Job ID = 2001546 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T19:41:56 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 : 23,321,657 reads read : 23,321,657 reads written : 23,321,657 rm: cannot remove ‘[DSE]RR*’: 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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:10:36 23321657 reads; of these: 23321657 (100.00%) were unpaired; of these: 734014 (3.15%) aligned 0 times 17128729 (73.45%) aligned exactly 1 time 5458914 (23.41%) aligned >1 times 96.85% overall alignment rate Time searching: 00:10:38 Overall time: 00:10:38 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1477409 / 22587643 = 0.0654 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 @ Fri, 05 Jul 2019 05:03:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101889/ERX101889.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101889/ERX101889.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101889/ERX101889.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101889/ERX101889.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 05 Jul 2019 05:03:30: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:03:30: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:03:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101889/ERX101889.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101889/ERX101889.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101889/ERX101889.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101889/ERX101889.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 05 Jul 2019 05:03:32: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:03:32: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:03:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101889/ERX101889.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101889/ERX101889.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101889/ERX101889.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101889/ERX101889.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 05 Jul 2019 05:03:32: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:03:32: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:03:42: 1000000 INFO @ Fri, 05 Jul 2019 05:03:43: 1000000 INFO @ Fri, 05 Jul 2019 05:03:45: 1000000 INFO @ Fri, 05 Jul 2019 05:03:53: 2000000 INFO @ Fri, 05 Jul 2019 05:03:54: 2000000 INFO @ Fri, 05 Jul 2019 05:03:56: 2000000 INFO @ Fri, 05 Jul 2019 05:04:04: 3000000 INFO @ Fri, 05 Jul 2019 05:04:04: 3000000 INFO @ Fri, 05 Jul 2019 05:04:06: 3000000 INFO @ Fri, 05 Jul 2019 05:04:13: 4000000 INFO @ Fri, 05 Jul 2019 05:04:14: 4000000 INFO @ Fri, 05 Jul 2019 05:04:16: 4000000 INFO @ Fri, 05 Jul 2019 05:04:22: 5000000 INFO @ Fri, 05 Jul 2019 05:04:23: 5000000 INFO @ Fri, 05 Jul 2019 05:04:26: 5000000 INFO @ Fri, 05 Jul 2019 05:04:32: 6000000 INFO @ Fri, 05 Jul 2019 05:04:33: 6000000 INFO @ Fri, 05 Jul 2019 05:04:37: 6000000 INFO @ Fri, 05 Jul 2019 05:04:41: 7000000 INFO @ Fri, 05 Jul 2019 05:04:41: 7000000 INFO @ Fri, 05 Jul 2019 05:04:47: 7000000 INFO @ Fri, 05 Jul 2019 05:04:52: 8000000 INFO @ Fri, 05 Jul 2019 05:04:52: 8000000 INFO @ Fri, 05 Jul 2019 05:04:59: 8000000 INFO @ Fri, 05 Jul 2019 05:05:02: 9000000 INFO @ Fri, 05 Jul 2019 05:05:04: 9000000 INFO @ Fri, 05 Jul 2019 05:05:10: 9000000 INFO @ Fri, 05 Jul 2019 05:05:12: 10000000 INFO @ Fri, 05 Jul 2019 05:05:15: 10000000 INFO @ Fri, 05 Jul 2019 05:05:19: 10000000 INFO @ Fri, 05 Jul 2019 05:05:22: 11000000 INFO @ Fri, 05 Jul 2019 05:05:25: 11000000 INFO @ Fri, 05 Jul 2019 05:05:29: 11000000 INFO @ Fri, 05 Jul 2019 05:05:32: 12000000 INFO @ Fri, 05 Jul 2019 05:05:35: 12000000 INFO @ Fri, 05 Jul 2019 05:05:40: 12000000 INFO @ Fri, 05 Jul 2019 05:05:42: 13000000 INFO @ Fri, 05 Jul 2019 05:05:45: 13000000 INFO @ Fri, 05 Jul 2019 05:05:50: 13000000 INFO @ Fri, 05 Jul 2019 05:05:52: 14000000 INFO @ Fri, 05 Jul 2019 05:05:53: 14000000 INFO @ Fri, 05 Jul 2019 05:06:00: 14000000 INFO @ Fri, 05 Jul 2019 05:06:02: 15000000 INFO @ Fri, 05 Jul 2019 05:06:02: 15000000 INFO @ Fri, 05 Jul 2019 05:06:10: 15000000 INFO @ Fri, 05 Jul 2019 05:06:11: 16000000 INFO @ Fri, 05 Jul 2019 05:06:11: 16000000 INFO @ Fri, 05 Jul 2019 05:06:20: 17000000 INFO @ Fri, 05 Jul 2019 05:06:21: 16000000 INFO @ Fri, 05 Jul 2019 05:06:21: 17000000 INFO @ Fri, 05 Jul 2019 05:06:30: 18000000 INFO @ Fri, 05 Jul 2019 05:06:31: 18000000 INFO @ Fri, 05 Jul 2019 05:06:31: 17000000 INFO @ Fri, 05 Jul 2019 05:06:39: 19000000 INFO @ Fri, 05 Jul 2019 05:06:41: 19000000 INFO @ Fri, 05 Jul 2019 05:06:42: 18000000 INFO @ Fri, 05 Jul 2019 05:06:49: 20000000 INFO @ Fri, 05 Jul 2019 05:06:50: 20000000 INFO @ Fri, 05 Jul 2019 05:06:52: 19000000 INFO @ Fri, 05 Jul 2019 05:06:58: 21000000 INFO @ Fri, 05 Jul 2019 05:06:59: 21000000 INFO @ Fri, 05 Jul 2019 05:06:59: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 05:06:59: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 05:06:59: #1 total tags in treatment: 21110234 INFO @ Fri, 05 Jul 2019 05:06:59: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:06:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 05:07:00: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 05:07:00: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 05:07:00: #1 total tags in