Job ID = 1294577 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T00:03:15 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 ) 2019-06-03T00:03:15 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 ) 2019-06-03T00:04:18 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 ) 2019-06-03T00:07:40 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 ) 2019-06-03T00:08:00 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 ) 2019-06-03T00:08:00 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 : 16,158,558 reads read : 16,158,558 reads written : 16,158,558 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: 00:06:27 16158558 reads; of these: 16158558 (100.00%) were unpaired; of these: 799898 (4.95%) aligned 0 times 11062214 (68.46%) aligned exactly 1 time 4296446 (26.59%) aligned >1 times 95.05% overall alignment rate Time searching: 00:06:27 Overall time: 00:06:27 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 8 files... [bam_rmdupse_core] 2084462 / 15358660 = 0.1357 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 09:21:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287752/SRX287752.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287752/SRX287752.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287752/SRX287752.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287752/SRX287752.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 09:21:26: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:21:26: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:21:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287752/SRX287752.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287752/SRX287752.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287752/SRX287752.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287752/SRX287752.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 09:21:26: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:21:26: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:21:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287752/SRX287752.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287752/SRX287752.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287752/SRX287752.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287752/SRX287752.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 09:21:26: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:21:26: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:21:36: 1000000 INFO @ Mon, 03 Jun 2019 09:21:36: 1000000 INFO @ Mon, 03 Jun 2019 09:21:36: 1000000 INFO @ Mon, 03 Jun 2019 09:21:46: 2000000 INFO @ Mon, 03 Jun 2019 09:21:46: 2000000 INFO @ Mon, 03 Jun 2019 09:21:46: 2000000 INFO @ Mon, 03 Jun 2019 09:21:56: 3000000 INFO @ Mon, 03 Jun 2019 09:21:57: 3000000 INFO @ Mon, 03 Jun 2019 09:21:57: 3000000 INFO @ Mon, 03 Jun 2019 09:22:06: 4000000 INFO @ Mon, 03 Jun 2019 09:22:07: 4000000 INFO @ Mon, 03 Jun 2019 09:22:07: 4000000 INFO @ Mon, 03 Jun 2019 09:22:16: 5000000 INFO @ Mon, 03 Jun 2019 09:22:17: 5000000 INFO @ Mon, 03 Jun 2019 09:22:17: 5000000 INFO @ Mon, 03 Jun 2019 09:22:25: 6000000 INFO @ Mon, 03 Jun 2019 09:22:27: 6000000 INFO @ Mon, 03 Jun 2019 09:22:27: 6000000 INFO @ Mon, 03 Jun 2019 09:22:35: 7000000 INFO @ Mon, 03 Jun 2019 09:22:36: 7000000 INFO @ Mon, 03 Jun 2019 09:22:36: 7000000 INFO @ Mon, 03 Jun 2019 09:22:44: 8000000 INFO @ Mon, 03 Jun 2019 09:22:46: 8000000 INFO @ Mon, 03 Jun 2019 09:22:46: 8000000 INFO @ Mon, 03 Jun 2019 09:22:53: 9000000 INFO @ Mon, 03 Jun 2019 09:22:55: 9000000 INFO @ Mon, 03 Jun 2019 09:22:56: 9000000 INFO @ Mon, 03 Jun 2019 09:23:02: 10000000 INFO @ Mon, 03 Jun 2019 09:23:04: 10000000 INFO @ Mon, 03 Jun 2019 09:23:04: 10000000 INFO @ Mon, 03 Jun 2019 09:23:11: 11000000 INFO @ Mon, 03 Jun 2019 09:23:12: 11000000 INFO @ Mon, 03 Jun 2019 09:23:12: 11000000 INFO @ Mon, 03 Jun 2019 09:23:20: 12000000 INFO @ Mon, 03 Jun 2019 09:23:21: 12000000 INFO @ Mon, 03 Jun 2019 09:23:21: 12000000 INFO @ Mon, 03 Jun 2019 09:23:29: 13000000 INFO @ Mon, 03 Jun 2019 09:23:29: 13000000 INFO @ Mon, 03 Jun 2019 09:23:29: 13000000 INFO @ Mon, 03 Jun 2019 09:23:31: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:23:31: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:23:31: #1 total tags in treatment: 13274198 INFO @ Mon, 03 Jun 2019 09:23:31: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:23:31: #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 09:23:31: #1 tags after filtering in treatment: 13274198 INFO @ Mon, 03 Jun 2019 09:23:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:23:31: #1 finished! INFO @ Mon, 03 Jun 2019 09:23:31: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:23:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:23:32: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:23:32: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:23:32: #1 total tags in treatment: 13274198 INFO @ Mon, 03 Jun 2019 09:23:32: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:23:32: #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 09:23:32: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:23:32: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:23:32: #1 total tags in treatment: 13274198 INFO @ Mon, 03 Jun 2019 09:23:32: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:23:32: #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 09:23:32: #1 tags after filtering in treatment: 13274198 INFO @ Mon, 03 Jun 2019 09:23:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:23:32: #1 finished! INFO @ Mon, 03 Jun 2019 09:23:32: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:23:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:23:32: #1 tags after filtering in treatment: 13274198 INFO @ Mon, 03 Jun 2019 09:23:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:23:32: #1 finished! INFO @ Mon, 03 Jun 2019 09:23:32: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:23:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:23:33: #2 number of paired peaks: 497 WARNING @ Mon, 03 Jun 2019 09:23:33: Fewer paired peaks (497) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 497 pairs to build model! INFO @ Mon, 03 Jun 2019 09:23:33: start model_add_line... INFO @ Mon, 03 Jun 2019 09:23:33: start X-correlation... INFO @ Mon, 03 Jun 2019 09:23:33: end of X-cor INFO @ Mon, 03 Jun 2019 09:23:33: #2 finished! INFO @ Mon, 03 Jun 2019 09:23:33: #2 predicted fragment length is 154 bps INFO @ Mon, 03 Jun 2019 09:23:33: #2 alternative fragment length(s) may be 154 bps INFO @ Mon, 03 Jun 2019 09:23:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287752/SRX287752.10_model.r INFO @ Mon, 03 Jun 2019 09:23:33: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:23:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:23:33: #2 number of paired peaks: 497 WARNING @ Mon, 03 Jun 2019 09:23:33: Fewer paired peaks (497) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 497 pairs to build model! INFO @ Mon, 03 Jun 2019 09:23:33: start model_add_line... INFO @ Mon, 03 Jun 2019 09:23:33: start X-correlation... INFO @ Mon, 03 Jun 2019 09:23:33: end of X-cor INFO @ Mon, 03 Jun 2019 09:23:33: #2 finished! INFO @ Mon, 03 Jun 2019 09:23:33: #2 predicted fragment length is 154 bps INFO @ Mon, 03 Jun 2019 09:23:33: #2 alternative fragment length(s) may be 154 bps INFO @ Mon, 03 Jun 2019 09:23:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287752/SRX287752.05_model.r INFO @ Mon, 03 Jun 2019 09:23:33: #2 number of paired peaks: 497 WARNING @ Mon, 03 Jun 2019 09:23:33: Fewer paired peaks (497) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 497 pairs to build model! INFO @ Mon, 03 Jun 2019 09:23:33: start model_add_line... INFO @ Mon, 03 Jun 2019 09:23:33: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:23:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:23:33: start X-correlation... INFO @ Mon, 03 Jun 2019 09:23:33: end of X-cor INFO @ Mon, 03 Jun 2019 09:23:33: #2 finished! INFO @ Mon, 03 Jun 2019 09:23:33: #2 predicted fragment length is 154 bps INFO @ Mon, 03 Jun 2019 09:23:33: #2 alternative fragment length(s) may be 154 bps INFO @ Mon, 03 Jun 2019 09:23:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287752/SRX287752.20_model.r INFO @ Mon, 03 Jun 2019 09:23:33: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:23:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:24:11: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:24:12: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:24:12: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:24:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287752/SRX287752.10_peaks.xls INFO @ Mon, 03 Jun 2019 09:24:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287752/SRX287752.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:24:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287752/SRX287752.10_summits.bed INFO @ Mon, 03 Jun 2019 09:24:30: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2385 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:24:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287752/SRX287752.20_peaks.xls INFO @ Mon, 03 Jun 2019 09:24:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287752/SRX287752.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:24:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287752/SRX287752.20_summits.bed INFO @ Mon, 03 Jun 2019 09:24:31: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1712 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:24:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287752/SRX287752.05_peaks.xls INFO @ Mon, 03 Jun 2019 09:24:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287752/SRX287752.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:24:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287752/SRX287752.05_summits.bed INFO @ Mon, 03 Jun 2019 09:24:31: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3216 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。