Job ID = 2001679 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T23:26:00 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 60,752,511 reads read : 60,752,511 reads written : 60,752,511 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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:39:01 60752511 reads; of these: 60752511 (100.00%) were unpaired; of these: 1703519 (2.80%) aligned 0 times 52629087 (86.63%) aligned exactly 1 time 6419905 (10.57%) aligned >1 times 97.20% overall alignment rate Time searching: 00:39:04 Overall time: 00:39:04 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 28 files... [bam_rmdupse_core] 33596594 / 59048992 = 0.5690 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 09:46:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101994/ERX101994.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101994/ERX101994.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101994/ERX101994.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101994/ERX101994.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 09:46:08: #1 read tag files... INFO @ Fri, 05 Jul 2019 09:46:08: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 09:46:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101994/ERX101994.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101994/ERX101994.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101994/ERX101994.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101994/ERX101994.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 09:46:08: #1 read tag files... INFO @ Fri, 05 Jul 2019 09:46:08: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 09:46:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101994/ERX101994.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101994/ERX101994.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101994/ERX101994.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101994/ERX101994.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 09:46:08: #1 read tag files... INFO @ Fri, 05 Jul 2019 09:46:08: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 09:46:15: 1000000 INFO @ Fri, 05 Jul 2019 09:46:15: 1000000 INFO @ Fri, 05 Jul 2019 09:46:17: 1000000 INFO @ Fri, 05 Jul 2019 09:46:23: 2000000 INFO @ Fri, 05 Jul 2019 09:46:23: 2000000 INFO @ Fri, 05 Jul 2019 09:46:25: 2000000 INFO @ Fri, 05 Jul 2019 09:46:30: 3000000 INFO @ Fri, 05 Jul 2019 09:46:30: 3000000 INFO @ Fri, 05 Jul 2019 09:46:34: 3000000 INFO @ Fri, 05 Jul 2019 09:46:37: 4000000 INFO @ Fri, 05 Jul 2019 09:46:37: 4000000 INFO @ Fri, 05 Jul 2019 09:46:42: 4000000 INFO @ Fri, 05 Jul 2019 09:46:44: 5000000 INFO @ Fri, 05 Jul 2019 09:46:44: 5000000 INFO @ Fri, 05 Jul 2019 09:46:50: 5000000 INFO @ Fri, 05 Jul 2019 09:46:51: 6000000 INFO @ Fri, 05 Jul 2019 09:46:51: 6000000 INFO @ Fri, 05 Jul 2019 09:46:58: 7000000 INFO @ Fri, 05 Jul 2019 09:46:58: 6000000 INFO @ Fri, 05 Jul 2019 09:46:58: 7000000 INFO @ Fri, 05 Jul 2019 09:47:05: 8000000 INFO @ Fri, 05 Jul 2019 09:47:06: 8000000 INFO @ Fri, 05 Jul 2019 09:47:06: 7000000 INFO @ Fri, 05 Jul 2019 09:47:12: 9000000 INFO @ Fri, 05 Jul 2019 09:47:13: 9000000 INFO @ Fri, 05 Jul 2019 09:47:14: 8000000 INFO @ Fri, 05 Jul 2019 09:47:19: 10000000 INFO @ Fri, 05 Jul 2019 09:47:20: 10000000 INFO @ Fri, 05 Jul 2019 09:47:21: 9000000 INFO @ Fri, 05 Jul 2019 09:47:26: 11000000 INFO @ Fri, 05 Jul 2019 09:47:27: 11000000 INFO @ Fri, 05 Jul 2019 09:47:28: 10000000 INFO @ Fri, 05 Jul 2019 09:47:33: 12000000 INFO @ Fri, 05 Jul 2019 09:47:34: 12000000 INFO @ Fri, 05 Jul 2019 09:47:35: 11000000 INFO @ Fri, 05 Jul 2019 09:47:40: 13000000 INFO @ Fri, 05 Jul 2019 09:47:41: 13000000 INFO @ Fri, 05 Jul 2019 09:47:42: 