Job ID = 2001643 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T21:55:53 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 : 29,718,418 reads read : 29,718,418 reads written : 29,718,418 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: 00:11:55 29718418 reads; of these: 29718418 (100.00%) were unpaired; of these: 576490 (1.94%) aligned 0 times 20577299 (69.24%) aligned exactly 1 time 8564629 (28.82%) aligned >1 times 98.06% overall alignment rate Time searching: 00:11:58 Overall time: 00:11:58 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] 1157443 / 29141928 = 0.0397 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 07:17:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101958/ERX101958.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101958/ERX101958.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101958/ERX101958.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101958/ERX101958.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 07:17:36: #1 read tag files... INFO @ Fri, 05 Jul 2019 07:17:36: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 07:17:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101958/ERX101958.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101958/ERX101958.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101958/ERX101958.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101958/ERX101958.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 07:17:36: #1 read tag files... INFO @ Fri, 05 Jul 2019 07:17:36: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 07:17:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101958/ERX101958.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101958/ERX101958.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101958/ERX101958.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101958/ERX101958.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 07:17:37: #1 read tag files... INFO @ Fri, 05 Jul 2019 07:17:37: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 07:17:44: 1000000 INFO @ Fri, 05 Jul 2019 07:17:44: 1000000 INFO @ Fri, 05 Jul 2019 07:17:44: 1000000 INFO @ Fri, 05 Jul 2019 07:17:51: 2000000 INFO @ Fri, 05 Jul 2019 07:17:51: 2000000 INFO @ Fri, 05 Jul 2019 07:17:51: 2000000 INFO @ Fri, 05 Jul 2019 07:17:58: 3000000 INFO @ Fri, 05 Jul 2019 07:17:58: 3000000 INFO @ Fri, 05 Jul 2019 07:17:59: 3000000 INFO @ Fri, 05 Jul 2019 07:18:05: 4000000 INFO @ Fri, 05 Jul 2019 07:18:06: 4000000 INFO @ Fri, 05 Jul 2019 07:18:06: 4000000 INFO @ Fri, 05 Jul 2019 07:18:11: 5000000 INFO @ Fri, 05 Jul 2019 07:18:13: 5000000 INFO @ Fri, 05 Jul 2019 07:18:13: 5000000 INFO @ Fri, 05 Jul 2019 07:18:18: 6000000 INFO @ Fri, 05 Jul 2019 07:18:20: 6000000 INFO @ Fri, 05 Jul 2019 07:18:20: 6000000 INFO @ Fri, 05 Jul 2019 07:18:25: 7000000 INFO @ Fri, 05 Jul 2019 07:18:27: 7000000 INFO @ Fri, 05 Jul 2019 07:18:28: 7000000 INFO @ Fri, 05 Jul 2019 07:18:32: 8000000 INFO @ Fri, 05 Jul 2019 07:18:34: 8000000 INFO @ Fri, 05 Jul 2019 07:18:35: 8000000 INFO @ Fri, 05 Jul 2019 07:18:38: 9000000 INFO @ Fri, 05 Jul 2019 07:18:42: 9000000 INFO @ Fri, 05 Jul 2019 07:18:42: 9000000 INFO @ Fri, 05 Jul 2019 07:18:45: 10000000 INFO @ Fri, 05 Jul 2019 07:18:49: 10000000 INFO @ Fri, 05 Jul 2019 07:18:49: 10000000 INFO @ Fri, 05 Jul 2019 07:18:52: 11000000 INFO @ Fri, 05 Jul 2019 07:18:56: 11000000 INFO @ Fri, 05 Jul 2019 07:18:56: 11000000 INFO @ Fri, 05 Jul 2019 07:18:59: 12000000 INFO @ Fri, 05 Jul 2019 07:19:03: 12000000 INFO @ Fri, 05 Jul 2019 07:19:04: 12000000 INFO @ Fri, 05 Jul 2019 07:19:05: 13000000 INFO @ Fri, 05 Jul 2019 07:19:10: 13000000 INFO @ Fri, 05 Jul 2019 07:19:11: 13000000 INFO @ Fri, 05 Jul 2019 07:19:12: 14000000 INFO @ Fri, 