Job ID = 2001533 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T19:21:55 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 ) 2019-07-04T19:25:24 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 : 26,629,918 reads read : 26,629,918 reads written : 26,629,918 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: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:04:51 26629918 reads; of these: 26629918 (100.00%) were unpaired; of these: 587530 (2.21%) aligned 0 times 23545158 (88.42%) aligned exactly 1 time 2497230 (9.38%) aligned >1 times 97.79% overall alignment rate Time searching: 00:04:52 Overall time: 00:04:52 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] 13479584 / 26042388 = 0.5176 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 04:38:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101877/ERX101877.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101877/ERX101877.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101877/ERX101877.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101877/ERX101877.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 04:38:23: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:38:23: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:38:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101877/ERX101877.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101877/ERX101877.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101877/ERX101877.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101877/ERX101877.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 04:38:24: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:38:24: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:38:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101877/ERX101877.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101877/ERX101877.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101877/ERX101877.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101877/ERX101877.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 04:38:25: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:38:25: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:38:32: 1000000 INFO @ Fri, 05 Jul 2019 04:38:33: 1000000 INFO @ Fri, 05 Jul 2019 04:38:34: 1000000 INFO @ Fri, 05 Jul 2019 04:38:40: 2000000 INFO @ Fri, 05 Jul 2019 04:38:42: 2000000 INFO @ Fri, 05 Jul 2019 04:38:42: 2000000 INFO @ Fri, 05 Jul 2019 04:38:49: 3000000 INFO @ Fri, 05 Jul 2019 04:38:50: 3000000 INFO @ Fri, 05 Jul 2019 04:38:51: 3000000 INFO @ Fri, 05 Jul 2019 04:38:58: 4000000 INFO @ Fri, 05 Jul 2019 04:38:58: 4000000 INFO @ Fri, 05 Jul 2019 04:39:00: 4000000 INFO @ Fri, 05 Jul 2019 04:39:07: 5000000 INFO @ Fri, 05 Jul 2019 04:39:07: 5000000 INFO @ Fri, 05 Jul 2019 04:39:09: 5000000 INFO @ Fri, 05 Jul 2019 04:39:15: 6000000 INFO @ Fri, 05 Jul 2019 04:39:16: 6000000 INFO @ Fri, 05 Jul 2019 04:39:18: 6000000 INFO @ Fri, 05 Jul 2019 04:39:24: 7000000 INFO @ Fri, 05 Jul 2019 04:39:25: 7000000 INFO @ Fri, 05 Jul 2019 04:39:27: 7000000 INFO @ Fri, 05 Jul 2019 04:39:32: 8000000 INFO @ Fri, 05 Jul 2019 04:39:35: 8000000 INFO @ Fri, 05 Jul 2019 04:39:36: 8000000 INFO @ Fri, 05 Jul 2019 04:39:40: 9000000 INFO @ Fri, 05 Jul 2019 04:39:44: 9000000 INFO @ Fri, 05 Jul 2019 04:39:45: 9000000 INFO @ Fri, 05 Jul 2019 04:39:48: 10000000 INFO @ Fri, 05 Jul 2019 04:39:53: 10000000 INFO @ Fri, 05 Jul 2019 04:39:54: 10000000 INFO @ Fri, 05 Jul 2019 04:39:57: 11000000 INFO @ Fri, 05 Jul 2019 04:40:02: 11000000 INFO @ Fri, 05 Jul 2019 04:40:03: 11000000 INFO @ Fri, 05 Jul 2019 04:40:05: 12000000 INFO @ Fri, 05 Jul 2019 04:40:09: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:40:09: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:40:09: #1 total tags in treatment: 12562804 INFO @ Fri, 05 Jul 2019 04:40:09: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:40:09: #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 04:40:10: #1 tags after filtering in treatment: 12562519 INFO @ Fri, 05 Jul 2019 04:40:10: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:40:10: #1 finished! INFO @ Fri, 05 Jul 2019 04:40:10: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:40:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:40:11: 12000000 INFO @ Fri, 05 Jul 2019 04:40:12: 12000000 INFO @ Fri, 05 Jul 2019 04:40:13: #2 number of paired peaks: 44034 INFO @ Fri, 05 Jul 2019 04:40:13: start model_add_line... INFO @ Fri, 05 Jul 2019 04:40:13: start X-correlation... INFO @ Fri, 05 Jul 2019 04:40:13: end of X-cor INFO @ Fri, 05 Jul 2019 04:40:13: #2 finished! INFO @ Fri, 05 Jul 2019 04:40:13: #2 predicted fragment length is 142 bps INFO @ Fri, 05 Jul 2019 04:40:13: #2 alternative