12000000 INFO @ Fri, 05 Jul 2019 09:47:47: 14000000 INFO @ Fri, 05 Jul 2019 09:47:49: 14000000 INFO @ Fri, 05 Jul 2019 09:47:49: 13000000 INFO @ Fri, 05 Jul 2019 09:47:54: 15000000 INFO @ Fri, 05 Jul 2019 09:47:56: 15000000 INFO @ Fri, 05 Jul 2019 09:47:56: 14000000 INFO @ Fri, 05 Jul 2019 09:48:01: 16000000 INFO @ Fri, 05 Jul 2019 09:48:03: 16000000 INFO @ Fri, 05 Jul 2019 09:48:03: 15000000 INFO @ Fri, 05 Jul 2019 09:48:08: 17000000 INFO @ Fri, 05 Jul 2019 09:48:10: 17000000 INFO @ Fri, 05 Jul 2019 09:48:10: 16000000 INFO @ Fri, 05 Jul 2019 09:48:15: 18000000 INFO @ Fri, 05 Jul 2019 09:48:17: 18000000 INFO @ Fri, 05 Jul 2019 09:48:17: 17000000 INFO @ Fri, 05 Jul 2019 09:48:22: 19000000 INFO @ Fri, 05 Jul 2019 09:48:24: 19000000 INFO @ Fri, 05 Jul 2019 09:48:24: 18000000 INFO @ Fri, 05 Jul 2019 09:48:30: 20000000 INFO @ Fri, 05 Jul 2019 09:48:31: 20000000 INFO @ Fri, 05 Jul 2019 09:48:31: 19000000 INFO @ Fri, 05 Jul 2019 09:48:37: 21000000 INFO @ Fri, 05 Jul 2019 09:48:38: 21000000 INFO @ Fri, 05 Jul 2019 09:48:39: 20000000 INFO @ Fri, 05 Jul 2019 09:48:44: 22000000 INFO @ Fri, 05 Jul 2019 09:48:45: 22000000 INFO @ Fri, 05 Jul 2019 09:48:46: 21000000 INFO @ Fri, 05 Jul 2019 09:48:51: 23000000 INFO @ Fri, 05 Jul 2019 09:48:53: 22000000 INFO @ Fri, 05 Jul 2019 09:48:53: 23000000 INFO @ Fri, 05 Jul 2019 09:48:58: 24000000 INFO @ Fri, 05 Jul 2019 09:49:00: 23000000 INFO @ Fri, 05 Jul 2019 09:49:00: 24000000 INFO @ Fri, 05 Jul 2019 09:49:05: 25000000 INFO @ Fri, 05 Jul 2019 09:49:07: 24000000 INFO @ Fri, 05 Jul 2019 09:49:07: 25000000 INFO @ Fri, 05 Jul 2019 09:49:08: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 09:49:08: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 09:49:08: #1 total tags in treatment: 25452398 INFO @ Fri, 05 Jul 2019 09:49:08: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 09:49:08: #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 09:49:09: #1 tags after filtering in treatment: 25452166 INFO @ Fri, 05 Jul 2019 09:49:09: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 09:49:09: #1 finished! INFO @ Fri, 05 Jul 2019 09:49:09: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 09:49:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 09:49:10: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 09:49:10: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 09:49:10: #1 total tags in treatment: 25452398 INFO @ Fri, 05 Jul 2019 09:49:10: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 09:49:10: #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 09:49:11: #1 tags after filtering in treatment: 25452166 INFO @ Fri, 05 Jul 2019 09:49:11: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 09:49:11: #1 finished! INFO @ Fri, 05 Jul 2019 09:49:11: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 09:49:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 09:49:14: 25000000 INFO @ Fri, 05 Jul 2019 09:49:15: #2 number of paired peaks: 59933 INFO @ Fri, 05 Jul 2019 09:49:15: start model_add_line... INFO @ Fri, 05 Jul 2019 09:49:16: start X-correlation... INFO @ Fri, 05 Jul 2019 09:49:16: end of X-cor INFO @ Fri, 05 Jul 2019 09:49:16: #2 finished! INFO @ Fri, 05 Jul 2019 09:49:16: #2 predicted fragment length is 112 bps INFO @ Fri, 05 Jul 2019 09:49:16: #2 alternative fragment length(s) may be 112 bps INFO @ Fri, 05 Jul 2019 09:49:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101994/ERX101994.20_model.r INFO @ Fri, 05 Jul 2019 09:49:16: #3 Call peaks... INFO @ Fri, 05 Jul 2019 09:49:16: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 09:49:17: #2 number of paired peaks: 59933 INFO @ Fri, 05 Jul 2019 09:49:17: start model_add_line... INFO @ Fri, 05 