Job ID = 1293726 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,461,294 reads read : 18,461,294 reads written : 18,461,294 2019-06-02T16:57:42 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 ) 2019-06-02T16:58:04 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 ) 2019-06-02T16:58:04 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( ) 2019-06-02T16:58:04 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 ) 2019-06-02T16:58:04 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 ) 2019-06-02T16:58:58 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 ) 2019-06-02T17:10:18 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 29,540,947 reads read : 29,540,947 reads written : 29,540,947 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: 00:13:47 48002241 reads; of these: 48002241 (100.00%) were unpaired; of these: 10733542 (22.36%) aligned 0 times 29595189 (61.65%) aligned exactly 1 time 7673510 (15.99%) aligned >1 times 77.64% overall alignment rate Time searching: 00:13:47 Overall time: 00:13:47 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] 13119754 / 37268699 = 0.3520 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 02:38:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX111810/SRX111810.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX111810/SRX111810.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX111810/SRX111810.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX111810/SRX111810.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 02:38:52: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:38:52: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:38:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX111810/SRX111810.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX111810/SRX111810.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX111810/SRX111810.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX111810/SRX111810.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 02:38:52: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:38:52: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:38:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX111810/SRX111810.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX111810/SRX111810.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX111810/SRX111810.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX111810/SRX111810.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 02:38:52: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:38:52: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:39:00: 1000000 INFO @ Mon, 03 Jun 2019 02:39:00: 1000000 INFO @ Mon, 03 Jun 2019 02:39:01: 1000000 INFO @ Mon, 03 Jun 2019 02:39:07: 2000000 INFO @ Mon, 03 Jun 2019 02:39:08: 2000000 INFO @ Mon, 03 Jun 2019 02:39:08: 2000000 INFO @ Mon, 03 Jun 2019 02:39:14: 3000000 INFO @ Mon, 03 Jun 2019 02:39:16: 3000000 INFO @ Mon, 03 Jun 2019 02:39:16: 3000000 INFO @ Mon, 03 Jun 2019 02:39:21: 4000000 INFO @ Mon, 03 Jun 2019 02:39:24: 4000000 INFO @ Mon, 03 Jun 2019 02:39:24: 4000000 INFO @ Mon, 03 Jun 2019 02:39:27: 5000000 INFO @ Mon, 03 Jun 2019 02:39:31: 5000000 INFO @ Mon, 03 Jun 2019 02:39:32: 5000000 INFO @ Mon, 03 Jun 2019 02:39:34: 6000000 INFO @ Mon, 03 Jun 2019 02:39:39: 6000000 INFO @ Mon, 03 Jun 2019 02:39:39: 6000000 INFO @ Mon, 03 Jun 2019 02:39:41: 7000000 INFO @ Mon, 03 Jun 2019 02:39:47: 7000000 INFO @ Mon, 03 Jun 2019 02:39:47: 7000000 INFO @ Mon, 03 Jun 2019 02:39:48: 8000000 INFO @ Mon, 03 Jun 2019 02:39:54: 8000000 INFO @ Mon, 03 Jun 2019 02:39:55: 9000000 INFO @ Mon, 03 Jun 2019 02:39:55: 8000000 INFO @ Mon, 03 Jun 2019 02:40:02: 9000000 INFO @ Mon, 03 Jun 2019 02:40:02: 10000000 INFO @ Mon, 03 Jun 2019 02:40:04: 9000000 INFO @ Mon, 03 Jun 2019 02:40:09: 11000000 INFO @ Mon, 03 Jun 2019 02:40:10: 10000000 INFO @ Mon, 03 Jun 2019 02:40:13: 10000000 INFO @ Mon, 03 Jun 2019 02:40:16: 12000000 INFO @ Mon, 03 Jun 2019 02:40:17: 11000000 INFO @ Mon, 03 Jun 2019 02:40:22: 11000000 INFO @ Mon, 03 Jun 2019 02:40:23: 13000000 INFO @ Mon, 03 Jun 2019 02:40:25: 12000000 INFO @ Mon, 03 Jun 2019 02:40:29: 14000000 INFO @ Mon, 03 Jun 2019 02:40:31: 12000000 INFO @ Mon, 03 Jun 2019 02:40:33: 13000000 INFO @ Mon, 03 Jun 2019 02:40:36: 15000000 INFO @ Mon, 03 Jun 2019 02:40:40: 13000000 INFO @ Mon, 03 Jun 2019 02:40:40: 14000000 INFO @ Mon, 03 Jun 2019 02:40:43: 16000000 INFO @ Mon, 03 Jun 2019 02:40:47: 15000000 INFO @ Mon, 03 Jun 2019 02:40:48: 14000000 INFO @ Mon, 03 Jun 2019 02:40:49: 17000000 INFO @ Mon, 03 