Job ID = 1293695 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T16:35:44 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' 2019-06-02T16:35:44 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/SRR390223/SRR390223.2' 2019-06-02T16:35:55 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR390223' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-02T16:35:55 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) spots read : 20,222,375 reads read : 20,222,375 reads written : 20,222,375 spots read : 24,290,557 reads read : 24,290,557 reads written : 24,290,557 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: 00:08:55 44512932 reads; of these: 44512932 (100.00%) were unpaired; of these: 10659103 (23.95%) aligned 0 times 29906487 (67.19%) aligned exactly 1 time 3947342 (8.87%) aligned >1 times 76.05% overall alignment rate Time searching: 00:08:55 Overall time: 00:08:55 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] 10203388 / 33853829 = 0.3014 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 02:12:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX111779/SRX111779.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX111779/SRX111779.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX111779/SRX111779.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX111779/SRX111779.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 02:12:04: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:12:04: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:12:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX111779/SRX111779.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX111779/SRX111779.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX111779/SRX111779.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX111779/SRX111779.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 02:12:04: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:12:04: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:12:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX111779/SRX111779.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX111779/SRX111779.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX111779/SRX111779.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX111779/SRX111779.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 02:12:04: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:12:04: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:12:13: 1000000 INFO @ Mon, 03 Jun 2019 02:12:13: 1000000 INFO @ Mon, 03 Jun 2019 02:12:13: 1000000 INFO @ Mon, 03 Jun 2019 02:12:21: 2000000 INFO @ Mon, 03 Jun 2019 02:12:22: 2000000 INFO @ Mon, 03 Jun 2019 02:12:22: 2000000 INFO @ Mon, 03 Jun 2019 02:12:30: 3000000 INFO @ Mon, 03 Jun 2019 02:12:31: 3000000 INFO @ Mon, 03 Jun 2019 02:12:32: 3000000 INFO @ Mon, 03 Jun 2019 02:12:38: 4000000 INFO @ Mon, 03 Jun 2019 02:12:40: 4000000 INFO @ Mon, 03 Jun 2019 02:12:41: 4000000 INFO @ Mon, 03 Jun 2019 02:12:46: 5000000 INFO @ Mon, 03 Jun 2019 02:12:48: 5000000 INFO @ Mon, 03 Jun 2019 02:12:49: 5000000 INFO @ Mon, 03 Jun 2019 02:12:54: 6000000 INFO @ Mon, 03 Jun 2019 02:12:56: 6000000 INFO @ Mon, 03 Jun 2019 02:12:57: 6000000 INFO @ Mon, 03 Jun 2019 02:13:02: 7000000 INFO @ Mon, 03 Jun 2019 02:13:05: 7000000 INFO @ Mon, 03 Jun 2019 02:13:06: 7000000 INFO @ Mon, 03 Jun 2019 02:13:10: 8000000 INFO @ Mon, 03 Jun 2019 02:13:13: 8000000 INFO @ Mon, 03 Jun 2019 02:13:14: 8000000 INFO @ Mon, 03 Jun 2019 02:13:18: 9000000 INFO @ Mon, 03 Jun 2019 02:13:22: 9000000 INFO @ Mon, 03 Jun 2019 02:13:22: 9000000 INFO @ Mon, 03 Jun 2019 02:13:26: 10000000 INFO @ Mon, 03 Jun 2019 02:13:31: 10000000 INFO @ Mon, 03 Jun 2019 02:13:31: 10000000 INFO @ Mon, 03 Jun 2019 02:13:34: 11000000 INFO @ Mon, 03 Jun 2019 02:13:39: 11000000 INFO @ Mon, 03 Jun 2019 02:13:40: 11000000 INFO @ Mon, 03 Jun 2019 02:13:43: 12000000 INFO @ Mon, 03 Jun 2019 02:13:48: 12000000 INFO @ Mon, 03 Jun 2019 02:13:48: 12000000 INFO @ Mon, 03 Jun 2019 02:13:51: 13000000 INFO @ Mon, 03 Jun 2019 02:13:57: 13000000 INFO @ Mon, 03 Jun 2019 02:13:57: 13000000 INFO @ Mon, 03 Jun 2019 02:14:00: 14000000 INFO @ Mon, 03 Jun 2019 02:14:06: 14000000 INFO @ Mon, 03 Jun 2019 02:14:07: 14000000 INFO @ Mon, 03 Jun 2019 02:14:08: 15000000 INFO @ Mon, 03 Jun 2019 02:14:15: 15000000 INFO @ Mon, 03 Jun 2019 02:14:16: 15000000 INFO @ Mon, 03 Jun 2019 02:14:16: 16000000 INFO @ Mon, 03 Jun 2019 02:14:24: 16000000 INFO @ Mon, 03 Jun 2019 02:14:24: 17000000 INFO @ Mon, 03 Jun 2019 02:14:25: 16000000 INFO @ Mon, 03 Jun 2019 02:14:32: 17000000 INFO @ Mon, 03 Jun 2019 02:14:32: 18000000 INFO @ Mon, 03 Jun 2019 02:14:33: 17000000 INFO @ Mon, 03 Jun 2019 02:14:40: 18000000 INFO @ Mon, 03 Jun 2019 02:14:41: 19000000 INFO @ Mon, 03 Jun 2019 02:14:41: 18000000 INFO @ Mon, 03 Jun 2019 02:14:48: 19000000 INFO @ Mon, 03 Jun 2019 02:14:49: 19000000 INFO @ Mon, 03 Jun 2019 02:14:50: 20000000 INFO @ Mon, 03 Jun 2019 02:14:56: 20000000 INFO @ Mon, 03 Jun 2019 02:14:57: 20000000 INFO @ Mon, 03 Jun 2019 02:14:59: 21000000 INFO @ Mon, 03 Jun 2019 02:15:03: 21000000 INFO @ Mon, 03 Jun 2019 02:15:05: 21000000 INFO @ Mon, 03 Jun 2019 02:15:08: 22000000 INFO @ Mon, 03 Jun 2019 02:15:10: 22000000 INFO @ Mon, 03 Jun 2019 02:15:13: 22000000 INFO @ Mon, 03 Jun 2019 02:15:17: 23000000 INFO @ Mon, 03 Jun 2019 02:15:17: 23000000 INFO @ Mon, 03 Jun 2019 02:15:20: 23000000 INFO @ Mon, 03 Jun 2019 02:15:22: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 02:15:22: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 02:15:22: #1 total tags in treatment: 23650441 INFO @ Mon, 03 Jun 2019 02:15:22: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:15:22: #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 02:15:23: #1 tags after filtering in treatment: 23650441 INFO @ Mon, 03 Jun 2019 02:15:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:15:23: #1 finished! INFO @ Mon, 03 Jun 2019 02:15:23: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:15:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:15:23: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 02:15:23: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 02:15:23: #1 total tags in treatment: 23650441 INFO @ Mon, 03 Jun 2019 02:15:23: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:15:23: #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 02:15:24: #1 tags after filtering in treatment: 23650441 INFO @ Mon, 03 Jun 2019 02:15:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:15:24: #1 finished! INFO @ Mon, 03 Jun 2019 02:15:24: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:15:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:15:25: #2 number of paired peaks: 51 WARNING @ Mon, 03 Jun 2019 02:15:25: Too few paired peaks (51) 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 02:15:25: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX111779/SRX111779.05_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/SRX111779/SRX111779.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111779/SRX111779.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111779/SRX111779.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:15:26: #2 number of paired peaks: 51 WARNING @ Mon, 03 Jun 2019 02:15:26: Too few paired peaks (51) 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 02:15:26: Process for pairing-model is terminated! INFO @ Mon, 03 Jun 2019 02:15:26: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 02:15:26: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 02:15:26: #1 total tags in treatment: 23650441 INFO @ Mon, 03 Jun 2019 02:15:26: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:15:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) cut: /home/okishinya/chipatlas/results/dm3/SRX111779/SRX111779.10_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/SRX111779/SRX111779.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111779/SRX111779.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111779/SRX111779.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:15:26: #1 tags after filtering in treatment: 23650441 INFO @ Mon, 03 Jun 2019 02:15:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:15:26: #1 finished! INFO @ Mon, 03 Jun 2019 02:15:26: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:15:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:15:28: #2 number of paired peaks: 51 WARNING @ Mon, 03 Jun 2019 02:15:28: Too few paired peaks (51) 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 02:15:28: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX111779/SRX111779.20_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/SRX111779/SRX111779.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111779/SRX111779.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111779/SRX111779.20_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。