Job ID = 1293696 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T16:35:46 fasterq-dump.2.9.6 sys: connection not found while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download-internal.ncbi.nlm.nih.gov:443' 2019-06-02T16:35:46 fasterq-dump.2.9.6 err: connection not found while validating within network system module - error with https open 'https://sra-download-internal.ncbi.nlm.nih.gov/sos/sra-pub-run-2/SRR390225/SRR390225.2' 2019-06-02T16:35:56 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR390225' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) spots read : 22,761,404 reads read : 22,761,404 reads written : 22,761,404 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:05:29 22761404 reads; of these: 22761404 (100.00%) were unpaired; of these: 1496191 (6.57%) aligned 0 times 18494474 (81.25%) aligned exactly 1 time 2770739 (12.17%) aligned >1 times 93.43% overall alignment rate Time searching: 00:05:30 Overall time: 00:05:30 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 3935533 / 21265213 = 0.1851 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 @ Mon, 03 Jun 2019 01:50:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX111780/SRX111780.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX111780/SRX111780.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX111780/SRX111780.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX111780/SRX111780.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 01:50:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:50:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:50:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX111780/SRX111780.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX111780/SRX111780.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX111780/SRX111780.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX111780/SRX111780.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 01:50:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:50:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:50:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX111780/SRX111780.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX111780/SRX111780.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX111780/SRX111780.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX111780/SRX111780.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 01:50:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:50:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:50:08: 1000000 INFO @ Mon, 03 Jun 2019 01:50:09: 1000000 INFO @ Mon, 03 Jun 2019 01:50:09: 1000000 INFO @ Mon, 03 Jun 2019 01:50:16: 2000000 INFO @ Mon, 03 Jun 2019 01:50:18: 2000000 INFO @ Mon, 03 Jun 2019 01:50:18: 2000000 INFO @ Mon, 03 Jun 2019 01:50:24: 3000000 INFO @ Mon, 03 Jun 2019 01:50:28: 3000000 INFO @ Mon, 03 Jun 2019 01:50:28: 3000000 INFO @ Mon, 03 Jun 2019 01:50:31: 4000000 INFO @ Mon, 03 Jun 2019 01:50:37: 4000000 INFO @ Mon, 03 Jun 2019 01:50:37: 4000000 INFO @ Mon, 03 Jun 2019 01:50:39: 5000000 INFO @ Mon, 03 Jun 2019 01:50:46: 5000000 INFO @ Mon, 03 Jun 2019 01:50:46: 5000000 INFO @ Mon, 03 Jun 2019 01:50:47: 6000000 INFO @ Mon, 03 Jun 2019 01:50:55: 7000000 INFO @ Mon, 03 Jun 2019 01:50:55: 6000000 INFO @ Mon, 03 Jun 2019 01:50:55: 6000000 INFO @ Mon, 03 Jun 2019 01:51:02: 8000000 INFO @ Mon, 03 Jun 2019 01:51:04: 7000000 INFO @ Mon, 03 Jun 2019 01:51:04: 7000000 INFO @ Mon, 03 Jun 2019 01:51:10: 9000000 INFO @ Mon, 03 Jun 2019 01:51:13: 8000000 INFO @ Mon, 03 Jun 2019 01:51:14: 8000000 INFO @ Mon, 03 Jun 2019 01:51:18: 10000000 INFO @ Mon, 03 Jun 2019 01:51:22: 9000000 INFO @ Mon, 03 Jun 2019 01:51:23: 9000000 INFO @ Mon, 03 Jun 2019 01:51:26: 11000000 INFO @ Mon, 03 Jun 2019 01:51:31: 10000000 INFO @ Mon, 03 Jun 2019 01:51:32: 10000000 INFO @ Mon, 03 Jun 2019 01:51:33: 12000000 INFO @ Mon, 03 Jun 2019 01:51:40: 11000000 INFO @ Mon, 03 Jun 2019 01:51:41: 11000000 INFO @ Mon, 03 Jun 2019 01:51:41: 13000000 INFO @ Mon, 03 Jun 2019 01:51:48: 14000000 INFO @ Mon, 03 Jun 2019 01:51:49: 12000000 INFO @ Mon, 03 Jun 2019 01:51:49: 12000000 INFO @ Mon, 03 Jun 2019 01:51:56: 15000000 INFO @ Mon, 03 Jun 2019 01:51:58: 13000000 INFO @ Mon, 03 Jun 2019 01:51:58: 13000000 INFO @ Mon, 03 Jun 2019 01:52:04: 16000000 INFO @ Mon, 03 Jun 2019 01:52:06: 14000000 INFO @ Mon, 03 Jun 2019 01:52:06: 14000000 INFO @ Mon, 03 Jun 2019 01:52:12: 17000000 INFO @ Mon, 03 Jun 2019 01:52:14: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 01:52:14: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 01:52:14: #1 total tags in treatment: 17329680 INFO @ Mon, 03 Jun 2019 01:52:14: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:52:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 01:52:14: #1 tags after filtering in treatment: 17329680 INFO @ Mon, 03 Jun 2019 01:52:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:52:14: #1 finished! INFO @ Mon, 03 Jun 2019 01:52:14: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:52:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:52:15: 15000000 INFO @ Mon, 03 Jun 2019 01:52:15: 15000000 INFO @ Mon, 03 Jun 2019 01:52:16: #2 number of paired peaks: 39 WARNING @ Mon, 03 Jun 2019 01:52:16: Too few paired peaks (39) 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 @ Mon, 03 Jun 2019 01:52:16: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX111780/SRX111780.05_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/dm3/SRX111780/SRX111780.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111780/SRX111780.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111780/SRX111780.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:52:24: 16000000 INFO @ Mon, 03 Jun 2019 01:52:24: 16000000 INFO @ Mon, 03 Jun 2019 01:52:33: 17000000 INFO @ Mon, 03 Jun 2019 01:52:33: 17000000 INFO @ Mon, 03 Jun 2019 01:52:36: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 01:52:36: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 01:52:36: #1 total tags in treatment: 17329680 INFO @ Mon, 03 Jun 2019 01:52:36: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:52:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 01:52:36: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 01:52:36: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 01:52:36: #1 total tags in treatment: 17329680 INFO @ Mon, 03 Jun 2019 01:52:36: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:52:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 01:52:36: #1 tags after filtering in treatment: 17329680 INFO @ Mon, 03 Jun 2019 01:52:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:52:36: #1 finished! INFO @ Mon, 03 Jun 2019 01:52:36: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:52:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:52:36: #1 tags after filtering in treatment: 17329680 INFO @ Mon, 03 Jun 2019 01:52:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:52:36: #1 finished! INFO @ Mon, 03 Jun 2019 01:52:36: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:52:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:52:37: #2 number of paired peaks: 39 WARNING @ Mon, 03 Jun 2019 01:52:37: Too few paired peaks (39) 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 @ Mon, 03 Jun 2019 01:52:37: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX111780/SRX111780.10_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/dm3/SRX111780/SRX111780.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111780/SRX111780.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111780/SRX111780.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:52:38: #2 number of paired peaks: 39 WARNING @ Mon, 03 Jun 2019 01:52:38: Too few paired peaks (39) 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 @ Mon, 03 Jun 2019 01:52:38: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX111780/SRX111780.20_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/dm3/SRX111780/SRX111780.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111780/SRX111780.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111780/SRX111780.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。