Job ID = 1293971 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T18:35:29 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' 2019-06-02T18:35:29 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/SRR504959/SRR504959.1' 2019-06-02T18:35:40 fasterq-dump.2.9.6 err: cmn_iter.c cmn_get_acc_type( 'SRR504959', 'NAME' ).VDBManagerOpenTableRead() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) spots read : 37,203,045 reads read : 37,203,045 reads written : 37,203,045 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: 00:16:59 37203045 reads; of these: 37203045 (100.00%) were unpaired; of these: 1496109 (4.02%) aligned 0 times 25042332 (67.31%) aligned exactly 1 time 10664604 (28.67%) aligned >1 times 95.98% overall alignment rate Time searching: 00:16:59 Overall time: 00:16:59 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 16 files... [bam_rmdupse_core] 8729268 / 35706936 = 0.2445 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 04:06:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX152103/SRX152103.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX152103/SRX152103.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX152103/SRX152103.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX152103/SRX152103.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 04:06:43: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:06:43: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:06:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX152103/SRX152103.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX152103/SRX152103.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX152103/SRX152103.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX152103/SRX152103.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 04:06:43: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:06:43: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:06:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX152103/SRX152103.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX152103/SRX152103.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX152103/SRX152103.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX152103/SRX152103.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 04:06:43: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:06:43: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:06:50: 1000000 INFO @ Mon, 03 Jun 2019 04:06:51: 1000000 INFO @ Mon, 03 Jun 2019 04:06:52: 1000000 INFO @ Mon, 03 Jun 2019 04:06:57: 2000000 INFO @ Mon, 03 Jun 2019 04:06:59: 2000000 INFO @ Mon, 03 Jun 2019 04:07:00: 2000000 INFO @ Mon, 03 Jun 2019 04:07:03: 3000000 INFO @ Mon, 03 Jun 2019 04:07:06: 3000000 INFO @ Mon, 03 Jun 2019 04:07:08: 3000000 INFO @ Mon, 03 Jun 2019 04:07:10: 4000000 INFO @ Mon, 03 Jun 2019 04:07:13: 4000000 INFO @ Mon, 03 Jun 2019 04:07:16: 4000000 INFO @ Mon, 03 Jun 2019 04:07:17: 5000000 INFO @ Mon, 03 Jun 2019 04:07:20: 5000000 INFO @ Mon, 03 Jun 2019 04:07:24: 6000000 INFO @ Mon, 03 Jun 2019 04:07:24: 5000000 INFO @ Mon, 03 Jun 2019 04:07:28: 6000000 INFO @ Mon, 03 Jun 2019 04:07:30: 7000000 INFO @ Mon, 03 Jun 2019 04:07:33: 6000000 INFO @ Mon, 03 Jun 2019 04:07:36: 7000000 INFO @ Mon, 03 Jun 2019 04:07:37: 8000000 INFO @ Mon, 03 Jun 2019 04:07:41: 7000000 INFO @ Mon, 03 Jun 2019 04:07:43: 8000000 INFO @ Mon, 03 Jun 2019 04:07:44: 9000000 INFO @ Mon, 03 Jun 2019 04:07:49: 8000000 INFO @ Mon, 03 Jun 2019 04:07:50: 9000000 INFO @ Mon, 03 Jun 2019 04:07:50: 10000000 INFO @ Mon, 03 Jun 2019 04:07:57: 9000000 INFO @ Mon, 03 Jun 2019 04:07:57: 11000000 INFO @ Mon, 03 Jun 2019 04:07:58: 10000000 INFO @ Mon, 03 Jun 2019 04:08:04: 12000000 INFO @ Mon, 03 Jun 2019 04:08:05: 10000000 INFO @ Mon, 03 Jun 2019 04:08:06: 11000000 INFO @ Mon, 03 Jun 2019 04:08:11: 13000000 INFO @ Mon, 03 Jun 2019 04:08:13: 12000000 INFO @ Mon, 03 Jun 2019 04:08:14: 11000000 INFO @ Mon, 03 Jun 2019 04:08:17: 14000000 INFO @ Mon, 03 Jun 2019 04:08:20: 13000000 INFO @ Mon, 03 Jun 2019 04:08:22: 12000000 INFO @ Mon, 03 Jun 2019 04:08:24: 15000000 INFO @ Mon, 03 Jun 2019 04:08:27: 14000000 INFO @ Mon, 03 Jun 2019 04:08:31: 13000000 INFO @ Mon, 03 Jun 2019 04:08:31: 16000000 INFO @ Mon, 03 Jun 2019 04:08:35: 15000000 INFO @ Mon, 03 Jun 2019 04:08:38: 17000000 INFO @ Mon, 03 Jun 2019 04:08:39: 14000000 INFO @ Mon, 03 Jun 2019 04:08:42: 16000000 INFO @ Mon, 03 Jun 2019 04:08:44: 18000000 INFO @ Mon, 03 Jun 2019 04:08:47: 15000000 INFO @ Mon, 03 Jun 2019 04:08:49: 17000000 INFO @ Mon, 03 Jun 2019 04:08:51: 19000000 INFO @ Mon, 03 Jun 2019 