Job ID = 1294251 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T20:49:34 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 ) 2019-06-02T20:49:34 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 : 21,806,275 reads read : 43,612,550 reads written : 21,806,275 reads 0-length : 21,806,275 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: 00:08:49 21806275 reads; of these: 21806275 (100.00%) were unpaired; of these: 565304 (2.59%) aligned 0 times 15640858 (71.73%) aligned exactly 1 time 5600113 (25.68%) aligned >1 times 97.41% overall alignment rate Time searching: 00:08:49 Overall time: 00:08:49 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] 4413472 / 21240971 = 0.2078 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 06:09:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2035282/SRX2035282.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2035282/SRX2035282.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2035282/SRX2035282.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2035282/SRX2035282.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 06:09:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:09:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:09:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2035282/SRX2035282.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2035282/SRX2035282.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2035282/SRX2035282.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2035282/SRX2035282.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 06:09:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:09:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:09:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2035282/SRX2035282.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2035282/SRX2035282.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2035282/SRX2035282.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2035282/SRX2035282.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 06:09:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:09:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:09:08: 1000000 INFO @ Mon, 03 Jun 2019 06:09:11: 1000000 INFO @ Mon, 03 Jun 2019 06:09:11: 1000000 INFO @ Mon, 03 Jun 2019 06:09:16: 2000000 INFO @ Mon, 03 Jun 2019 06:09:22: 2000000 INFO @ Mon, 03 Jun 2019 06:09:22: 2000000 INFO @ Mon, 03 Jun 2019 06:09:23: 3000000 INFO @ Mon, 03 Jun 2019 06:09:31: 4000000 INFO @ Mon, 03 Jun 2019 06:09:33: 3000000 INFO @ Mon, 03 Jun 2019 06:09:33: 3000000 INFO @ Mon, 03 Jun 2019 06:09:38: 5000000 INFO @ Mon, 03 Jun 2019 06:09:44: 4000000 INFO @ Mon, 03 Jun 2019 06:09:44: 4000000 INFO @ Mon, 03 Jun 2019 06:09:45: 6000000 INFO @ Mon, 03 Jun 2019 06:09:53: 7000000 INFO @ Mon, 03 Jun 2019 06:09:55: 5000000 INFO @ Mon, 03 Jun 2019 06:09:55: 5000000 INFO @ Mon, 03 Jun 2019 06:10:00: 8000000 INFO @ Mon, 03 Jun 2019 06:10:06: 6000000 INFO @ Mon, 03 Jun 2019 06:10:06: 6000000 INFO @ Mon, 03 Jun 2019 06:10:08: 9000000 INFO @ Mon, 03 Jun 2019 06:10:15: 10000000 INFO @ Mon, 03 Jun 2019 06:10:17: 7000000 INFO @ Mon, 03 Jun 2019 06:10:17: 7000000 INFO @ Mon, 03 Jun 2019 06:10:22: 11000000 INFO @ Mon, 03 Jun 2019 06:10:28: 8000000 INFO @ Mon, 03 Jun 2019 06:10:28: 8000000 INFO @ Mon, 03 Jun 2019 06:10:30: 12000000 INFO @ Mon, 03 Jun 2019 06:10:37: 13000000 INFO @ Mon, 03 Jun 2019 06:10:38: 9000000 INFO @ Mon, 03 Jun 2019 06:10:38: 9000000 INFO @ Mon, 03 Jun 2019 06:10:44: 14000000 INFO @ Mon, 03 Jun 2019 06:10:49: 10000000 INFO @ Mon, 03 Jun 2019 06:10:49: 10000000 INFO @ Mon, 03 Jun 2019 06:10:52: 15000000 INFO @ Mon, 03 Jun 2019 06:10:59: 16000000 INFO @ Mon, 03 Jun 2019 06:10:59: 11000000 INFO @ Mon, 03 Jun 2019 06:10:59: 11000000 INFO @ Mon, 03 Jun 2019 06:11:05: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 06:11:05: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 06:11:05: #1 total tags in treatment: 16827499 INFO @ Mon, 03 Jun 2019 06:11:05: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:11:05: #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 06:11:05: #1 tags after filtering in treatment: 16827499 INFO @ Mon, 03 Jun 2019 06:11:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:11:05: #1 finished! INFO @ Mon, 03 Jun 2019 06:11:05: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:11:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:11:07: #2 number of paired peaks: 418 WARNING @ Mon, 03 Jun 2019 06:11:07: Fewer paired peaks (418) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 418 pairs to build model! INFO @ Mon, 03 Jun 2019 06:11:07: start model_add_line... INFO @ Mon, 03 Jun 2019 06:11:07: start X-correlation... INFO @ Mon, 03 Jun 2019 06:11:07: end of X-cor INFO @ Mon, 03 Jun 2019 06:11:07: #2 finished! INFO @ Mon, 03 Jun 2019 06:11:07: #2 predicted fragment length is 129 bps INFO @ Mon, 03 Jun 2019 06:11:07: #2 alternative fragment length(s) may be 129 bps INFO @ Mon, 03 Jun 2019 06:11:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2035282/SRX2035282.05_model.r INFO @ Mon, 03 Jun 2019 