Job ID = 1306125 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T12:33:18 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 ) 2019-06-03T12:33:18 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 ) 2019-06-03T12:33:18 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 ) 2019-06-03T12:35:44 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 ) 2019-06-03T12:37:27 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 ) 2019-06-03T12:40:05 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 : 31,833,913 reads read : 31,833,913 reads written : 31,833,913 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: 00:16:31 31833913 reads; of these: 31833913 (100.00%) were unpaired; of these: 10381100 (32.61%) aligned 0 times 8466915 (26.60%) aligned exactly 1 time 12985898 (40.79%) aligned >1 times 67.39% overall alignment rate Time searching: 00:16:31 Overall time: 00:16:31 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] 7496544 / 21452813 = 0.3494 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 22:11:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495323/SRX495323.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495323/SRX495323.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495323/SRX495323.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495323/SRX495323.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 22:11:23: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:11:23: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:11:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495323/SRX495323.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495323/SRX495323.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495323/SRX495323.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495323/SRX495323.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 22:11:23: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:11:23: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:11:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495323/SRX495323.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495323/SRX495323.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495323/SRX495323.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495323/SRX495323.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 22:11:23: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:11:23: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:11:31: 1000000 INFO @ Mon, 03 Jun 2019 22:11:31: 1000000 INFO @ Mon, 03 Jun 2019 22:11:31: 1000000 INFO @ Mon, 03 Jun 2019 22:11:38: 2000000 INFO @ Mon, 03 Jun 2019 22:11:38: 2000000 INFO @ Mon, 03 Jun 2019 22:11:38: 2000000 INFO @ Mon, 03 Jun 2019 22:11:46: 3000000 INFO @ Mon, 03 Jun 2019 22:11:46: 3000000 INFO @ Mon, 03 Jun 2019 22:11:46: 3000000 INFO @ Mon, 03 Jun 2019 22:11:53: 4000000 INFO @ Mon, 03 Jun 2019 22:11:54: 4000000 INFO @ Mon, 03 Jun 2019 22:11:54: 4000000 INFO @ Mon, 03 Jun 2019 22:12:01: 5000000 INFO @ Mon, 03 Jun 2019 22:12:01: 5000000 INFO @ Mon, 03 Jun 2019 22:12:01: 5000000 INFO @ Mon, 03 Jun 2019 22:12:08: 6000000 INFO @ Mon, 03 Jun 2019 22:12:08: 6000000 INFO @ Mon, 03 Jun 2019 22:12:09: 6000000 INFO @ Mon, 03 Jun 2019 22:12:15: 7000000 INFO @ Mon, 03 Jun 2019 22:12:16: 7000000 INFO @ Mon, 03 Jun 2019 22:12:16: 7000000 INFO @ Mon, 03 Jun 2019 22:12:22: 8000000 INFO @ Mon, 03 Jun 2019 22:12:23: 8000000 INFO @ Mon, 03 Jun 2019 22:12:23: 8000000 INFO @ Mon, 03 Jun 2019 22:12:29: 9000000 INFO @ Mon, 03 Jun 2019 22:12:30: 9000000 INFO @ Mon, 03 Jun 2019 22:12:30: 9000000 INFO @ Mon, 03 Jun 2019 22:12:36: 10000000 INFO @ Mon, 03 Jun 2019 22:12:37: 10000000 INFO @ Mon, 03 Jun 2019 22:12:37: 10000000 INFO @ Mon, 03 Jun 2019 22:12:43: 11000000 INFO @ Mon, 03 Jun 2019 22:12:44: 11000000 INFO @ Mon, 03 Jun 2019 22:12:44: 11000000 INFO @ Mon, 03 Jun 2019 22:12:50: 12000000 INFO @ Mon, 03 Jun 2019 22:12:52: 12000000 INFO @ Mon, 03 Jun 2019 22:12:52: 12000000 INFO @ Mon, 03 Jun 2019 22:12:57: 13000000 INFO @ Mon, 03 Jun 2019 22:12:59: 13000000 INFO @ Mon, 03 Jun 2019 22:12:59: 13000000 INFO @ Mon, 03 Jun 2019 22:13:04: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 22:13:04: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 22:13:04: #1 total tags in treatment: 13956269 INFO @ Mon, 03 Jun 2019 22:13:04: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:13:04: #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 22:13:04: #1 tags after filtering in treatment: 13956269 INFO @ Mon, 03 Jun 2019 22:13:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:13:04: #1 finished! INFO @ Mon, 03 Jun 2019 22:13:04: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:13:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:13:05: #2 number of paired peaks: 445 WARNING @ Mon, 03 Jun 2019 22:13:05: Fewer paired peaks (445) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 445 pairs to build model! INFO @ Mon, 03 Jun 2019 22:13:05: start model_add_line... INFO @ Mon, 03 Jun 2019 22:13:06: start X-correlation... INFO @ Mon, 03 Jun 2019 22:13:06: end of X-cor INFO @ Mon, 03 Jun 2019 22:13:06: #2 finished! INFO @ Mon, 03 Jun 2019 22:13:06: #2 predicted fragment length is 3 bps INFO @ Mon, 03 Jun 2019 22:13:06: #2 alternative fragment length(s) may be 3,11,39 