Job ID = 2640607 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T09:01:53 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 : 23,604,208 reads read : 47,208,416 reads written : 23,604,208 reads 0-length : 23,604,208 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: 00:00:01 Multiseed full-index search: 00:18:38 23604208 reads; of these: 23604208 (100.00%) were unpaired; of these: 543408 (2.30%) aligned 0 times 19697757 (83.45%) aligned exactly 1 time 3363043 (14.25%) aligned >1 times 97.70% overall alignment rate Time searching: 00:18:42 Overall time: 00:18:42 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 12 files... [bam_rmdupse_core] 5146536 / 23060800 = 0.2232 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:33:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375035/SRX5375035.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375035/SRX5375035.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375035/SRX5375035.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375035/SRX5375035.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 @ Sat, 24 Aug 2019 18:33:14: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:33:14: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:33:21: 1000000 INFO @ Sat, 24 Aug 2019 18:33:28: 2000000 INFO @ Sat, 24 Aug 2019 18:33:35: 3000000 INFO @ Sat, 24 Aug 2019 18:33:42: 4000000 INFO @ Sat, 24 Aug 2019 18:33:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375035/SRX5375035.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375035/SRX5375035.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375035/SRX5375035.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375035/SRX5375035.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 @ Sat, 24 Aug 2019 18:33:44: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:33:44: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:33:49: 5000000 INFO @ Sat, 24 Aug 2019 18:33:52: 1000000 INFO @ Sat, 24 Aug 2019 18:33:57: 6000000 INFO @ Sat, 24 Aug 2019 18:34:00: 2000000 INFO @ Sat, 24 Aug 2019 18:34:04: 7000000 INFO @ Sat, 24 Aug 2019 18:34:08: 3000000 INFO @ Sat, 24 Aug 2019 18:34:11: 8000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:34:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375035/SRX5375035.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375035/SRX5375035.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375035/SRX5375035.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375035/SRX5375035.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 @ Sat, 24 Aug 2019 18:34:14: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:34:14: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:34:17: 4000000 INFO @ Sat, 24 Aug 2019 18:34:19: 9000000 INFO @ Sat, 24 Aug 2019 18:34:22: 1000000 INFO @ Sat, 24 Aug 2019 18:34:26: 5000000 INFO @ Sat, 24 Aug 2019 18:34:27: 10000000 INFO @ Sat, 24 Aug 2019 18:34:31: 2000000 INFO @ Sat, 24 Aug 2019 18:34:34: 6000000 INFO @ Sat, 24 Aug 2019 18:34:36: 11000000 INFO @ Sat, 24 Aug 2019 18:34:39: 3000000 INFO @ Sat, 24 Aug 2019 18:34:43: 7000000 INFO @ Sat, 24 Aug 2019 18:34:46: 12000000 INFO @ Sat, 24 Aug 2019 18:34:47: 4000000 INFO @ Sat, 24 Aug 2019 18:34:51: 8000000 INFO @ Sat, 24 Aug 2019 18:34:55: 13000000 INFO @ Sat, 24 Aug 2019 18:34:56: 5000000 INFO @ Sat, 24 Aug 2019 18:35:00: 9000000 INFO @ Sat, 24 Aug 2019 18:35:04: 6000000 INFO @ Sat, 24 Aug 2019 18:35:05: 14000000 INFO @ Sat, 24 Aug 2019 18:35:08: 10000000 INFO @ Sat, 24 Aug 2019 18:35:12: 7000000 INFO @ Sat, 24 Aug 2019 18:35:14: 15000000 INFO @ Sat, 24 Aug 2019 18:35:16: 11000000 INFO @ Sat, 24 Aug 2019 18:35:21: 8000000 INFO @ Sat, 24 Aug 2019 18:35:23: 16000000 INFO @ Sat, 24 Aug 2019 18:35:24: 12000000 INFO @ Sat, 24 Aug 2019 18:35:29: 9000000 INFO @ Sat, 24 Aug 2019 18:35:33: 13000000 INFO @ Sat, 24 Aug 2019 18:35:33: 17000000 INFO @ Sat, 24 Aug 2019 18:35:37: 10000000 INFO @ Sat, 24 Aug 2019 18:35:41: 14000000 INFO @ Sat, 24 Aug 2019 18:35:42: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:35:42: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:35:42: #1 total tags in treatment: 17914264 INFO @ Sat, 24 Aug 2019 18:35:42: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:35:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:35:43: #1 tags after filtering in treatment: 17914056 INFO @ Sat, 24 Aug 2019 18:35:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:35:43: #1 finished! INFO @ Sat, 24 Aug 2019 18:35:43: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:35:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:35:45: 11000000 INFO @ Sat, 24 Aug 2019 18:35:49: 15000000 INFO @ Sat, 24 Aug 2019 18:35:49: #2 number of paired peaks: 112246 INFO @ Sat, 24 Aug 2019 18:35:49: start model_add_line... INFO @ Sat, 24 Aug 2019 18:35:49: start X-correlation... INFO @ Sat, 24 Aug 2019 18:35:49: end of X-cor INFO @ Sat, 24 Aug 2019 18:35:49: #2 finished! INFO @ Sat, 24 Aug 2019 18:35:49: #2 predicted fragment length is 173 bps INFO @ Sat, 24 Aug 2019 18:35:49: #2 alternative