Job ID = 4289609 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T06:00:29 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 ) spots read : 30,778,562 reads read : 61,557,124 reads written : 30,778,562 reads 0-length : 30,778,562 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: 00:06:01 30778562 reads; of these: 30778562 (100.00%) were unpaired; of these: 2171741 (7.06%) aligned 0 times 21353815 (69.38%) aligned exactly 1 time 7253006 (23.57%) aligned >1 times 92.94% overall alignment rate Time searching: 00:06:01 Overall time: 00:06:01 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] 16173203 / 28606821 = 0.5654 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 15:14:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7106980/SRX7106980.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7106980/SRX7106980.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7106980/SRX7106980.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7106980/SRX7106980.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 15:14:30: #1 read tag files... INFO @ Tue, 10 Dec 2019 15:14:30: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 15:14:39: 1000000 INFO @ Tue, 10 Dec 2019 15:14:47: 2000000 INFO @ Tue, 10 Dec 2019 15:14:55: 3000000 INFO @ Tue, 10 Dec 2019 15:15:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7106980/SRX7106980.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7106980/SRX7106980.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7106980/SRX7106980.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7106980/SRX7106980.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 15:15:00: #1 read tag files... INFO @ Tue, 10 Dec 2019 15:15:00: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 15:15:03: 4000000 INFO @ Tue, 10 Dec 2019 15:15:09: 1000000 INFO @ Tue, 10 Dec 2019 15:15:11: 5000000 INFO @ Tue, 10 Dec 2019 15:15:17: 2000000 INFO @ Tue, 10 Dec 2019 15:15:20: 6000000 INFO @ Tue, 10 Dec 2019 15:15:25: 3000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 15:15:29: 7000000 INFO @ Tue, 10 Dec 2019 15:15:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7106980/SRX7106980.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7106980/SRX7106980.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7106980/SRX7106980.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7106980/SRX7106980.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 15:15:30: #1 read tag files... INFO @ Tue, 10 Dec 2019 15:15:30: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 15:15:32: 4000000 INFO @ Tue, 10 Dec 2019 15:15:37: 8000000 INFO @ Tue, 10 Dec 2019 15:15:39: 1000000 INFO @ Tue, 10 Dec 2019 15:15:40: 5000000 INFO @ Tue, 10 Dec 2019 15:15:46: 9000000 INFO @ Tue, 10 Dec 2019 15:15:48: 6000000 INFO @ Tue, 10 Dec 2019 15:15:48: 2000000 INFO @ Tue, 10 Dec 2019 15:15:55: 7000000 INFO @ Tue, 10 Dec 2019 15:15:55: 10000000 INFO @ Tue, 10 Dec 2019 15:15:56: 3000000 INFO @ Tue, 10 Dec 2019 15:16:02: 8000000 INFO @ Tue, 10 Dec 2019 15:16:04: 11000000 INFO @ Tue, 10 Dec 2019 15:16:05: 4000000 INFO @ Tue, 10 Dec 2019 15:16:10: 9000000 INFO @ Tue, 10 Dec 2019 15:16:13: 12000000 INFO @ Tue, 10 Dec 2019 15:16:14: 5000000 INFO @ Tue, 10 Dec 2019 15:16:17: #1 tag size is determined as 50 bps INFO @ Tue, 10 Dec 2019 15:16:17: #1 tag size = 50 INFO @ Tue, 10 Dec 2019 15:16:17: #1 total tags in treatment: 12433618 INFO @ Tue, 10 Dec 2019 15:16:17: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 15:16:17: #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 15:16:17: #1 tags after filtering in treatment: 12433618 INFO @ Tue, 10 Dec 2019 15:16:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 15:16:17: #1 finished! INFO @ Tue, 10 Dec 2019 15:16:17: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 15:16:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 15:16:17: 10000000 INFO @ Tue, 10 Dec 2019 15:16:18: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 15:16:18: 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 15:16:18: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7106980/SRX7106980.05_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/SRX7106980/SRX7106980.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7106980/SRX7106980.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7106980/SRX7106980.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 15:16:22: 6000000 INFO @ Tue, 10 Dec 2019 15:16:24: 11000000 INFO @ Tue, 10 Dec 2019 15:16:31: 7000000 INFO @ Tue, 10 Dec 2019 15:16:32: 12000000 INFO @ Tue, 10 Dec 2019 15:16:35: #1 tag size is determined as 50 bps INFO @ Tue, 10 Dec 2019 15:16:35: #1 tag size = 50 INFO @ Tue, 10 Dec 2019 15:16:35: #1 total tags in treatment: 12433618 INFO @ Tue, 10 Dec 2019 15:16:35: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 15:16:35: #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 15:16:35: #1 tags after filtering in treatment: 12433618 INFO @ Tue, 10 Dec 2019 15:16:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 15:16:35: #1 finished! INFO @ Tue, 10 Dec 2019 15:16:35: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 15:16:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 15:16:36: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 15:16:36: 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 15:16:36: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7106980/SRX7106980.10_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/SRX7106980/SRX7106980.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7106980/SRX7106980.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7106980/SRX7106980.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 15:16:40: 8000000 INFO @ Tue, 10 Dec 2019 15:16:48: 9000000 INFO @ Tue, 10 Dec 2019 15:16:57: 10000000 INFO @ Tue, 10 Dec 2019 15:17:06: 11000000 INFO @ Tue, 10 Dec 2019 15:17:14: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 10 Dec 2019 15:17:18: #1 tag size is determined as 50 bps INFO @ Tue, 10 Dec 2019 15:17:18: #1 tag size = 50 INFO @ Tue, 10 Dec 2019 15:17:18: #1 total tags in treatment: 12433618 INFO @ Tue, 10 Dec 2019 15:17:18: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 15:17:18: #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 15:17:18: #1 tags after filtering in treatment: 12433618 INFO @ Tue, 10 Dec 2019 15:17:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 15:17:18: #1 finished! INFO @ Tue, 10 Dec 2019 15:17:18: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 15:17:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 15:17:19: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 15:17:19: 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 15:17:19: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7106980/SRX7106980.20_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/SRX7106980/SRX7106980.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7106980/SRX7106980.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7106980/SRX7106980.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。