Jul 2019 09:49:17: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 09:49:17: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 09:49:17: #1 total tags in treatment: 25452398 INFO @ Fri, 05 Jul 2019 09:49:17: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 09:49:17: #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 09:49:18: start X-correlation... INFO @ Fri, 05 Jul 2019 09:49:18: end of X-cor INFO @ Fri, 05 Jul 2019 09:49:18: #2 finished! INFO @ Fri, 05 Jul 2019 09:49:18: #2 predicted fragment length is 112 bps INFO @ Fri, 05 Jul 2019 09:49:18: #2 alternative fragment length(s) may be 112 bps INFO @ Fri, 05 Jul 2019 09:49:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101994/ERX101994.10_model.r INFO @ Fri, 05 Jul 2019 09:49:18: #3 Call peaks... INFO @ Fri, 05 Jul 2019 09:49:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 09:49:18: #1 tags after filtering in treatment: 25452166 INFO @ Fri, 05 Jul 2019 09:49:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 09:49:18: #1 finished! INFO @ Fri, 05 Jul 2019 09:49:18: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 09:49:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 09:49:24: #2 number of paired peaks: 59933 INFO @ Fri, 05 Jul 2019 09:49:24: start model_add_line... INFO @ Fri, 05 Jul 2019 09:49:24: start X-correlation... INFO @ Fri, 05 Jul 2019 09:49:24: end of X-cor INFO @ Fri, 05 Jul 2019 09:49:24: #2 finished! INFO @ Fri, 05 Jul 2019 09:49:24: #2 predicted fragment length is 112 bps INFO @ Fri, 05 Jul 2019 09:49:24: #2 alternative fragment length(s) may be 112 bps INFO @ Fri, 05 Jul 2019 09:49:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101994/ERX101994.05_model.r INFO @ Fri, 05 Jul 2019 09:49:25: #3 Call peaks... INFO @ Fri, 05 Jul 2019 09:49:25: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 09:50:27: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 09:50:30: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 09:50:36: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 09:51:06: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101994/ERX101994.20_peaks.xls INFO @ Fri, 05 Jul 2019 09:51:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101994/ERX101994.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 09:51:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101994/ERX101994.20_summits.bed INFO @ Fri, 05 Jul 2019 09:51:07: Done! pass1 - making usageList (118 chroms): 12 millis pass2 - checking and writing primary data (33391 records, 4 fields): 48 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 09:51:10: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101994/ERX101994.10_peaks.xls INFO @ Fri, 05 Jul 2019 09:51:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101994/ERX101994.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 09:51:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101994/ERX101994.10_summits.bed INFO @ Fri, 05 Jul 2019 09:51:11: Done! pass1 - making usageList (138 chroms): 9 millis pass2 - checking and writing primary data (45973 records, 4 fields): 63 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 09:51:16: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101994/ERX101994.05_peaks.xls INFO @ Fri, 05 Jul 2019 09:51:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101994/ERX101994.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 09:51:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101994/ERX101994.05_summits.bed INFO @ Fri, 05 Jul 2019 09:51:18: Done! pass1 - making usageList (166 chroms): 12 millis pass2 - checking and writing primary data (57656 records, 4 fields): 345 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。