Job ID = 2011001 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T16:35:41 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 ) 2019-07-05T16:35:41 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 : 26,835,569 reads read : 53,671,138 reads written : 26,835,569 reads 0-length : 26,835,569 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: 00:05:14 26835569 reads; of these: 26835569 (100.00%) were unpaired; of these: 901556 (3.36%) aligned 0 times 22218458 (82.79%) aligned exactly 1 time 3715555 (13.85%) aligned >1 times 96.64% overall alignment rate Time searching: 00:05:14 Overall time: 00:05:14 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_rmdupse_core] 12294798 / 25934013 = 0.4741 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 01:56:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4409369/SRX4409369.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4409369/SRX4409369.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4409369/SRX4409369.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4409369/SRX4409369.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 01:56:04: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:56:04: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:56:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4409369/SRX4409369.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4409369/SRX4409369.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4409369/SRX4409369.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4409369/SRX4409369.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 01:56:04: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:56:04: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:56:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4409369/SRX4409369.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4409369/SRX4409369.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4409369/SRX4409369.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4409369/SRX4409369.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 01:56:05: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:56:05: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:56:14: 1000000 INFO @ Sat, 06 Jul 2019 01:56:17: 1000000 INFO @ Sat, 06 Jul 2019 01:56:17: 1000000 INFO @ Sat, 06 Jul 2019 01:56:23: 2000000 INFO @ Sat, 06 Jul 2019 01:56:30: 2000000 INFO @ Sat, 06 Jul 2019 01:56:30: 2000000 INFO @ Sat, 06 Jul 2019 01:56:31: 3000000 INFO @ Sat, 06 Jul 2019 01:56:39: 4000000 INFO @ Sat, 06 Jul 2019 01:56:42: 3000000 INFO @ Sat, 06 Jul 2019 01:56:42: 3000000 INFO @ Sat, 06 Jul 2019 01:56:47: 5000000 INFO @ Sat, 06 Jul 2019 01:56:54: 4000000 INFO @ Sat, 06 Jul 2019 01:56:54: 4000000 INFO @ Sat, 06 Jul 2019 01:56:55: 6000000 INFO @ Sat, 06 Jul 2019 01:57:03: 7000000 INFO @ Sat, 06 Jul 2019 01:57:06: 5000000 INFO @ Sat, 06 Jul 2019 01:57:07: 5000000 INFO @ Sat, 06 Jul 2019 01:57:12: 8000000 INFO @ Sat, 06 Jul 2019 01:57:19: 6000000 INFO @ Sat, 06 Jul 2019 01:57:19: 6000000 INFO @ Sat, 06 Jul 2019 01:57:20: 9000000 INFO @ Sat, 06 Jul 2019 01:57:28: 10000000 INFO @ Sat, 06 Jul 2019 01:57:31: 7000000 INFO @ Sat, 06 Jul 2019 01:57:31: 7000000 INFO @ Sat, 06 Jul 2019 01:57:37: 11000000 INFO @ Sat, 06 Jul 2019 01:57:45: 8000000 INFO @ Sat, 06 Jul 2019 01:57:45: 8000000 INFO @ Sat, 06 Jul 2019 01:57:45: 12000000 INFO @ Sat, 06 Jul 2019 01:57:54: 13000000 INFO @ Sat, 06 Jul 2019 01:57:58: 9000000 INFO @ Sat, 06 Jul 2019 01:57:58: 9000000 INFO @ Sat, 06 Jul 2019 01:57:59: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 01:57:59: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 01:57:59: #1 total tags in treatment: 13639215 INFO @ Sat, 06 Jul 2019 01:57:59: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:57:59: #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 01:57:59: #1 tags after filtering in treatment: 13639215 INFO @ Sat, 06 Jul 2019 01:57:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 01:57:59: #1 finished! INFO @ Sat, 06 Jul 2019 01:57:59: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:57:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:58:00: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 01:58:00: 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 01:58:00: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4409369/SRX4409369.20_peaks.narrowPeak: No such file or directory INFO @ Sat, 06 Jul 2019 01:58:10: 10000000 INFO @ Sat, 06 Jul 2019 01:58:11: 10000000 BedGraph に変換しました。 INFO @ Sat, 06 Jul 2019 01:58:23: 11000000 INFO @ Sat, 06 Jul 2019 01:58:23: 11000000 BigWig に変換中... pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4409369/SRX4409369.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4409369/SRX4409369.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4409369/SRX4409369.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 01:58:36: 12000000 INFO @ Sat, 06 Jul 2019 01:58:36: 12000000 BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 01:58:48: 13000000 INFO @ Sat, 06 Jul 2019 01:58:48: 13000000 INFO @ Sat, 06 Jul 2019 01:58:55: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 01:58:55: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 01:58:55: #1 total tags in treatment: 13639215 INFO @ Sat, 06 Jul 2019 01:58:55: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:58:55: #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 01:58:55: #1 tags after filtering in treatment: 13639215 INFO @ Sat, 06 Jul 2019 01:58:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 01:58:55: #1 finished! INFO @ Sat, 06 Jul 2019 01:58:55: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:58:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:58:55: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 01:58:55: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 01:58:55: #1 total tags in treatment: 13639215 INFO @ Sat, 06 Jul 2019 01:58:55: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:58:55: #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 01:58:56: #1 tags after filtering in treatment: 13639215 INFO @ Sat, 06 Jul 2019 01:58:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 01:58:56: #1 finished! INFO @ Sat, 06 Jul 2019 01:58:56: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:58:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:58:56: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 01:58:56: 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 01:58:56: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4409369/SRX4409369.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4409369/SRX4409369.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4409369/SRX4409369.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4409369/SRX4409369.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 01:58:57: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 01:58:57: 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 @ Sat, 06 Jul 2019 01:58:57: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4409369/SRX4409369.10_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4409369/SRX4409369.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4409369/SRX4409369.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4409369/SRX4409369.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling