Job ID = 1293725 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 11,625,498 reads read : 11,625,498 reads written : 11,625,498 2019-06-02T17:01:15 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-06-02T17:01:15 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-06-02T17:07:54 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-06-02T17:07:54 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-06-02T17:09:16 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 21,010,599 reads read : 21,010,599 reads written : 21,010,599 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: 00:08:53 32636097 reads; of these: 32636097 (100.00%) were unpaired; of these: 1272364 (3.90%) aligned 0 times 25103432 (76.92%) aligned exactly 1 time 6260301 (19.18%) aligned >1 times 96.10% overall alignment rate Time searching: 00:08:53 Overall time: 00:08:53 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] 9003059 / 31363733 = 0.2871 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 02:31:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX111805/SRX111805.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX111805/SRX111805.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX111805/SRX111805.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX111805/SRX111805.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 02:31:27: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:31:27: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:31:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX111805/SRX111805.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX111805/SRX111805.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX111805/SRX111805.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX111805/SRX111805.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 02:31:27: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:31:27: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:31:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX111805/SRX111805.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX111805/SRX111805.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX111805/SRX111805.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX111805/SRX111805.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 02:31:27: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:31:27: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:31:35: 1000000 INFO @ Mon, 03 Jun 2019 02:31:35: 1000000 INFO @ Mon, 03 Jun 2019 02:31:36: 1000000 INFO @ Mon, 03 Jun 2019 02:31:43: 2000000 INFO @ Mon, 03 Jun 2019 02:31:43: 2000000 INFO @ Mon, 03 Jun 2019 02:31:44: 2000000 INFO @ Mon, 03 Jun 2019 02:31:50: 3000000 INFO @ Mon, 03 Jun 2019 02:31:50: 3000000 INFO @ Mon, 03 Jun 2019 02:31:52: 3000000 INFO @ Mon, 03 Jun 2019 02:31:58: 4000000 INFO @ Mon, 03 Jun 2019 02:31:58: 4000000 INFO @ Mon, 03 Jun 2019 02:32:00: 4000000 INFO @ Mon, 03 Jun 2019 02:32:06: 5000000 INFO @ Mon, 03 Jun 2019 02:32:06: 5000000 INFO @ Mon, 03 Jun 2019 02:32:09: 5000000 INFO @ Mon, 03 Jun 2019 02:32:13: 6000000 INFO @ Mon, 03 Jun 2019 02:32:14: 6000000 INFO @ Mon, 03 Jun 2019 02:32:17: 6000000 INFO @ Mon, 03 Jun 2019 02:32:21: 7000000 INFO @ Mon, 03 Jun 2019 02:32:21: 7000000 INFO @ Mon, 03 Jun 2019 02:32:25: 7000000 INFO @ Mon, 03 Jun 2019 02:32:29: 8000000 INFO @ Mon, 03 Jun 2019 02:32:29: 8000000 INFO @ Mon, 03 Jun 2019 02:32:34: 8000000 INFO @ Mon, 03 Jun 2019 02:32:36: 9000000 INFO @ Mon, 03 Jun 2019 02:32:36: 9000000 INFO @ Mon, 03 Jun 2019 02:32:42: 9000000 INFO @ Mon, 03 Jun 2019 02:32:44: 10000000 INFO @ Mon, 03 Jun 2019 02:32:44: 10000000 INFO @ Mon, 03 Jun 2019 02:32:50: 10000000 INFO @ Mon, 03 Jun 2019 02:32:52: 11000000 INFO @ Mon, 03 Jun 2019 02:32:52: 11000000 INFO @ Mon, 03 Jun 2019 02:32:59: 11000000 INFO @ Mon, 03 Jun 2019 02:32:59: 12000000 INFO @ Mon, 03 Jun 2019 02:32:59: 12000000 INFO @ Mon, 03 Jun 2019 02:33:07: 13000000 INFO @ Mon, 03 Jun 2019 02:33:07: 12000000 INFO @ Mon, 03 Jun 2019 02:33:07: 13000000 INFO @ Mon, 03 Jun 2019 02:33:15: 14000000 INFO @ Mon, 03 Jun 2019 02:33:15: 14000000 INFO @ Mon, 03 Jun 2019 02:33:16: 13000000 INFO @ Mon, 03 Jun 2019 02:33:23: 15000000 INFO @ Mon, 03 Jun 2019 02:33:24: 15000000 INFO @ Mon, 03 Jun 2019 02:33:24: 14000000 INFO @ Mon, 03 Jun 2019 02:33:31: 16000000 INFO @ Mon, 03 Jun 