, 06 Jul 2019 00:10:36: 18000000 INFO @ Sat, 06 Jul 2019 00:10:39: 21000000 INFO @ Sat, 06 Jul 2019 00:10:43: 19000000 INFO @ Sat, 06 Jul 2019 00:10:44: 19000000 INFO @ Sat, 06 Jul 2019 00:10:46: 22000000 INFO @ Sat, 06 Jul 2019 00:10:51: 20000000 INFO @ Sat, 06 Jul 2019 00:10:52: 20000000 INFO @ Sat, 06 Jul 2019 00:10:53: 23000000 INFO @ Sat, 06 Jul 2019 00:10:58: 21000000 INFO @ Sat, 06 Jul 2019 00:11:00: 21000000 INFO @ Sat, 06 Jul 2019 00:11:00: 24000000 INFO @ Sat, 06 Jul 2019 00:11:06: 22000000 INFO @ Sat, 06 Jul 2019 00:11:07: 25000000 INFO @ Sat, 06 Jul 2019 00:11:08: 22000000 INFO @ Sat, 06 Jul 2019 00:11:14: 26000000 INFO @ Sat, 06 Jul 2019 00:11:14: 23000000 INFO @ Sat, 06 Jul 2019 00:11:16: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 00:11:21: 27000000 INFO @ Sat, 06 Jul 2019 00:11:22: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 00:11:22: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 00:11:22: #1 total tags in treatment: 13198278 INFO @ Sat, 06 Jul 2019 00:11:22: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:11:22: #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 00:11:22: 24000000 INFO @ Sat, 06 Jul 2019 00:11:22: #1 tags after filtering in treatment: 8451432 INFO @ Sat, 06 Jul 2019 00:11:22: #1 Redundant rate of treatment: 0.36 INFO @ Sat, 06 Jul 2019 00:11:22: #1 finished! INFO @ Sat, 06 Jul 2019 00:11:22: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:11:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:11:23: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:11:23: 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 00:11:23: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX381285/SRX381285.20_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/SRX381285/SRX381285.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381285/SRX381285.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381285/SRX381285.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:11:24: 24000000 INFO @ Sat, 06 Jul 2019 00:11:30: 25000000 INFO @ Sat, 06 Jul 2019 00:11:31: 25000000 BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 00:11:37: 26000000 INFO @ Sat, 06 Jul 2019 00:11:39: 26000000 INFO @ Sat, 06 Jul 2019 00:11:45: 27000000 INFO @ Sat, 06 Jul 2019 00:11:46: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 00:11:46: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 00:11:46: #1 total tags in treatment: 13198278 INFO @ Sat, 06 Jul 2019 00:11:46: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:11:46: #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 00:11:46: #1 tags after filtering in treatment: 8451432 INFO @ Sat, 06 Jul 2019 00:11:46: #1 Redundant rate of treatment: 0.36 INFO @ Sat, 06 Jul 2019 00:11:46: #1 finished! INFO @ Sat, 06 Jul 2019 00:11:46: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:11:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:11:47: 27000000 INFO @ Sat, 06 Jul 2019 00:11:47: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:11:47: 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 00:11:47: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX381285/SRX381285.05_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/SRX381285/SRX381285.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381285/SRX381285.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381285/SRX381285.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:11:47: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 00:11:47: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 00:11:47: #1 total tags in treatment: 13198278 INFO @ Sat, 06 Jul 2019 00:11:47: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:11:47: #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 00:11:48: #1 tags after filtering in treatment: 8451432 INFO @ Sat, 06 Jul 2019 00:11:48: #1 Redundant rate of treatment: 0.36 INFO @ Sat, 06 Jul 2019 00:11:48: #1 finished! INFO @ Sat, 06 Jul 2019 00:11:48: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:11:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:11:48: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:11:48: 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 00:11:48: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX381285/SRX381285.10_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/SRX381285/SRX381285.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381285/SRX381285.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381285/SRX381285.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling