Job ID = 4289430 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T05:26:25 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 ) 2019-12-10T05:26:25 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 ) 2019-12-10T05:26:25 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 : 19,742,022 reads read : 19,742,022 reads written : 19,742,022 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: 00:03:41 19742022 reads; of these: 19742022 (100.00%) were unpaired; of these: 1824820 (9.24%) aligned 0 times 16355821 (82.85%) aligned exactly 1 time 1561381 (7.91%) aligned >1 times 90.76% overall alignment rate Time searching: 00:03:41 Overall time: 00:03:41 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_rmdupse_core] 7702627 / 17917202 = 0.4299 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 14:45:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6678261/SRX6678261.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6678261/SRX6678261.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6678261/SRX6678261.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6678261/SRX6678261.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 @ Tue, 10 Dec 2019 14:45:16: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:45:16: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:45:26: 1000000 INFO @ Tue, 10 Dec 2019 14:45:36: 2000000 INFO @ Tue, 10 Dec 2019 14:45:45: 3000000 INFO @ Tue, 10 Dec 2019 14:45:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6678261/SRX6678261.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6678261/SRX6678261.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6678261/SRX6678261.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6678261/SRX6678261.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 @ Tue, 10 Dec 2019 14:45:46: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:45:46: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:45:53: 1000000 INFO @ Tue, 10 Dec 2019 14:45:54: 4000000 INFO @ Tue, 10 Dec 2019 14:45:59: 2000000 INFO @ Tue, 10 Dec 2019 14:46:04: 5000000 INFO @ Tue, 10 Dec 2019 14:46:06: 3000000 INFO @ Tue, 10 Dec 2019 14:46:13: 4000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 14:46:14: 6000000 INFO @ Tue, 10 Dec 2019 14:46:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6678261/SRX6678261.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6678261/SRX6678261.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6678261/SRX6678261.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6678261/SRX6678261.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 @ Tue, 10 Dec 2019 14:46:16: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:46:16: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:46:20: 5000000 INFO @ Tue, 10 Dec 2019 14:46:23: 7000000 INFO @ Tue, 10 Dec 2019 14:46:26: 1000000 INFO @ Tue, 10 Dec 2019 14:46:27: 6000000 INFO @ Tue, 10 Dec 2019 14:46:33: 8000000 INFO @ Tue, 10 Dec 2019 14:46:33: 7000000 INFO @ Tue, 10 Dec 2019 14:46:37: 2000000 INFO @ Tue, 10 Dec 2019 14:46:40: 8000000 INFO @ Tue, 10 Dec 2019 14:46:42: 9000000 INFO @ Tue, 10 Dec 2019 14:46:47: 9000000 INFO @ Tue, 10 Dec 2019 14:46:47: 3000000 INFO @ Tue, 10 Dec 2019 14:46:51: 10000000 INFO @ Tue, 10 Dec 2019 14:46:53: 10000000 INFO @ Tue, 10 Dec 2019 14:46:54: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:46:54: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:46:54: #1 total tags in treatment: 10214575 INFO @ Tue, 10 Dec 2019 14:46:54: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:46:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 14:46:54: #1 tags after filtering in treatment: 10214575 INFO @ Tue, 10 Dec 2019 14:46:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:46:54: #1 finished! INFO @ Tue, 10 Dec 2019 14:46:54: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:46:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:46:55: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:46:55: 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 @ Tue, 10 Dec 2019 14:46:55: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6678261/SRX6678261.05_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/SRX6678261/SRX6678261.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678261/SRX6678261.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678261/SRX6678261.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:46:55: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:46:55: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:46:55: #1 total tags in treatment: 10214575 INFO @ Tue, 10 Dec 2019 14:46:55: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:46:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 14:46:55: #1 tags after filtering in treatment: 10214575 INFO @ Tue, 10 Dec 2019 14:46:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:46:55: #1 finished! INFO @ Tue, 10 Dec 2019 14:46:55: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:46:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:46:56: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:46:56: 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 @ Tue, 10 Dec 2019 14:46:56: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6678261/SRX6678261.10_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/SRX6678261/SRX6678261.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678261/SRX6678261.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678261/SRX6678261.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:46:57: 4000000 INFO @ Tue, 10 Dec 2019 14:47:08: 5000000 INFO @ Tue, 10 Dec 2019 14:47:18: 6000000 INFO @ Tue, 10 Dec 2019 14:47:28: 7000000 INFO @ Tue, 10 Dec 2019 14:47:38: 8000000 INFO @ Tue, 10 Dec 2019 14:47:49: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 10 Dec 2019 14:47:59: 10000000 INFO @ Tue, 10 Dec 2019 14:48:01: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:48:01: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:48:01: #1 total tags in treatment: 10214575 INFO @ Tue, 10 Dec 2019 14:48:01: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:48:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 14:48:01: #1 tags after filtering in treatment: 10214575 INFO @ Tue, 10 Dec 2019 14:48:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:48:01: #1 finished! INFO @ Tue, 10 Dec 2019 14:48:01: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:48:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:48:02: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:48:02: 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 @ Tue, 10 Dec 2019 14:48:02: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6678261/SRX6678261.20_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/SRX6678261/SRX6678261.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678261/SRX6678261.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678261/SRX6678261.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。