Job ID = 1301376 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T10:50:38 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 ) 2019-06-03T10:50:38 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 ) 2019-06-03T10:57:07 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 ) 2019-06-03T10:57:07 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 ) 2019-06-03T10:57:07 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 ) 2019-06-03T11:03:45 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 : 31,816,837 reads read : 31,816,837 reads written : 31,816,837 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: 00:08:42 31816837 reads; of these: 31816837 (100.00%) were unpaired; of these: 9034612 (28.40%) aligned 0 times 18693067 (58.75%) aligned exactly 1 time 4089158 (12.85%) aligned >1 times 71.60% overall alignment rate Time searching: 00:08:42 Overall time: 00:08:42 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] 16678504 / 22782225 = 0.7321 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 20:20:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX485212/SRX485212.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX485212/SRX485212.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX485212/SRX485212.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX485212/SRX485212.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 20:20:45: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:20:45: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:20:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX485212/SRX485212.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX485212/SRX485212.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX485212/SRX485212.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX485212/SRX485212.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 20:20:45: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:20:45: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:20:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX485212/SRX485212.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX485212/SRX485212.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX485212/SRX485212.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX485212/SRX485212.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 20:20:45: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:20:45: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:20:54: 1000000 INFO @ Mon, 03 Jun 2019 20:20:54: 1000000 INFO @ Mon, 03 Jun 2019 20:20:55: 1000000 INFO @ Mon, 03 Jun 2019 20:21:01: 2000000 INFO @ Mon, 03 Jun 2019 20:21:03: 2000000 INFO @ Mon, 03 Jun 2019 20:21:03: 2000000 INFO @ Mon, 03 Jun 2019 20:21:09: 3000000 INFO @ Mon, 03 Jun 2019 20:21:11: 3000000 INFO @ Mon, 03 Jun 2019 20:21:12: 3000000 INFO @ Mon, 03 Jun 2019 20:21:16: 4000000 INFO @ Mon, 03 Jun 2019 20:21:19: 4000000 INFO @ Mon, 03 Jun 2019 20:21:20: 4000000 INFO @ Mon, 03 Jun 2019 20:21:24: 5000000 INFO @ Mon, 03 Jun 2019 20:21:27: 5000000 INFO @ Mon, 03 Jun 2019 20:21:28: 5000000 INFO @ Mon, 03 Jun 2019 20:21:31: 6000000 INFO @ Mon, 03 Jun 2019 20:21:32: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:21:32: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:21:32: #1 total tags in treatment: 6103721 INFO @ Mon, 03 Jun 2019 20:21:32: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:21:32: #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 20:21:32: #1 tags after filtering in treatment: 6103721 INFO @ Mon, 03 Jun 2019 20:21:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:21:32: #1 finished! INFO @ Mon, 03 Jun 2019 20:21:32: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:21:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:21:33: #2 number of paired peaks: 919 WARNING @ Mon, 03 Jun 2019 20:21:33: Fewer paired peaks (919) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 919 pairs to build model! INFO @ Mon, 03 Jun 2019 20:21:33: start model_add_line... INFO @ Mon, 03 Jun 2019 20:21:33: start X-correlation... INFO @ Mon, 03 Jun 2019 20:21:33: end of X-cor INFO @ Mon, 03 Jun 2019 20:21:33: #2 finished! INFO @ Mon, 03 Jun 2019 20:21:33: #2 predicted fragment length is 134 bps INFO @ Mon, 03 Jun 2019 20:21:33: #2 alternative fragment length(s) may be 134 bps INFO @ Mon, 03 Jun 2019 20:21:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX485212/SRX485212.20_model.r INFO @ Mon, 03 Jun 2019 20:21:33: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:21:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:21:35: 6000000 INFO @ Mon, 03 Jun 2019 20:21:36: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:21:36: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:21:36: #1 total tags in treatment: 6103721 INFO @ Mon, 03 Jun 2019 20:21:36: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:21:36: #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 20:21:36: #1 tags after filtering in treatment: 6103721 INFO @ Mon, 03 Jun 2019 20:21:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:21:36: #1 finished! INFO @ Mon, 03 Jun 2019 20:21:36: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:21:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:21:36: 6000000 INFO @ Mon, 03 Jun 2019 20:21:36: #2 number of paired peaks: 919 WARNING @ Mon, 03 Jun 2019 20:21:36: Fewer paired peaks (919) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 919 pairs to build model! INFO @ Mon, 03 Jun 2019 20:21:36: start model_add_line... INFO @ Mon, 03 Jun 2019 20:21:36: start X-correlation... INFO @ Mon, 03 Jun 2019 20:21:36: end of X-cor INFO @ Mon, 03 Jun 2019 20:21:36: #2 finished! INFO @ Mon, 03 Jun 2019 20:21:36: #2 predicted fragment length is 134 bps INFO @ Mon, 03 Jun 2019 20:21:36: #2 alternative fragment length(s) may be 134 bps INFO @ Mon, 03 Jun 2019 20:21:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX485212/SRX485212.10_model.r INFO @ Mon, 03 Jun 2019 20:21:36: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:21:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:21:37: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:21:37: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:21:37: #1 total tags in treatment: 6103721 INFO @ Mon, 03 Jun 2019 20:21:37: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:21:37: #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 20:21:37: #1 tags after filtering in treatment: 6103721 INFO @ Mon, 03 Jun 2019 20:21:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:21:37: #1 finished! INFO @ Mon, 03 Jun 2019 20:21:37: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:21:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:21:38: #2 number of paired peaks: 919 WARNING @ Mon, 03 Jun 2019 20:21:38: Fewer paired peaks (919) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 919 pairs to build model! INFO @ Mon, 03 Jun 2019 20:21:38: start model_add_line... INFO @ Mon, 03 Jun 2019 20:21:38: start X-correlation... INFO @ Mon, 03 Jun 2019 20:21:38: end of X-cor INFO @ Mon, 03 Jun 2019 20:21:38: #2 finished! INFO @ Mon, 03 Jun 2019 20:21:38: #2 predicted fragment length is 134 bps INFO @ Mon, 03 Jun 2019 20:21:38: #2 alternative fragment length(s) may be 134 bps INFO @ Mon, 03 Jun 2019 20:21:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX485212/SRX485212.05_model.r INFO @ Mon, 03 Jun 2019 20:21:38: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:21:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:21:52: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:21:56: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:21:57: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:22:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX485212/SRX485212.20_peaks.xls INFO @ Mon, 03 Jun 2019 20:22:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX485212/SRX485212.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:22:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX485212/SRX485212.20_summits.bed INFO @ Mon, 03 Jun 2019 20:22:01: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (797 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:22:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX485212/SRX485212.10_peaks.xls INFO @ Mon, 03 Jun 2019 20:22:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX485212/SRX485212.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:22:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX485212/SRX485212.10_summits.bed INFO @ Mon, 03 Jun 2019 20:22:05: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1376 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:22:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX485212/SRX485212.05_peaks.xls INFO @ Mon, 03 Jun 2019 20:22:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX485212/SRX485212.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:22:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX485212/SRX485212.05_summits.bed INFO @ Mon, 03 Jun 2019 20:22:06: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2595 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。