Job ID = 2001551 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T19:37:27 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 ) spots read : 22,104,573 reads read : 22,104,573 reads written : 22,104,573 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: 00:00:01 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:03 Multiseed full-index search: 00:10:04 22104573 reads; of these: 22104573 (100.00%) were unpaired; of these: 502035 (2.27%) aligned 0 times 16551806 (74.88%) aligned exactly 1 time 5050732 (22.85%) aligned >1 times 97.73% overall alignment rate Time searching: 00:10:11 Overall time: 00:10:11 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] 1221417 / 21602538 = 0.0565 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 05:04:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101894/ERX101894.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101894/ERX101894.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101894/ERX101894.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101894/ERX101894.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 05:04:46: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:04:46: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:04:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101894/ERX101894.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101894/ERX101894.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101894/ERX101894.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101894/ERX101894.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 05:04:46: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:04:46: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:04:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101894/ERX101894.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101894/ERX101894.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101894/ERX101894.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101894/ERX101894.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 05:04:47: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:04:47: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:04:56: 1000000 INFO @ Fri, 05 Jul 2019 05:04:56: 1000000 INFO @ Fri, 05 Jul 2019 05:04:57: 1000000 INFO @ Fri, 05 Jul 2019 05:05:06: 2000000 INFO @ Fri, 05 Jul 2019 05:05:07: 2000000 INFO @ Fri, 05 Jul 2019 05:05:08: 2000000 INFO @ Fri, 05 Jul 2019 05:05:16: 3000000 INFO @ Fri, 05 Jul 2019 05:05:17: 3000000 INFO @ Fri, 05 Jul 2019 05:05:18: 3000000 INFO @ Fri, 05 Jul 2019 05:05:25: 4000000 INFO @ Fri, 05 Jul 2019 05:05:27: 4000000 INFO @ Fri, 05 Jul 2019 05:05:28: 4000000 INFO @ Fri, 05 Jul 2019 05:05:34: 5000000 INFO @ Fri, 05 Jul 2019 05:05:37: 5000000 INFO @ Fri, 05 Jul 2019 05:05:38: 5000000 INFO @ Fri, 05 Jul 2019 05:05:43: 6000000 INFO @ Fri, 05 Jul 2019 05:05:48: 6000000 INFO @ Fri, 05 Jul 2019 05:05:48: 6000000 INFO @ Fri, 05 Jul 2019 05:05:52: 7000000 INFO @ Fri, 05 Jul 2019 05:05:58: 7000000 INFO @ Fri, 05 Jul 2019 05:05:59: 7000000 INFO @ Fri, 05 Jul 2019 05:06:01: 8000000 INFO @ Fri, 05 Jul 2019 05:06:08: 8000000 INFO @ Fri, 05 Jul 2019 05:06:09: 8000000 INFO @ Fri, 05 Jul 2019 05:06:10: 9000000 INFO @ Fri, 05 Jul 2019 05:06:19: 9000000 INFO @ Fri, 05 Jul 2019 05:06:19: 9000000 INFO @ Fri, 05 Jul 2019 05:06:20: 10000000 INFO @ Fri, 05 Jul 2019 05:06:29: 10000000 INFO @ Fri, 05 Jul 2019 05:06:29: 10000000 INFO @ Fri, 05 Jul 2019 05:06:30: 11000000 INFO @ Fri, 05 Jul 2019 05:06:39: 11000000 INFO @ Fri, 05 Jul 2019 05:06:39: 11000000 INFO @ Fri, 05 Jul 2019 05:06:40: 12000000 INFO @ Fri, 05 Jul 2019 05:06:49: 12000000 INFO @ Fri, 05 Jul 2019 05:06:49: 12000000 INFO @ Fri, 05 Jul 2019 05:06:49: 13000000 INFO @ Fri, 05 Jul 2019 05:06:59: 14000000 INFO @ Fri, 05 Jul 2019 05:07:00: 13000000 INFO @ Fri, 05 Jul 2019 05:07:00: 13000000 INFO @ Fri, 05 Jul 2019 05:07:08: 15000000 INFO @ Fri, 05 Jul 2019 05:07:10: 14000000 INFO @ Fri, 05 Jul 2019 05:07:10: 14000000 INFO @ Fri, 05 Jul 2019 05:07:18: 16000000 INFO @ Fri, 05 Jul 2019 05:07:19: 15000000 INFO @ Fri, 05 Jul 2019 05:07:20: 15000000 INFO @ Fri, 05 Jul 2019 05:07:27: 17000000 INFO @ Fri, 05 Jul 2019 05:07:30: 16000000 INFO @ Fri, 05 Jul 2019 05:07:31: 16000000 INFO @ Fri, 05 Jul 2019 05:07:38: 18000000 INFO @ Fri, 05 Jul 2019 05:07:40: 17000000 INFO @ Fri, 05 Jul 2019 05:07:42: 17000000 INFO @ Fri, 05 Jul 2019 05:07:48: 19000000 INFO @ Fri, 05 Jul 2019 05:07:49: 18000000 INFO @ Fri, 05 Jul 2019 05:07:51: 18000000 INFO @ Fri, 05 Jul 2019 05:07:58: 20000000 INFO @ Fri, 05 Jul 2019 05:07:59: 19000000 INFO @ Fri, 05 Jul 2019 05:08:02: 19000000 INFO @ Fri, 05 Jul 2019 05:08:02: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 05:08:02: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 05:08:02: #1 total tags in treatment: 20381121 INFO @ Fri, 05 Jul 2019 05:08:02: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:08:02: #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 05:08:03: #1 tags after filtering in treatment: 20380964 INFO @ Fri, 05 Jul 2019 05:08:03: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:08:03: #1 finished! INFO @ Fri, 05 Jul 2019 