2019 02:33:31: 16000000 INFO @ Mon, 03 Jun 2019 02:33:32: 15000000 INFO @ Mon, 03 Jun 2019 02:33:39: 17000000 INFO @ Mon, 03 Jun 2019 02:33:39: 17000000 INFO @ Mon, 03 Jun 2019 02:33:41: 16000000 INFO @ Mon, 03 Jun 2019 02:33:47: 18000000 INFO @ Mon, 03 Jun 2019 02:33:50: 18000000 INFO @ Mon, 03 Jun 2019 02:33:50: 17000000 INFO @ Mon, 03 Jun 2019 02:33:55: 19000000 INFO @ Mon, 03 Jun 2019 02:33:58: 18000000 INFO @ Mon, 03 Jun 2019 02:33:59: 19000000 INFO @ Mon, 03 Jun 2019 02:34:02: 20000000 INFO @ Mon, 03 Jun 2019 02:34:07: 19000000 INFO @ Mon, 03 Jun 2019 02:34:07: 20000000 INFO @ Mon, 03 Jun 2019 02:34:11: 21000000 INFO @ Mon, 03 Jun 2019 02:34:16: 20000000 INFO @ Mon, 03 Jun 2019 02:34:16: 21000000 INFO @ Mon, 03 Jun 2019 02:34:20: 22000000 INFO @ Mon, 03 Jun 2019 02:34:23: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 02:34:23: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 02:34:23: #1 total tags in treatment: 22360674 INFO @ Mon, 03 Jun 2019 02:34:23: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:34:23: #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 02:34:24: #1 tags after filtering in treatment: 22360674 INFO @ Mon, 03 Jun 2019 02:34:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:34:24: #1 finished! INFO @ Mon, 03 Jun 2019 02:34:24: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:34:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:34:25: 21000000 INFO @ Mon, 03 Jun 2019 02:34:25: 22000000 INFO @ Mon, 03 Jun 2019 02:34:26: #2 number of paired peaks: 48 WARNING @ Mon, 03 Jun 2019 02:34:26: Too few paired peaks (48) 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 02:34:26: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX111805/SRX111805.20_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/SRX111805/SRX111805.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111805/SRX111805.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111805/SRX111805.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:34:27: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 02:34:27: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 02:34:27: #1 total tags in treatment: 22360674 INFO @ Mon, 03 Jun 2019 02:34:27: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:34:27: #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 02:34:28: #1 tags after filtering in treatment: 22360674 INFO @ Mon, 03 Jun 2019 02:34:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:34:28: #1 finished! INFO @ Mon, 03 Jun 2019 02:34:28: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:34:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:34:30: #2 number of paired peaks: 48 WARNING @ Mon, 03 Jun 2019 02:34:30: Too few paired peaks (48) 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 02:34:30: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX111805/SRX111805.05_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/SRX111805/SRX111805.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111805/SRX111805.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111805/SRX111805.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:34:33: 22000000 INFO @ Mon, 03 Jun 2019 02:34:36: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 02:34:36: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 02:34:36: #1 total tags in treatment: 22360674 INFO @ Mon, 03 Jun 2019 02:34:36: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:34:36: #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 02:34:36: #1 tags after filtering in treatment: 22360674 INFO @ Mon, 03 Jun 2019 02:34:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:34:36: #1 finished! INFO @ Mon, 03 Jun 2019 02:34:36: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:34:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:34:38: #2 number of paired peaks: 48 WARNING @ Mon, 03 Jun 2019 02:34:38: Too few paired peaks (48) 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 02:34:38: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX111805/SRX111805.10_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/SRX111805/SRX111805.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111805/SRX111805.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111805/SRX111805.10_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。