05 Jul 2019 07:19:17: 14000000 INFO @ Fri, 05 Jul 2019 07:19:18: 14000000 INFO @ Fri, 05 Jul 2019 07:19:19: 15000000 INFO @ Fri, 05 Jul 2019 07:19:25: 15000000 INFO @ Fri, 05 Jul 2019 07:19:25: 15000000 INFO @ Fri, 05 Jul 2019 07:19:25: 16000000 INFO @ Fri, 05 Jul 2019 07:19:32: 16000000 INFO @ Fri, 05 Jul 2019 07:19:32: 17000000 INFO @ Fri, 05 Jul 2019 07:19:32: 16000000 INFO @ Fri, 05 Jul 2019 07:19:39: 17000000 INFO @ Fri, 05 Jul 2019 07:19:39: 18000000 INFO @ Fri, 05 Jul 2019 07:19:40: 17000000 INFO @ Fri, 05 Jul 2019 07:19:46: 19000000 INFO @ Fri, 05 Jul 2019 07:19:46: 18000000 INFO @ Fri, 05 Jul 2019 07:19:47: 18000000 INFO @ Fri, 05 Jul 2019 07:19:52: 20000000 INFO @ Fri, 05 Jul 2019 07:19:53: 19000000 INFO @ Fri, 05 Jul 2019 07:19:54: 19000000 INFO @ Fri, 05 Jul 2019 07:19:59: 21000000 INFO @ Fri, 05 Jul 2019 07:20:01: 20000000 INFO @ Fri, 05 Jul 2019 07:20:01: 20000000 INFO @ Fri, 05 Jul 2019 07:20:05: 22000000 INFO @ Fri, 05 Jul 2019 07:20:08: 21000000 INFO @ Fri, 05 Jul 2019 07:20:08: 21000000 INFO @ Fri, 05 Jul 2019 07:20:12: 23000000 INFO @ Fri, 05 Jul 2019 07:20:14: 22000000 INFO @ Fri, 05 Jul 2019 07:20:15: 22000000 INFO @ Fri, 05 Jul 2019 07:20:18: 24000000 INFO @ Fri, 05 Jul 2019 07:20:22: 23000000 INFO @ Fri, 05 Jul 2019 07:20:22: 23000000 INFO @ Fri, 05 Jul 2019 07:20:25: 25000000 INFO @ Fri, 05 Jul 2019 07:20:29: 24000000 INFO @ Fri, 05 Jul 2019 07:20:29: 24000000 INFO @ Fri, 05 Jul 2019 07:20:32: 26000000 INFO @ Fri, 05 Jul 2019 07:20:36: 25000000 INFO @ Fri, 05 Jul 2019 07:20:36: 25000000 INFO @ Fri, 05 Jul 2019 07:20:39: 27000000 INFO @ Fri, 05 Jul 2019 07:20:42: 26000000 INFO @ Fri, 05 Jul 2019 07:20:43: 26000000 INFO @ Fri, 05 Jul 2019 07:20:46: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 07:20:46: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 07:20:46: #1 total tags in treatment: 27984485 INFO @ Fri, 05 Jul 2019 07:20:46: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 07:20:46: #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 07:20:46: #1 tags after filtering in treatment: 27984358 INFO @ Fri, 05 Jul 2019 07:20:46: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 07:20:46: #1 finished! INFO @ Fri, 05 Jul 2019 07:20:46: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 07:20:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 07:20:49: 27000000 INFO @ Fri, 05 Jul 2019 07:20:50: 27000000 INFO @ Fri, 05 Jul 2019 07:20:50: #2 number of paired peaks: 19086 INFO @ Fri, 05 Jul 2019 07:20:50: start model_add_line... INFO @ Fri, 05 Jul 2019 07:20:51: start X-correlation... INFO @ Fri, 05 Jul 2019 07:20:51: end of X-cor INFO @ Fri, 05 Jul 2019 07:20:51: #2 finished! INFO @ Fri, 05 Jul 2019 07:20:51: #2 predicted fragment length is 122 bps INFO @ Fri, 05 Jul 2019 07:20:51: #2 alternative fragment length(s) may be 122 bps INFO @ Fri, 05 Jul 2019 07:20:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101958/ERX101958.20_model.r INFO @ Fri, 05 Jul 2019 07:20:51: #3 Call peaks... INFO @ Fri, 05 Jul 2019 07:20:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 07:20:56: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 07:20:56: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 07:20:56: #1 total tags in treatment: 27984485 INFO @ Fri, 05 Jul 2019 07:20:56: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 07:20:56: #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 07:20:57: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 07:20:57: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 07:20:57: #1 total tags in treatment: 27984485 INFO @ Fri, 05 Jul 2019 07:20:57: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 07:20:57: #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 