05:08:03: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:08:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:08:09: 20000000 INFO @ Fri, 05 Jul 2019 05:08:09: #2 number of paired peaks: 67084 INFO @ Fri, 05 Jul 2019 05:08:09: start model_add_line... INFO @ Fri, 05 Jul 2019 05:08:09: start X-correlation... INFO @ Fri, 05 Jul 2019 05:08:09: end of X-cor INFO @ Fri, 05 Jul 2019 05:08:09: #2 finished! INFO @ Fri, 05 Jul 2019 05:08:09: #2 predicted fragment length is 135 bps INFO @ Fri, 05 Jul 2019 05:08:09: #2 alternative fragment length(s) may be 4,135 bps INFO @ Fri, 05 Jul 2019 05:08:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101894/ERX101894.05_model.r INFO @ Fri, 05 Jul 2019 05:08:09: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:08:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:08:13: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 05:08:13: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 05:08:13: #1 total tags in treatment: 20381121 INFO @ Fri, 05 Jul 2019 05:08:13: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:08:13: #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 05:08:13: 20000000 INFO @ Fri, 05 Jul 2019 05:08:14: #1 tags after filtering in treatment: 20380964 INFO @ Fri, 05 Jul 2019 05:08:14: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:08:14: #1 finished! INFO @ Fri, 05 Jul 2019 05:08:14: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:08:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:08:17: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 05:08:17: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 05:08:17: #1 total tags in treatment: 20381121 INFO @ Fri, 05 Jul 2019 05:08:17: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:08:17: #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 05:08:17: #1 tags after filtering in treatment: 20380964 INFO @ Fri, 05 Jul 2019 05:08:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:08:17: #1 finished! INFO @ Fri, 05 Jul 2019 05:08:17: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:08:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:08:19: #2 number of paired peaks: 67084 INFO @ Fri, 05 Jul 2019 05:08:19: start model_add_line... INFO @ Fri, 05 Jul 2019 05:08:19: start X-correlation... INFO @ Fri, 05 Jul 2019 05:08:19: end of X-cor INFO @ Fri, 05 Jul 2019 05:08:19: #2 finished! INFO @ Fri, 05 Jul 2019 05:08:19: #2 predicted fragment length is 135 bps INFO @ Fri, 05 Jul 2019 05:08:19: #2 alternative fragment length(s) may be 4,135 bps INFO @ Fri, 05 Jul 2019 05:08:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101894/ERX101894.10_model.r INFO @ Fri, 05 Jul 2019 05:08:19: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:08:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:08:22: #2 number of paired peaks: 67084 INFO @ Fri, 05 Jul 2019 05:08:22: start model_add_line... INFO @ Fri, 05 Jul 2019 05:08:23: start X-correlation... INFO @ Fri, 05 Jul 2019 05:08:23: end of X-cor INFO @ Fri, 05 Jul 2019 05:08:23: #2 finished! INFO @ Fri, 05 Jul 2019 05:08:23: #2 predicted fragment length is 135 bps INFO @ Fri, 05 Jul 2019 05:08:23: #2 alternative fragment length(s) may be 4,135 bps INFO @ Fri, 05 Jul 2019 05:08:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101894/ERX101894.20_model.r INFO @ Fri, 05 Jul 2019 05:08:23: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:08:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:09:21: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 05:09:30: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 05:09:35: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 05:09:59: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101894/ERX101894.05_peaks.xls INFO @ Fri, 05 Jul 2019 05:09:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101894/ERX101894.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 05:09:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101894/ERX101894.05_summits.bed INFO @ Fri, 05 Jul 2019 05:09:59: Done! pass1 - making usageList (57 chroms): 2 millis pass2 - checking and writing primary data (4776 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 05:10:09: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101894/ERX101894.10_peaks.xls INFO @ Fri, 05 Jul 2019 05:10:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101894/ERX101894.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 05:10:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101894/ERX101894.10_summits.bed INFO @ Fri, 05 Jul 2019 05:10:10: Done! pass1 - making usageList (36 chroms): 6 millis pass2 - checking and writing primary data (1140 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 05:10:14: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101894/ERX101894.20_peaks.xls INFO @ Fri, 05 Jul 2019 05:10:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101894/ERX101894.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 05:10:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101894/ERX101894.20_summits.bed INFO @ Fri, 05 Jul 2019 05:10:14: Done! pass1 - making usageList (27 chroms): 2 millis pass2 - checking and writing primary data (143 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。