bps INFO @ Mon, 03 Jun 2019 22:13:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495323/SRX495323.05_model.r WARNING @ Mon, 03 Jun 2019 22:13:06: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:13:06: #2 You may need to consider one of the other alternative d(s): 3,11,39 WARNING @ Mon, 03 Jun 2019 22:13:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 22:13:06: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:13:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:13:06: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 22:13:06: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 22:13:06: #1 total tags in treatment: 13956269 INFO @ Mon, 03 Jun 2019 22:13:06: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:13:06: #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 22:13:06: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 22:13:06: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 22:13:06: #1 total tags in treatment: 13956269 INFO @ Mon, 03 Jun 2019 22:13:06: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:13:06: #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 22:13:06: #1 tags after filtering in treatment: 13956269 INFO @ Mon, 03 Jun 2019 22:13:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:13:06: #1 finished! INFO @ Mon, 03 Jun 2019 22:13:06: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:13:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:13:06: #1 tags after filtering in treatment: 13956269 INFO @ Mon, 03 Jun 2019 22:13:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:13:06: #1 finished! INFO @ Mon, 03 Jun 2019 22:13:06: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:13:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:13:07: #2 number of paired peaks: 445 WARNING @ Mon, 03 Jun 2019 22:13:07: Fewer paired peaks (445) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 445 pairs to build model! INFO @ Mon, 03 Jun 2019 22:13:07: start model_add_line... INFO @ Mon, 03 Jun 2019 22:13:07: start X-correlation... INFO @ Mon, 03 Jun 2019 22:13:07: end of X-cor INFO @ Mon, 03 Jun 2019 22:13:07: #2 finished! INFO @ Mon, 03 Jun 2019 22:13:07: #2 predicted fragment length is 3 bps INFO @ Mon, 03 Jun 2019 22:13:07: #2 alternative fragment length(s) may be 3,11,39 bps INFO @ Mon, 03 Jun 2019 22:13:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495323/SRX495323.10_model.r WARNING @ Mon, 03 Jun 2019 22:13:07: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:13:07: #2 You may need to consider one of the other alternative d(s): 3,11,39 WARNING @ Mon, 03 Jun 2019 22:13:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 22:13:07: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:13:07: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:13:08: #2 number of paired peaks: 445 WARNING @ Mon, 03 Jun 2019 22:13:08: Fewer paired peaks (445) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 445 pairs to build model! INFO @ Mon, 03 Jun 2019 22:13:08: start model_add_line... INFO @ Mon, 03 Jun 2019 22:13:08: start X-correlation... INFO @ Mon, 03 Jun 2019 22:13:08: end of X-cor INFO @ Mon, 03 Jun 2019 22:13:08: #2 finished! INFO @ Mon, 03 Jun 2019 22:13:08: #2 predicted fragment length is 3 bps INFO @ Mon, 03 Jun 2019 22:13:08: #2 alternative fragment length(s) may be 3,11,39 bps INFO @ Mon, 03 Jun 2019 22:13:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495323/SRX495323.20_model.r WARNING @ Mon, 03 Jun 2019 22:13:08: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:13:08: #2 You may need to consider one of the other alternative d(s): 3,11,39 WARNING @ Mon, 03 Jun 2019 22:13:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 22:13:08: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:13:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:13:42: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:13:44: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:13:44: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:13:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495323/SRX495323.05_peaks.xls INFO @ Mon, 03 Jun 2019 22:13:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495323/SRX495323.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:13:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495323/SRX495323.05_summits.bed INFO @ Mon, 03 Jun 2019 22:13:59: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:14:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495323/SRX495323.10_peaks.xls INFO @ Mon, 03 Jun 2019 22:14:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495323/SRX495323.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:14:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495323/SRX495323.10_summits.bed INFO @ Mon, 03 Jun 2019 22:14:01: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:14:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495323/SRX495323.20_peaks.xls INFO @ Mon, 03 Jun 2019 22:14:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495323/SRX495323.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:14:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495323/SRX495323.20_summits.bed INFO @ Mon, 03 Jun 2019 22:14:01: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。