treatment: 21110234 INFO @ Fri, 05 Jul 2019 05:07:00: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:07:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 05:07:00: #1 tags after filtering in treatment: 21110077 INFO @ Fri, 05 Jul 2019 05:07:00: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:07:00: #1 finished! INFO @ Fri, 05 Jul 2019 05:07:00: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:07:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:07:00: #1 tags after filtering in treatment: 21110077 INFO @ Fri, 05 Jul 2019 05:07:00: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:07:00: #1 finished! INFO @ Fri, 05 Jul 2019 05:07:00: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:07:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:07:03: 20000000 INFO @ Fri, 05 Jul 2019 05:07:05: #2 number of paired peaks: 57152 INFO @ Fri, 05 Jul 2019 05:07:05: start model_add_line... INFO @ Fri, 05 Jul 2019 05:07:05: start X-correlation... INFO @ Fri, 05 Jul 2019 05:07:05: end of X-cor INFO @ Fri, 05 Jul 2019 05:07:05: #2 finished! INFO @ Fri, 05 Jul 2019 05:07:05: #2 predicted fragment length is 128 bps INFO @ Fri, 05 Jul 2019 05:07:05: #2 alternative fragment length(s) may be 128 bps INFO @ Fri, 05 Jul 2019 05:07:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101889/ERX101889.10_model.r INFO @ Fri, 05 Jul 2019 05:07:05: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:07:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:07:06: #2 number of paired peaks: 57152 INFO @ Fri, 05 Jul 2019 05:07:06: start model_add_line... INFO @ Fri, 05 Jul 2019 05:07:06: start X-correlation... INFO @ Fri, 05 Jul 2019 05:07:06: end of X-cor INFO @ Fri, 05 Jul 2019 05:07:06: #2 finished! INFO @ Fri, 05 Jul 2019 05:07:06: #2 predicted fragment length is 128 bps INFO @ Fri, 05 Jul 2019 05:07:06: #2 alternative fragment length(s) may be 128 bps INFO @ Fri, 05 Jul 2019 05:07:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101889/ERX101889.05_model.r INFO @ Fri, 05 Jul 2019 05:07:06: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:07:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:07:13: 21000000 INFO @ Fri, 05 Jul 2019 05:07:14: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 05:07:14: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 05:07:14: #1 total tags in treatment: 21110234 INFO @ Fri, 05 Jul 2019 05:07:14: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:07:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 05:07:14: #1 tags after filtering in treatment: 21110077 INFO @ Fri, 05 Jul 2019 05:07:14: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:07:14: #1 finished! INFO @ Fri, 05 Jul 2019 05:07:14: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:07:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:07:20: #2 number of paired peaks: 57152 INFO @ Fri, 05 Jul 2019 05:07:20: start model_add_line... INFO @ Fri, 05 Jul 2019 05:07:20: start X-correlation... INFO @ Fri, 05 Jul 2019 05:07:20: end of X-cor INFO @ Fri, 05 Jul 2019 05:07:20: #2 finished! INFO @ Fri, 05 Jul 2019 05:07:20: #2 predicted fragment length is 128 bps INFO @ Fri, 05 Jul 2019 05:07:20: #2 alternative fragment length(s) may be 128 bps INFO @ Fri, 05 Jul 2019 05:07:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101889/ERX101889.20_model.r INFO @ Fri, 05 Jul 2019 05:07:20: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:07:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:08:22: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 05:08:28: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 05:08:36: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 05:09:01: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101889/ERX101889.10_peaks.xls INFO @ Fri, 05 Jul 2019 05:09:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101889/ERX101889.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 05:09:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101889/ERX101889.10_summits.bed INFO @ Fri, 05 Jul 2019 05:09:01: Done! pass1 - making usageList (40 chroms): 1 millis pass2 - checking and writing primary data (1523 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 05:09:08: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101889/ERX101889.05_peaks.xls INFO @ Fri, 05 Jul 2019 05:09:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101889/ERX101889.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 05:09:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101889/ERX101889.05_summits.bed INFO @ Fri, 05 Jul 2019 05:09:08: Done! pass1 - making usageList (72 chroms): 2 millis pass2 - checking and writing primary data (6362 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 05:09:14: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101889/ERX101889.20_peaks.xls INFO @ Fri, 05 Jul 2019 05:09:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101889/ERX101889.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 05:09:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101889/ERX101889.20_summits.bed INFO @ Fri, 05 Jul 2019 05:09:14: Done! pass1 - making usageList (29 chroms): 1 millis pass2 - checking and writing primary data (183 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。