Job ID = 1293790 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T17:20:27 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' 2019-06-02T17:20:27 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/SRR392964/SRR392964.2' 2019-06-02T17:20:38 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR392964' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-02T17:20:38 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) spots read : 17,086,468 reads read : 17,086,468 reads written : 17,086,468 spots read : 21,583,839 reads read : 21,583,839 reads written : 21,583,839 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: 00:09:46 38670307 reads; of these: 38670307 (100.00%) were unpaired; of these: 6886587 (17.81%) aligned 0 times 25406448 (65.70%) aligned exactly 1 time 6377272 (16.49%) aligned >1 times 82.19% overall alignment rate Time searching: 00:09:46 Overall time: 00:09:46 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 12 files... [bam_rmdupse_core] 8823583 / 31783720 = 0.2776 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 02:53:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX113339/SRX113339.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX113339/SRX113339.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX113339/SRX113339.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX113339/SRX113339.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 02:53:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:53:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:53:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX113339/SRX113339.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX113339/SRX113339.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX113339/SRX113339.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX113339/SRX113339.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 02:53:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:53:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:53:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX113339/SRX113339.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX113339/SRX113339.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX113339/SRX113339.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX113339/SRX113339.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 02:53:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:53:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:53:06: 1000000 INFO @ Mon, 03 Jun 2019 02:53:07: 1000000 INFO @ Mon, 03 Jun 2019 02:53:07: 1000000 INFO @ Mon, 03 Jun 2019 02:53:13: 2000000 INFO @ Mon, 03 Jun 2019 02:53:13: 2000000 INFO @ Mon, 03 Jun 2019 02:53:14: 2000000 INFO @ Mon, 03 Jun 2019 02:53:19: 3000000 INFO @ Mon, 03 Jun 2019 02:53:20: 3000000 INFO @ Mon, 03 Jun 2019 02:53:21: 3000000 INFO @ Mon, 03 Jun 2019 02:53:25: 4000000 INFO @ Mon, 03 Jun 2019 02:53:26: 4000000 INFO @ Mon, 03 Jun 2019 02:53:27: 4000000 INFO @ Mon, 03 Jun 2019 02:53:32: 5000000 INFO @ Mon, 03 Jun 2019 02:53:33: 5000000 INFO @ Mon, 03 Jun 2019 02:53:34: 5000000 INFO @ Mon, 03 Jun 2019 02:53:38: 6000000 INFO @ Mon, 03 Jun 2019 02:53:39: 6000000 INFO @ Mon, 03 Jun 2019 02:53:41: 6000000 INFO @ Mon, 03 Jun 2019 02:53:44: 7000000 INFO @ Mon, 03 Jun 2019 02:53:46: 7000000 INFO @ Mon, 03 Jun 2019 02:53:48: 7000000 INFO @ Mon, 03 Jun 2019 02:53:51: 8000000 INFO @ Mon, 03 Jun 2019 02:53:52: 8000000 INFO @ Mon, 03 Jun 2019 02:53:54: 8000000 INFO @ Mon, 03 Jun 2019 02:53:57: 9000000 INFO @ Mon, 03 Jun 2019 02:53:59: 9000000 INFO @ Mon, 03 Jun 2019 02:54:01: 9000000 INFO @ Mon, 03 Jun 2019 02:54:04: 10000000 INFO @ Mon, 03 Jun 2019 02:54:06: 10000000 INFO @ Mon, 03 Jun 2019 02:54:08: 10000000 INFO @ Mon, 03 Jun 2019 02:54:10: 11000000 INFO @ Mon, 03 Jun 2019 02:54:13: 11000000 INFO @ Mon, 03 Jun 2019 02:54:15: 11000000 INFO @ Mon, 03 Jun 2019 02:54:17: 12000000 INFO @ Mon, 03 Jun 2019 02:54:20: 12000000 INFO @ Mon, 03 Jun 2019 02:54:22: 12000000 INFO @ Mon, 03 Jun 2019 02:54:23: 13000000 INFO @ Mon, 03 Jun 2019 02:54:26: 13000000 INFO @ Mon, 03 Jun 2019 02:54:29: 13000000 INFO @ Mon, 03 Jun 2019 02:54:29: 14000000 INFO @ Mon, 03 Jun 2019 02:54:33: 14000000 INFO @ Mon, 03 Jun 2019 02:54:36: 15000000 INFO @ Mon, 03 Jun 2019 02:54:36: 14000000 INFO @ Mon, 03 Jun 2019 02:54:39: 15000000 INFO @ Mon, 03 Jun 2019 02:54:42: 16000000 