Job ID = 2640592 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T08:58:44 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 ) 2019-08-24T08:58:44 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 ) 2019-08-24T08:58:44 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 ) 2019-08-24T08:58:44 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 : 27,284,943 reads read : 54,569,886 reads written : 27,284,943 reads 0-length : 27,284,943 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: 00:20:18 27284943 reads; of these: 27284943 (100.00%) were unpaired; of these: 571994 (2.10%) aligned 0 times 20979363 (76.89%) aligned exactly 1 time 5733586 (21.01%) aligned >1 times 97.90% overall alignment rate Time searching: 00:20:22 Overall time: 00:20:22 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] 5072568 / 26712949 = 0.1899 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:30:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375028/SRX5375028.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375028/SRX5375028.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375028/SRX5375028.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375028/SRX5375028.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 18:30:52: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:30:52: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:30:59: 1000000 INFO @ Sat, 24 Aug 2019 18:31:06: 2000000 INFO @ Sat, 24 Aug 2019 18:31:13: 3000000 INFO @ Sat, 24 Aug 2019 18:31:20: 4000000 INFO @ Sat, 24 Aug 2019 18:31:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375028/SRX5375028.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375028/SRX5375028.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375028/SRX5375028.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375028/SRX5375028.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 18:31:22: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:31:22: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:31:27: 5000000 INFO @ Sat, 24 Aug 2019 18:31:32: 1000000 INFO @ Sat, 24 Aug 2019 18:31:35: 6000000 INFO @ Sat, 24 Aug 2019 18:31:42: 2000000 INFO @ Sat, 24 Aug 2019 18:31:42: 7000000 INFO @ Sat, 24 Aug 2019 18:31:49: 8000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:31:52: 3000000 INFO @ Sat, 24 Aug 2019 18:31:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375028/SRX5375028.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375028/SRX5375028.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375028/SRX5375028.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375028/SRX5375028.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 18:31:52: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:31:52: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:31:57: 9000000 INFO @ Sat, 24 Aug 2019 18:32:01: 1000000 INFO @ Sat, 24 Aug 2019 18:32:01: 4000000 INFO @ Sat, 24 Aug 2019 18:32:06: 10000000 INFO @ Sat, 24 Aug 2019 18:32:09: 2000000 INFO @ Sat, 24 Aug 2019 18:32:11: 5000000 INFO @ Sat, 24 Aug 2019 18:32:15: 11000000 INFO @ Sat, 24 Aug 2019 18:32:18: 3000000 INFO @ Sat, 24 Aug 2019 18:32:21: 6000000 INFO @ Sat, 24 Aug 2019 18:32:23: 12000000 INFO @ Sat, 24 Aug 2019 18:32:26: 4000000 INFO @ Sat, 24 Aug 2019 18:32:31: 7000000 INFO @ Sat, 24 Aug 2019 18:32:31: 13000000 INFO @ Sat, 24 Aug 2019 18:32:35: 5000000 INFO @ Sat, 24 Aug 2019 18:32:39: 14000000 INFO @ Sat, 24 Aug 2019 18:32:41: 8000000 INFO @ Sat, 24 Aug 2019 18:32:42: 6000000 INFO @ Sat, 24 Aug 2019 18:32:47: 15000000 INFO @ Sat, 24 Aug 2019 18:32:50: 7000000 INFO @ Sat, 24 Aug 2019 18:32:51: 9000000 INFO @ Sat, 24 Aug 2019 18:32:54: 16000000 INFO @ Sat, 24 Aug 2019 18:32:57: 8000000 INFO @ Sat, 24 Aug 2019 18:33:01: 10000000 INFO @ Sat, 24 Aug 2019 18:33:02: 17000000 INFO @ Sat, 24 Aug 2019 18:33:04: 9000000 INFO @ Sat, 24 Aug 2019 18:33:09: 18000000 INFO @ Sat, 24 Aug 2019 18:33:10: 11000000 INFO @ Sat, 24 Aug 2019 18:33:12: 10000000 INFO @ Sat, 24 Aug 2019 18:33:17: 19000000 INFO @ Sat, 24 Aug 2019 18:33:19: 11000000 INFO @ Sat, 24 Aug 2019 18:33:20: 12000000 INFO @ Sat, 24 Aug 2019 18:33:24: 20000000 INFO @ Sat, 24 Aug 2019 18:33:27: 12000000 INFO @ Sat, 24 Aug 2019 18:33:30: 13000000 INFO @ Sat, 24 Aug 2019 18:33:32: 21000000 INFO @ Sat, 24 Aug 2019 18:33:34: 13000000 INFO @ Sat, 24 Aug 2019 18:33:37: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:33:37: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:33:37: #1 total tags in treatment: 21640381 INFO @ Sat, 24 Aug 2019 18:33:37: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:33:37: #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 18:33:38: #1 tags after filtering in treatment: 21640239 INFO @ Sat, 24 Aug 2019 18:33:38: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:33:38: #1 finished! INFO @ Sat, 24 Aug 2019 18:33:38: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:33:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:33:39: 14000000 INFO @ Sat, 24 Aug 2019 18:33:41: 14000000 INFO @ Sat, 24 Aug 2019 18:33:42: #2 number of paired peaks: 37369 INFO @ Sat, 24 Aug 2019 18:33:42: start model_add_line... INFO @ Sat, 24 Aug 2019 18:33:42: start X-correlation... INFO @ Sat, 24 Aug 2019 18:33:42: end of X-cor INFO @ Sat, 24 Aug 2019 18:33:42: #2 finished! INFO @ Sat, 24 Aug 2019 18:33:42: #2 predicted fragment length