Jun 2019 02:40:55: 16000000 INFO @ Mon, 03 Jun 2019 02:40:56: 18000000 INFO @ Mon, 03 Jun 2019 02:40:57: 15000000 INFO @ Mon, 03 Jun 2019 02:41:02: 17000000 INFO @ Mon, 03 Jun 2019 02:41:03: 19000000 INFO @ Mon, 03 Jun 2019 02:41:05: 16000000 INFO @ Mon, 03 Jun 2019 02:41:10: 18000000 INFO @ Mon, 03 Jun 2019 02:41:10: 20000000 INFO @ Mon, 03 Jun 2019 02:41:14: 17000000 INFO @ Mon, 03 Jun 2019 02:41:17: 21000000 INFO @ Mon, 03 Jun 2019 02:41:18: 19000000 INFO @ Mon, 03 Jun 2019 02:41:22: 18000000 INFO @ Mon, 03 Jun 2019 02:41:24: 22000000 INFO @ Mon, 03 Jun 2019 02:41:25: 20000000 INFO @ Mon, 03 Jun 2019 02:41:31: 23000000 INFO @ Mon, 03 Jun 2019 02:41:31: 19000000 INFO @ Mon, 03 Jun 2019 02:41:33: 21000000 INFO @ Mon, 03 Jun 2019 02:41:38: 24000000 INFO @ Mon, 03 Jun 2019 02:41:39: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 02:41:39: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 02:41:39: #1 total tags in treatment: 24148945 INFO @ Mon, 03 Jun 2019 02:41:39: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:41:39: #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 02:41:39: #1 tags after filtering in treatment: 24148945 INFO @ Mon, 03 Jun 2019 02:41:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:41:39: #1 finished! INFO @ Mon, 03 Jun 2019 02:41:39: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:41:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:41:40: 20000000 INFO @ Mon, 03 Jun 2019 02:41:40: 22000000 INFO @ Mon, 03 Jun 2019 02:41:41: #2 number of paired peaks: 3 WARNING @ Mon, 03 Jun 2019 02:41:41: Too few paired peaks (3) 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 02:41:41: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX111810/SRX111810.20_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/SRX111810/SRX111810.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111810/SRX111810.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111810/SRX111810.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:41:48: 23000000 INFO @ Mon, 03 Jun 2019 02:41:48: 21000000 INFO @ Mon, 03 Jun 2019 02:41:55: 24000000 INFO @ Mon, 03 Jun 2019 02:41:57: 22000000 INFO @ Mon, 03 Jun 2019 02:41:57: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 02:41:57: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 02:41:57: #1 total tags in treatment: 24148945 INFO @ Mon, 03 Jun 2019 02:41:57: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:41:57: #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 02:41:57: #1 tags after filtering in treatment: 24148945 INFO @ Mon, 03 Jun 2019 02:41:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:41:57: #1 finished! INFO @ Mon, 03 Jun 2019 02:41:57: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:41:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:41:59: #2 number of paired peaks: 3 WARNING @ Mon, 03 Jun 2019 02:41:59: Too few paired peaks (3) 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 02:41:59: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX111810/SRX111810.10_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/SRX111810/SRX111810.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111810/SRX111810.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111810/SRX111810.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:42:05: 23000000 INFO @ Mon, 03 Jun 2019 02:42:13: 24000000 INFO @ Mon, 03 Jun 2019 02:42:15: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 02:42:15: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 02:42:15: #1 total tags in treatment: 24148945 INFO @ Mon, 03 Jun 2019 02:42:15: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:42:15: #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 02:42:15: #1 tags after filtering in treatment: 24148945 INFO @ Mon, 03 Jun 2019 02:42:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:42:15: #1 finished! INFO @ Mon, 03 Jun 2019 02:42:15: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:42:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:42:18: #2 number of paired peaks: 3 WARNING @ Mon, 03 Jun 2019 02:42:18: Too few paired peaks (3) 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 02:42:18: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX111810/SRX111810.05_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/SRX111810/SRX111810.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111810/SRX111810.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111810/SRX111810.05_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。