Job ID = 2001164 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T18:57:45 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 ) 2019-07-04T18:57:45 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 : 25,163,248 reads read : 25,163,248 reads written : 25,163,248 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: 00:00:00 Multiseed full-index search: 00:09:25 25163248 reads; of these: 25163248 (100.00%) were unpaired; of these: 640145 (2.54%) aligned 0 times 18522880 (73.61%) aligned exactly 1 time 6000223 (23.85%) aligned >1 times 97.46% overall alignment rate Time searching: 00:09:26 Overall time: 00:09:26 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] 1662167 / 24523103 = 0.0678 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 04:20:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101853/ERX101853.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101853/ERX101853.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101853/ERX101853.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101853/ERX101853.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 04:20:26: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:20:26: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:20:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101853/ERX101853.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101853/ERX101853.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101853/ERX101853.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101853/ERX101853.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 04:20:27: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:20:27: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:20:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101853/ERX101853.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101853/ERX101853.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101853/ERX101853.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101853/ERX101853.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 04:20:28: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:20:28: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:20:36: 1000000 INFO @ Fri, 05 Jul 2019 04:20:36: 1000000 INFO @ Fri, 05 Jul 2019 04:20:36: 1000000 INFO @ Fri, 05 Jul 2019 04:20:44: 2000000 INFO @ Fri, 05 Jul 2019 04:20:44: 2000000 INFO @ Fri, 05 Jul 2019 04:20:44: 2000000 INFO @ Fri, 05 Jul 2019 04:20:52: 3000000 INFO @ Fri, 05 Jul 2019 04:20:53: 3000000 INFO @ Fri, 05 Jul 2019 04:20:53: 3000000 INFO @ Fri, 05 Jul 2019 04:20:59: 4000000 INFO @ Fri, 05 Jul 2019 04:21:01: 4000000 INFO @ Fri, 05 Jul 2019 04:21:01: 4000000 INFO @ Fri, 05 Jul 2019 04:21:07: 5000000 INFO @ Fri, 05 Jul 2019 04:21:10: 5000000 INFO @ Fri, 05 Jul 2019 04:21:10: 5000000 INFO @ Fri, 05 Jul 2019 04:21:15: 6000000 INFO @ Fri, 05 Jul 2019 04:21:19: 6000000 INFO @ Fri, 05 Jul 2019 04:21:19: 6000000 INFO @ Fri, 05 Jul 2019 04:21:22: 7000000 INFO @ Fri, 05 Jul 2019 04:21:28: 7000000 INFO @ Fri, 05 Jul 2019 04:21:28: 7000000 INFO @ Fri, 05 Jul 2019 04:21:30: 8000000 INFO @ Fri, 05 Jul 2019 04:21:36: 8000000 INFO @ Fri, 05 Jul 2019 04:21:36: 8000000 INFO @ Fri, 05 Jul 2019 04:21:37: 9000000 INFO @ Fri, 05 Jul 2019 04:21:43: 9000000 INFO @ Fri, 05 Jul 2019 04:21:45: 10000000 INFO @ Fri, 05 Jul 2019 04:21:45: 9000000 INFO @ Fri, 05 Jul 2019 04:21:50: 10000000 INFO @ Fri, 05 Jul 2019 04:21:52: 11000000 INFO @ Fri, 05 Jul 2019 04:21:53: 10000000 INFO @ Fri, 05 Jul 2019 04:21:57: 11000000 INFO @ Fri, 05 Jul 2019 04:22:00: 12000000 INFO @ Fri, 05 Jul 2019 04:22:02: 11000000 INFO @ Fri, 05 Jul 2019 04:22:03: 12000000 INFO @ Fri, 05 Jul 2019 04:22:07: 13000000 INFO @ Fri, 05 Jul 2019 04:22:10: 12000000 INFO @ Fri, 05 Jul 2019 04:22:11: 13000000 INFO @ Fri, 05 Jul 2019 04:22:15: 14000000 INFO @ Fri, 05 Jul 2019 04:22:19: 13000000 INFO @ Fri, 05 Jul 2019 04:22:19: 14000000 INFO @ Fri, 05 Jul 2019 04:22:22: 15000000 INFO @ Fri, 05 Jul 2019 04:22:26: 15000000 INFO @ Fri, 05 Jul 2019 04:22:28: 14000000 INFO @ Fri, 05 Jul 2019 04:22:30: 16000000 INFO @ Fri, 05 Jul 2019 04:22:35: 16000000 INFO @ Fri, 05 Jul 2019 04:22:36: 15000000 INFO @ Fri, 05 Jul 2019 04:22:37: 17000000 INFO @ Fri, 05 Jul 2019 04:22:42: 17000000 INFO @ Fri, 05 Jul 2019 04:22:44: 16000000 INFO @ Fri, 05 Jul 2019 04:22:44: 18000000 INFO @ Fri, 05 Jul 2019 04:22:49: 18000000 INFO @ Fri, 05 Jul 2019 04:22:52: 19000000 INFO @ Fri, 05 Jul 2019 04:22:53: 17000000 INFO @ Fri, 05 Jul 2019 04:22:56: 19000000 INFO @ Fri, 05 Jul 2019 04:22:59: 20000000 INFO @ Fri, 05 Jul 2019 04:23:01: 18000000 INFO @ Fri, 05 Jul 2019 04:23:03: 20000000 INFO @ Fri, 05 Jul 2019 04:23:06: 21000000 INFO @ Fri, 05 Jul 2019 04:23:10: 19000000 INFO @ Fri, 05 Jul 2019 04:23:10: 21000000 INFO @ Fri, 05 Jul 2019 04:23:14: 22000000 INFO @ Fri, 05 Jul 2019 04:23:18: 20000000 INFO @ Fri, 05 Jul 2019 04:23:18: 22000000 INFO @ Fri, 05 Jul 2019 04:23:20: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:23:20: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:23:20: #1 total tags in treatment: 22860936 INFO @ Fri, 05 Jul 2019 04:23:20: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:23:20: #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 04:23:21: #1 tags after filtering in treatment: 22860788 INFO @ Fri, 05 Jul 2019 