04:08:55: 16000000 INFO @ Mon, 03 Jun 2019 04:08:56: 18000000 INFO @ Mon, 03 Jun 2019 04:08:58: 20000000 INFO @ Mon, 03 Jun 2019 04:09:03: 17000000 INFO @ Mon, 03 Jun 2019 04:09:03: 19000000 INFO @ Mon, 03 Jun 2019 04:09:05: 21000000 INFO @ Mon, 03 Jun 2019 04:09:11: 18000000 INFO @ Mon, 03 Jun 2019 04:09:11: 20000000 INFO @ Mon, 03 Jun 2019 04:09:11: 22000000 INFO @ Mon, 03 Jun 2019 04:09:18: 21000000 INFO @ Mon, 03 Jun 2019 04:09:18: 23000000 INFO @ Mon, 03 Jun 2019 04:09:19: 19000000 INFO @ Mon, 03 Jun 2019 04:09:25: 24000000 INFO @ Mon, 03 Jun 2019 04:09:25: 22000000 INFO @ Mon, 03 Jun 2019 04:09:27: 20000000 INFO @ Mon, 03 Jun 2019 04:09:32: 25000000 INFO @ Mon, 03 Jun 2019 04:09:32: 23000000 INFO @ Mon, 03 Jun 2019 04:09:35: 21000000 INFO @ Mon, 03 Jun 2019 04:09:39: 26000000 INFO @ Mon, 03 Jun 2019 04:09:40: 24000000 INFO @ Mon, 03 Jun 2019 04:09:43: 22000000 INFO @ Mon, 03 Jun 2019 04:09:46: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 04:09:46: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 04:09:46: #1 total tags in treatment: 26977668 INFO @ Mon, 03 Jun 2019 04:09:46: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:09:46: #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 04:09:47: #1 tags after filtering in treatment: 26977668 INFO @ Mon, 03 Jun 2019 04:09:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:09:47: #1 finished! INFO @ Mon, 03 Jun 2019 04:09:47: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:09:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:09:47: 25000000 INFO @ Mon, 03 Jun 2019 04:09:49: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 04:09:49: 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 @ Mon, 03 Jun 2019 04:09:49: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX152103/SRX152103.20_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/SRX152103/SRX152103.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX152103/SRX152103.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX152103/SRX152103.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:09:52: 23000000 INFO @ Mon, 03 Jun 2019 04:09:54: 26000000 INFO @ Mon, 03 Jun 2019 04:10:00: 24000000 INFO @ Mon, 03 Jun 2019 04:10:02: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 04:10:02: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 04:10:02: #1 total tags in treatment: 26977668 INFO @ Mon, 03 Jun 2019 04:10:02: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:10:02: #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 04:10:02: #1 tags after filtering in treatment: 26977668 INFO @ Mon, 03 Jun 2019 04:10:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:10:02: #1 finished! INFO @ Mon, 03 Jun 2019 04:10:02: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:10:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:10:04: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 04:10:04: 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 @ Mon, 03 Jun 2019 04:10:04: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX152103/SRX152103.10_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/SRX152103/SRX152103.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX152103/SRX152103.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX152103/SRX152103.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:10:08: 25000000 INFO @ Mon, 03 Jun 2019 04:10:16: 26000000 INFO @ Mon, 03 Jun 2019 04:10:24: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 04:10:24: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 04:10:24: #1 total tags in treatment: 26977668 INFO @ Mon, 03 Jun 2019 04:10:24: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:10:24: #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 04:10:24: #1 tags after filtering in treatment: 26977668 INFO @ Mon, 03 Jun 2019 04:10:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:10:24: #1 finished! INFO @ Mon, 03 Jun 2019 04:10:24: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:10:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:10:27: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 04:10:27: 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 @ Mon, 03 Jun 2019 04:10:27: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX152103/SRX152103.05_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/SRX152103/SRX152103.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX152103/SRX152103.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX152103/SRX152103.05_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。