fragment length(s) may be 4,142 bps INFO @ Fri, 05 Jul 2019 04:40:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101877/ERX101877.10_model.r INFO @ Fri, 05 Jul 2019 04:40:13: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:40:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:40:16: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:40:16: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:40:16: #1 total tags in treatment: 12562804 INFO @ Fri, 05 Jul 2019 04:40:16: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:40:16: #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 04:40:16: #1 tags after filtering in treatment: 12562519 INFO @ Fri, 05 Jul 2019 04:40:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:40:16: #1 finished! INFO @ Fri, 05 Jul 2019 04:40:16: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:40:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:40:17: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:40:17: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:40:17: #1 total tags in treatment: 12562804 INFO @ Fri, 05 Jul 2019 04:40:17: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:40:17: #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 04:40:18: #1 tags after filtering in treatment: 12562519 INFO @ Fri, 05 Jul 2019 04:40:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:40:18: #1 finished! INFO @ Fri, 05 Jul 2019 04:40:18: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:40:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:40:19: #2 number of paired peaks: 44034 INFO @ Fri, 05 Jul 2019 04:40:19: start model_add_line... INFO @ Fri, 05 Jul 2019 04:40:20: start X-correlation... INFO @ Fri, 05 Jul 2019 04:40:20: end of X-cor INFO @ Fri, 05 Jul 2019 04:40:20: #2 finished! INFO @ Fri, 05 Jul 2019 04:40:20: #2 predicted fragment length is 142 bps INFO @ Fri, 05 Jul 2019 04:40:20: #2 alternative fragment length(s) may be 4,142 bps INFO @ Fri, 05 Jul 2019 04:40:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101877/ERX101877.05_model.r INFO @ Fri, 05 Jul 2019 04:40:20: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:40:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:40:21: #2 number of paired peaks: 44034 INFO @ Fri, 05 Jul 2019 04:40:21: start model_add_line... INFO @ Fri, 05 Jul 2019 04:40:21: start X-correlation... INFO @ Fri, 05 Jul 2019 04:40:21: end of X-cor INFO @ Fri, 05 Jul 2019 04:40:21: #2 finished! INFO @ Fri, 05 Jul 2019 04:40:21: #2 predicted fragment length is 142 bps INFO @ Fri, 05 Jul 2019 04:40:21: #2 alternative fragment length(s) may be 4,142 bps INFO @ Fri, 05 Jul 2019 04:40:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101877/ERX101877.20_model.r INFO @ Fri, 05 Jul 2019 04:40:21: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:40:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:40:51: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:40:58: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:41:00: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:41:14: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101877/ERX101877.10_peaks.xls INFO @ Fri, 05 Jul 2019 04:41:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101877/ERX101877.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:41:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101877/ERX101877.10_summits.bed INFO @ Fri, 05 Jul 2019 04:41:15: Done! pass1 - making usageList (118 chroms): 8 millis pass2 - checking and writing primary data (35038 records, 4 fields): 49 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 04:41:22: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101877/ERX101877.05_peaks.xls INFO @ Fri, 05 Jul 2019 04:41:22: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101877/ERX101877.20_peaks.xls INFO @ Fri, 05 Jul 2019 04:41:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101877/ERX101877.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:41:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101877/ERX101877.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:41:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101877/ERX101877.05_summits.bed INFO @ Fri, 05 Jul 2019 04:41:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101877/ERX101877.20_summits.bed INFO @ Fri, 05 Jul 2019 04:41:23: Done! INFO @ Fri, 05 Jul 2019 04:41:23: Done! pass1 - making usageList (90 chroms): 10 millis pass2 - checking and writing primary data (24937 records, 4 fields): 41 millis CompletedMACS2peakCalling pass1 - making usageList (137 chroms): 15 millis pass2 - checking and writing primary data (43373 records, 4 fields): 67 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。