04:23:21: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:23:21: #1 finished! INFO @ Fri, 05 Jul 2019 04:23:21: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:23:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:23:26: #2 number of paired peaks: 56791 INFO @ Fri, 05 Jul 2019 04:23:26: start model_add_line... INFO @ Fri, 05 Jul 2019 04:23:26: start X-correlation... INFO @ Fri, 05 Jul 2019 04:23:26: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:23:26: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:23:26: #1 total tags in treatment: 22860936 INFO @ Fri, 05 Jul 2019 04:23:26: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:23:26: #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 04:23:26: end of X-cor INFO @ Fri, 05 Jul 2019 04:23:26: #2 finished! INFO @ Fri, 05 Jul 2019 04:23:26: #2 predicted fragment length is 132 bps INFO @ Fri, 05 Jul 2019 04:23:26: #2 alternative fragment length(s) may be 2,132,496 bps INFO @ Fri, 05 Jul 2019 04:23:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101853/ERX101853.20_model.r INFO @ Fri, 05 Jul 2019 04:23:26: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:23:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:23:26: 21000000 INFO @ Fri, 05 Jul 2019 04:23:27: #1 tags after filtering in treatment: 22860788 INFO @ Fri, 05 Jul 2019 04:23:27: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:23:27: #1 finished! INFO @ Fri, 05 Jul 2019 04:23:27: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:23:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:23:32: #2 number of paired peaks: 56791 INFO @ Fri, 05 Jul 2019 04:23:32: start model_add_line... INFO @ Fri, 05 Jul 2019 04:23:32: start X-correlation... INFO @ Fri, 05 Jul 2019 04:23:32: end of X-cor INFO @ Fri, 05 Jul 2019 04:23:32: #2 finished! INFO @ Fri, 05 Jul 2019 04:23:32: #2 predicted fragment length is 132 bps INFO @ Fri, 05 Jul 2019 04:23:32: #2 alternative fragment length(s) may be 2,132,496 bps INFO @ Fri, 05 Jul 2019 04:23:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101853/ERX101853.10_model.r INFO @ Fri, 05 Jul 2019 04:23:32: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:23:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:23:35: 22000000 INFO @ Fri, 05 Jul 2019 04:23:42: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:23:42: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:23:42: #1 total tags in treatment: 22860936 INFO @ Fri, 05 Jul 2019 04:23:42: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:23:42: #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 04:23:43: #1 tags after filtering in treatment: 22860788 INFO @ Fri, 05 Jul 2019 04:23:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:23:43: #1 finished! INFO @ Fri, 05 Jul 2019 04:23:43: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:23:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:23:48: #2 number of paired peaks: 56791 INFO @ Fri, 05 Jul 2019 04:23:48: start model_add_line... INFO @ Fri, 05 Jul 2019 04:23:48: start X-correlation... INFO @ Fri, 05 Jul 2019 04:23:48: end of X-cor INFO @ Fri, 05 Jul 2019 04:23:48: #2 finished! INFO @ Fri, 05 Jul 2019 04:23:48: #2 predicted fragment length is 132 bps INFO @ Fri, 05 Jul 2019 04:23:48: #2 alternative fragment length(s) may be 2,132,496 bps INFO @ Fri, 05 Jul 2019 04:23:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101853/ERX101853.05_model.r INFO @ Fri, 05 Jul 2019 04:23:48: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:23:48: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:24:40: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:24:46: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:25:02: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:25:17: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101853/ERX101853.20_peaks.xls INFO @ Fri, 05 Jul 2019 04:25:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101853/ERX101853.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:25:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101853/ERX101853.20_summits.bed INFO @ Fri, 05 Jul 2019 04:25:17: Done! pass1 - making usageList (27 chroms): 0 millis pass2 - checking and writing primary data (129 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 04:25:23: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101853/ERX101853.10_peaks.xls INFO @ Fri, 05 Jul 2019 04:25:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101853/ERX101853.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:25:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101853/ERX101853.10_summits.bed INFO @ Fri, 05 Jul 2019 04:25:23: Done! pass1 - making usageList (40 chroms): 2 millis pass2 - checking and writing primary data (1093 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 04:25:41: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101853/ERX101853.05_peaks.xls INFO @ Fri, 05 Jul 2019 04:25:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101853/ERX101853.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:25:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101853/ERX101853.05_summits.bed INFO @ Fri, 05 Jul 2019 04:25:41: Done! pass1 - making usageList (67 chroms): 1 millis pass2 - checking and writing primary data (4809 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。