is 164 bps INFO @ Sat, 24 Aug 2019 18:33:42: #2 alternative fragment length(s) may be 164 bps INFO @ Sat, 24 Aug 2019 18:33:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375028/SRX5375028.05_model.r INFO @ Sat, 24 Aug 2019 18:33:42: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:33:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:33:49: 15000000 INFO @ Sat, 24 Aug 2019 18:33:49: 15000000 INFO @ Sat, 24 Aug 2019 18:33:56: 16000000 INFO @ Sat, 24 Aug 2019 18:33:58: 16000000 INFO @ Sat, 24 Aug 2019 18:34:04: 17000000 INFO @ Sat, 24 Aug 2019 18:34:08: 17000000 INFO @ Sat, 24 Aug 2019 18:34:11: 18000000 INFO @ Sat, 24 Aug 2019 18:34:18: 18000000 INFO @ Sat, 24 Aug 2019 18:34:18: 19000000 INFO @ Sat, 24 Aug 2019 18:34:26: 20000000 INFO @ Sat, 24 Aug 2019 18:34:27: 19000000 INFO @ Sat, 24 Aug 2019 18:34:34: 21000000 INFO @ Sat, 24 Aug 2019 18:34:37: 20000000 INFO @ Sat, 24 Aug 2019 18:34:38: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:34:38: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:34:38: #1 total tags in treatment: 21640381 INFO @ Sat, 24 Aug 2019 18:34:38: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:34:38: #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 18:34:39: #1 tags after filtering in treatment: 21640239 INFO @ Sat, 24 Aug 2019 18:34:39: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:34:39: #1 finished! INFO @ Sat, 24 Aug 2019 18:34:39: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:34:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:34:43: #2 number of paired peaks: 37369 INFO @ Sat, 24 Aug 2019 18:34:43: start model_add_line... INFO @ Sat, 24 Aug 2019 18:34:43: start X-correlation... INFO @ Sat, 24 Aug 2019 18:34:43: end of X-cor INFO @ Sat, 24 Aug 2019 18:34:43: #2 finished! INFO @ Sat, 24 Aug 2019 18:34:43: #2 predicted fragment length is 164 bps INFO @ Sat, 24 Aug 2019 18:34:43: #2 alternative fragment length(s) may be 164 bps INFO @ Sat, 24 Aug 2019 18:34:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375028/SRX5375028.20_model.r INFO @ Sat, 24 Aug 2019 18:34:43: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:34:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:34:47: 21000000 INFO @ Sat, 24 Aug 2019 18:34:52: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:34:53: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:34:53: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:34:53: #1 total tags in treatment: 21640381 INFO @ Sat, 24 Aug 2019 18:34:53: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:34:53: #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 18:34:53: #1 tags after filtering in treatment: 21640239 INFO @ Sat, 24 Aug 2019 18:34:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:34:53: #1 finished! INFO @ Sat, 24 Aug 2019 18:34:53: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:34:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:34:57: #2 number of paired peaks: 37369 INFO @ Sat, 24 Aug 2019 18:34:57: start model_add_line... INFO @ Sat, 24 Aug 2019 18:34:57: start X-correlation... INFO @ Sat, 24 Aug 2019 18:34:58: end of X-cor INFO @ Sat, 24 Aug 2019 18:34:58: #2 finished! INFO @ Sat, 24 Aug 2019 18:34:58: #2 predicted fragment length is 164 bps INFO @ Sat, 24 Aug 2019 18:34:58: #2 alternative fragment length(s) may be 164 bps INFO @ Sat, 24 Aug 2019 18:34:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375028/SRX5375028.10_model.r INFO @ Sat, 24 Aug 2019 18:34:58: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:34:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:35:28: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375028/SRX5375028.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:35:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375028/SRX5375028.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:35:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375028/SRX5375028.05_summits.bed INFO @ Sat, 24 Aug 2019 18:35:29: Done! pass1 - making usageList (96 chroms): 4 millis pass2 - checking and writing primary data (17223 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:35:53: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:36:08: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:36:29: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375028/SRX5375028.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:36:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375028/SRX5375028.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:36:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375028/SRX5375028.20_summits.bed INFO @ Sat, 24 Aug 2019 18:36:29: Done! pass1 - making usageList (63 chroms): 3 millis pass2 - checking and writing primary data (9942 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:36:44: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375028/SRX5375028.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:36:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375028/SRX5375028.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:36:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375028/SRX5375028.10_summits.bed INFO @ Sat, 24 Aug 2019 18:36:45: Done! pass1 - making usageList (80 chroms): 7 millis pass2 - checking and writing primary data (13764 records, 4 fields): 23 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。