fragment length(s) may be 173 bps INFO @ Sat, 24 Aug 2019 18:35:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375035/SRX5375035.05_model.r INFO @ Sat, 24 Aug 2019 18:35:49: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:35:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:35:53: 12000000 INFO @ Sat, 24 Aug 2019 18:35:56: 16000000 INFO @ Sat, 24 Aug 2019 18:36:00: 13000000 INFO @ Sat, 24 Aug 2019 18:36:04: 17000000 INFO @ Sat, 24 Aug 2019 18:36:08: 14000000 INFO @ Sat, 24 Aug 2019 18:36:11: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:36:11: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:36:11: #1 total tags in treatment: 17914264 INFO @ Sat, 24 Aug 2019 18:36:11: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:36:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:36:12: #1 tags after filtering in treatment: 17914056 INFO @ Sat, 24 Aug 2019 18:36:12: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:36:12: #1 finished! INFO @ Sat, 24 Aug 2019 18:36:12: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:36:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:36:15: 15000000 INFO @ Sat, 24 Aug 2019 18:36:18: #2 number of paired peaks: 112246 INFO @ Sat, 24 Aug 2019 18:36:18: start model_add_line... INFO @ Sat, 24 Aug 2019 18:36:18: start X-correlation... INFO @ Sat, 24 Aug 2019 18:36:18: end of X-cor INFO @ Sat, 24 Aug 2019 18:36:18: #2 finished! INFO @ Sat, 24 Aug 2019 18:36:18: #2 predicted fragment length is 173 bps INFO @ Sat, 24 Aug 2019 18:36:18: #2 alternative fragment length(s) may be 173 bps INFO @ Sat, 24 Aug 2019 18:36:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375035/SRX5375035.10_model.r INFO @ Sat, 24 Aug 2019 18:36:18: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:36:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:36:23: 16000000 INFO @ Sat, 24 Aug 2019 18:36:30: 17000000 INFO @ Sat, 24 Aug 2019 18:36:37: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:36:37: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:36:37: #1 total tags in treatment: 17914264 INFO @ Sat, 24 Aug 2019 18:36:37: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:36:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:36:38: #1 tags after filtering in treatment: 17914056 INFO @ Sat, 24 Aug 2019 18:36:38: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:36:38: #1 finished! INFO @ Sat, 24 Aug 2019 18:36:38: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:36:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:36:44: #2 number of paired peaks: 112246 INFO @ Sat, 24 Aug 2019 18:36:44: start model_add_line... INFO @ Sat, 24 Aug 2019 18:36:44: start X-correlation... INFO @ Sat, 24 Aug 2019 18:36:44: end of X-cor INFO @ Sat, 24 Aug 2019 18:36:44: #2 finished! INFO @ Sat, 24 Aug 2019 18:36:44: #2 predicted fragment length is 173 bps INFO @ Sat, 24 Aug 2019 18:36:44: #2 alternative fragment length(s) may be 173 bps INFO @ Sat, 24 Aug 2019 18:36:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375035/SRX5375035.20_model.r INFO @ Sat, 24 Aug 2019 18:36:44: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:36:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:36:49: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:37:16: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:37:23: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375035/SRX5375035.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:37:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375035/SRX5375035.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:37:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375035/SRX5375035.05_summits.bed INFO @ Sat, 24 Aug 2019 18:37:24: Done! pass1 - making usageList (130 chroms): 13 millis pass2 - checking and writing primary data (44639 records, 4 fields): 61 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:37:42: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:37:46: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375035/SRX5375035.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:37:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375035/SRX5375035.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:37:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375035/SRX5375035.10_summits.bed INFO @ Sat, 24 Aug 2019 18:37:47: Done! pass1 - making usageList (88 chroms): 5 millis pass2 - checking and writing primary data (25021 records, 4 fields): 35 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:38:11: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375035/SRX5375035.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:38:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375035/SRX5375035.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:38:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375035/SRX5375035.20_summits.bed INFO @ Sat, 24 Aug 2019 18:38:12: Done! pass1 - making usageList (56 chroms): 3 millis pass2 - checking and writing primary data (8366 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。