06:11:07: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:11:07: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:11:10: 12000000 INFO @ Mon, 03 Jun 2019 06:11:10: 12000000 INFO @ Mon, 03 Jun 2019 06:11:21: 13000000 INFO @ Mon, 03 Jun 2019 06:11:21: 13000000 INFO @ Mon, 03 Jun 2019 06:11:31: 14000000 INFO @ Mon, 03 Jun 2019 06:11:31: 14000000 INFO @ Mon, 03 Jun 2019 06:11:42: 15000000 INFO @ Mon, 03 Jun 2019 06:11:42: 15000000 INFO @ Mon, 03 Jun 2019 06:11:52: 16000000 INFO @ Mon, 03 Jun 2019 06:11:52: 16000000 INFO @ Mon, 03 Jun 2019 06:11:54: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:12:01: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 06:12:01: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 06:12:01: #1 total tags in treatment: 16827499 INFO @ Mon, 03 Jun 2019 06:12:01: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:12:01: #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 06:12:01: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 06:12:01: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 06:12:01: #1 total tags in treatment: 16827499 INFO @ Mon, 03 Jun 2019 06:12:01: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:12:01: #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 06:12:01: #1 tags after filtering in treatment: 16827499 INFO @ Mon, 03 Jun 2019 06:12:01: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:12:01: #1 finished! INFO @ Mon, 03 Jun 2019 06:12:01: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:12:01: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:12:01: #1 tags after filtering in treatment: 16827499 INFO @ Mon, 03 Jun 2019 06:12:01: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:12:01: #1 finished! INFO @ Mon, 03 Jun 2019 06:12:01: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:12:01: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:12:02: #2 number of paired peaks: 418 WARNING @ Mon, 03 Jun 2019 06:12:02: Fewer paired peaks (418) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 418 pairs to build model! INFO @ Mon, 03 Jun 2019 06:12:02: start model_add_line... INFO @ Mon, 03 Jun 2019 06:12:03: #2 number of paired peaks: 418 WARNING @ Mon, 03 Jun 2019 06:12:03: Fewer paired peaks (418) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 418 pairs to build model! INFO @ Mon, 03 Jun 2019 06:12:03: start model_add_line... INFO @ Mon, 03 Jun 2019 06:12:03: start X-correlation... INFO @ Mon, 03 Jun 2019 06:12:03: end of X-cor INFO @ Mon, 03 Jun 2019 06:12:03: #2 finished! INFO @ Mon, 03 Jun 2019 06:12:03: #2 predicted fragment length is 129 bps INFO @ Mon, 03 Jun 2019 06:12:03: #2 alternative fragment length(s) may be 129 bps INFO @ Mon, 03 Jun 2019 06:12:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2035282/SRX2035282.10_model.r INFO @ Mon, 03 Jun 2019 06:12:03: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:12:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:12:03: start X-correlation... INFO @ Mon, 03 Jun 2019 06:12:03: end of X-cor INFO @ Mon, 03 Jun 2019 06:12:03: #2 finished! INFO @ Mon, 03 Jun 2019 06:12:03: #2 predicted fragment length is 129 bps INFO @ Mon, 03 Jun 2019 06:12:03: #2 alternative fragment length(s) may be 129 bps INFO @ Mon, 03 Jun 2019 06:12:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2035282/SRX2035282.20_model.r INFO @ Mon, 03 Jun 2019 06:12:03: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:12:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:12:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2035282/SRX2035282.05_peaks.xls INFO @ Mon, 03 Jun 2019 06:12:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2035282/SRX2035282.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:12:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2035282/SRX2035282.05_summits.bed INFO @ Mon, 03 Jun 2019 06:12:18: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (7616 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:12:49: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:12:49: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:13:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2035282/SRX2035282.10_peaks.xls INFO @ Mon, 03 Jun 2019 06:13:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2035282/SRX2035282.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:13:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2035282/SRX2035282.10_summits.bed INFO @ Mon, 03 Jun 2019 06:13:14: Done! INFO @ Mon, 03 Jun 2019 06:13:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2035282/SRX2035282.20_peaks.xls INFO @ Mon, 03 Jun 2019 06:13:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2035282/SRX2035282.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:13:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2035282/SRX2035282.20_summits.bed INFO @ Mon, 03 Jun 2019 06:13:14: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4829 records, 4 fields): 8 millis CompletedMACS2peakCalling pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2157 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。