07:20:57: #1 tags after filtering in treatment: 27984358 INFO @ Fri, 05 Jul 2019 07:20:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 07:20:57: #1 finished! INFO @ Fri, 05 Jul 2019 07:20:57: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 07:20:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 07:20:57: #1 tags after filtering in treatment: 27984358 INFO @ Fri, 05 Jul 2019 07:20:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 07:20:57: #1 finished! INFO @ Fri, 05 Jul 2019 07:20:57: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 07:20:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 07:21:01: #2 number of paired peaks: 19086 INFO @ Fri, 05 Jul 2019 07:21:01: start model_add_line... INFO @ Fri, 05 Jul 2019 07:21:01: start X-correlation... INFO @ Fri, 05 Jul 2019 07:21:01: end of X-cor INFO @ Fri, 05 Jul 2019 07:21:01: #2 finished! INFO @ Fri, 05 Jul 2019 07:21:01: #2 predicted fragment length is 122 bps INFO @ Fri, 05 Jul 2019 07:21:01: #2 alternative fragment length(s) may be 122 bps INFO @ Fri, 05 Jul 2019 07:21:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101958/ERX101958.05_model.r INFO @ Fri, 05 Jul 2019 07:21:01: #3 Call peaks... INFO @ Fri, 05 Jul 2019 07:21:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 07:21:01: #2 number of paired peaks: 19086 INFO @ Fri, 05 Jul 2019 07:21:01: start model_add_line... INFO @ Fri, 05 Jul 2019 07:21:02: start X-correlation... INFO @ Fri, 05 Jul 2019 07:21:02: end of X-cor INFO @ Fri, 05 Jul 2019 07:21:02: #2 finished! INFO @ Fri, 05 Jul 2019 07:21:02: #2 predicted fragment length is 122 bps INFO @ Fri, 05 Jul 2019 07:21:02: #2 alternative fragment length(s) may be 122 bps INFO @ Fri, 05 Jul 2019 07:21:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101958/ERX101958.10_model.r INFO @ Fri, 05 Jul 2019 07:21:02: #3 Call peaks... INFO @ Fri, 05 Jul 2019 07:21:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 07:22:21: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 07:22:29: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 07:22:29: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 07:23:07: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101958/ERX101958.20_peaks.xls INFO @ Fri, 05 Jul 2019 07:23:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101958/ERX101958.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 07:23:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101958/ERX101958.20_summits.bed INFO @ Fri, 05 Jul 2019 07:23:07: Done! pass1 - making usageList (20 chroms): 1 millis pass2 - checking and writing primary data (84 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 07:23:14: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101958/ERX101958.05_peaks.xls INFO @ Fri, 05 Jul 2019 07:23:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101958/ERX101958.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 07:23:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101958/ERX101958.05_summits.bed INFO @ Fri, 05 Jul 2019 07:23:14: Done! pass1 - making usageList (58 chroms): 2 millis pass2 - checking and writing primary data (2282 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 07:23:14: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101958/ERX101958.10_peaks.xls INFO @ Fri, 05 Jul 2019 07:23:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101958/ERX101958.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 07:23:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101958/ERX101958.10_summits.bed INFO @ Fri, 05 Jul 2019 07:23:14: Done! pass1 - making usageList (37 chroms): 1 millis pass2 - checking and writing primary data (426 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。