INFO @ Mon, 03 Jun 2019 02:54:42: 15000000 INFO @ Mon, 03 Jun 2019 02:54:46: 16000000 INFO @ Mon, 03 Jun 2019 02:54:48: 17000000 INFO @ Mon, 03 Jun 2019 02:54:49: 16000000 INFO @ Mon, 03 Jun 2019 02:54:52: 17000000 INFO @ Mon, 03 Jun 2019 02:54:55: 18000000 INFO @ Mon, 03 Jun 2019 02:54:56: 17000000 INFO @ Mon, 03 Jun 2019 02:54:59: 18000000 INFO @ Mon, 03 Jun 2019 02:55:01: 19000000 INFO @ Mon, 03 Jun 2019 02:55:03: 18000000 INFO @ Mon, 03 Jun 2019 02:55:06: 19000000 INFO @ Mon, 03 Jun 2019 02:55:08: 20000000 INFO @ Mon, 03 Jun 2019 02:55:10: 19000000 INFO @ Mon, 03 Jun 2019 02:55:12: 20000000 INFO @ Mon, 03 Jun 2019 02:55:14: 21000000 INFO @ Mon, 03 Jun 2019 02:55:17: 20000000 INFO @ Mon, 03 Jun 2019 02:55:19: 21000000 INFO @ Mon, 03 Jun 2019 02:55:21: 22000000 INFO @ Mon, 03 Jun 2019 02:55:24: 21000000 INFO @ Mon, 03 Jun 2019 02:55:27: 22000000 INFO @ Mon, 03 Jun 2019 02:55:27: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 02:55:27: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 02:55:27: #1 total tags in treatment: 22960137 INFO @ Mon, 03 Jun 2019 02:55:27: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:55:27: #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 02:55:28: #1 tags after filtering in treatment: 22960137 INFO @ Mon, 03 Jun 2019 02:55:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:55:28: #1 finished! INFO @ Mon, 03 Jun 2019 02:55:28: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:55:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:55:30: #2 number of paired peaks: 42 WARNING @ Mon, 03 Jun 2019 02:55:30: Too few paired peaks (42) 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 02:55:30: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX113339/SRX113339.20_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/dm3/SRX113339/SRX113339.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX113339/SRX113339.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX113339/SRX113339.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:55:31: 22000000 INFO @ Mon, 03 Jun 2019 02:55:33: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 02:55:33: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 02:55:33: #1 total tags in treatment: 22960137 INFO @ Mon, 03 Jun 2019 02:55:33: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:55:33: #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 02:55:34: #1 tags after filtering in treatment: 22960137 INFO @ Mon, 03 Jun 2019 02:55:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:55:34: #1 finished! INFO @ Mon, 03 Jun 2019 02:55:34: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:55:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:55:36: #2 number of paired peaks: 42 WARNING @ Mon, 03 Jun 2019 02:55:36: Too few paired peaks (42) 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 02:55:36: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX113339/SRX113339.10_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/SRX113339/SRX113339.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX113339/SRX113339.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX113339/SRX113339.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:55:37: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 02:55:37: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 02:55:37: #1 total tags in treatment: 22960137 INFO @ Mon, 03 Jun 2019 02:55:37: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:55:37: #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 02:55:38: #1 tags after filtering in treatment: 22960137 INFO @ Mon, 03 Jun 2019 02:55:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:55:38: #1 finished! INFO @ Mon, 03 Jun 2019 02:55:38: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:55:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:55:40: #2 number of paired peaks: 42 WARNING @ Mon, 03 Jun 2019 02:55:40: Too few paired peaks (42) 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 02:55:40: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX113339/SRX113339.05_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/SRX113339/SRX113339.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX113339/SRX113339.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX113339/SRX113339.05_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。