Job ID = 2001548 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T19:33:49 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 ) 2019-07-04T19:42:00 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 ) 2019-07-04T19:47:37 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 : 57,378,461 reads read : 57,378,461 reads written : 57,378,461 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:38:14 57378461 reads; of these: 57378461 (100.00%) were unpaired; of these: 1450226 (2.53%) aligned 0 times 50075370 (87.27%) aligned exactly 1 time 5852865 (10.20%) aligned >1 times 97.47% overall alignment rate Time searching: 00:38:15 Overall time: 00:38:15 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 24 files... [bam_rmdupse_core] 31588931 / 55928235 = 0.5648 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 05:53:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101891/ERX101891.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101891/ERX101891.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101891/ERX101891.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101891/ERX101891.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 05:53:02: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:53:02: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:53:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101891/ERX101891.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101891/ERX101891.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101891/ERX101891.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101891/ERX101891.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 05:53:02: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:53:02: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:53:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101891/ERX101891.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101891/ERX101891.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101891/ERX101891.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101891/ERX101891.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 05:53:02: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:53:02: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:53:12: 1000000 INFO @ Fri, 05 Jul 2019 05:53:13: 1000000 INFO @ Fri, 05 Jul 2019 05:53:14: 1000000 INFO @ Fri, 05 Jul 2019 05:53:22: 2000000 INFO @ Fri, 05 Jul 2019 05:53:22: 2000000 INFO @ Fri, 05 Jul 2019 05:53:25: 2000000 INFO @ Fri, 05 Jul 2019 05:53:32: 3000000 INFO @ Fri, 05 Jul 2019 05:53:32: 3000000 INFO @ Fri, 05 Jul 2019 05:53:37: 3000000 INFO @ Fri, 05 Jul 2019 05:53:41: 4000000 INFO @ Fri, 05 Jul 2019 05:53:41: 4000000 INFO @ Fri, 05 Jul 2019 05:53:48: 4000000 INFO @ Fri, 05 Jul 2019 05:53:50: 5000000 INFO @ Fri, 05 Jul 2019 05:53:51: 5000000 INFO @ Fri, 05 Jul 2019 05:54:00: 6000000 INFO @ Fri, 05 Jul 2019 05:54:00: 5000000 INFO @ Fri, 05 Jul 2019 05:54:00: 6000000 INFO @ Fri, 05 Jul 2019 05:54:09: 7000000 INFO @ Fri, 05 Jul 2019 05:54:09: 7000000 INFO @ Fri, 05 Jul 2019 05:54:11: 6000000 INFO @ Fri, 05 Jul 2019 05:54:18: 8000000 INFO @ Fri, 05 Jul 2019 05:54:19: 8000000 INFO @ Fri, 05 Jul 2019 05:54:22: 7000000 INFO @ Fri, 05 Jul 2019 05:54:27: 9000000 INFO @ Fri, 05 Jul 2019 05:54:28: 9000000 INFO @ Fri, 05 Jul 2019 05:54:34: 8000000 INFO @ Fri, 05 Jul 2019 05:54:37: 10000000 INFO @ Fri, 05 Jul 2019 05:54:37: 10000000 INFO @ Fri, 05 Jul 2019 05:54:45: 9000000 INFO @ Fri, 05 Jul 2019 05:54:46: 11000000 INFO @ Fri, 05 Jul 2019 05:54:46: 11000000 INFO @ Fri, 05 Jul 2019 05:54:55: 12000000 INFO @ Fri, 05 Jul 2019 05:54:55: 12000000 INFO @ Fri, 05 Jul 2019 05:54:56: 10000000 INFO @ Fri, 05 Jul 2019 05:55:04: 13000000 INFO @ Fri, 05 Jul 2019 05:55:05: 13000000 INFO @ Fri, 05 Jul 2019 05:55:07: 11000000 INFO @ Fri, 05 Jul 2019 05:55:14: 14000000 INFO @ Fri, 05 Jul 2019 05:55:14: 14000000 INFO @ Fri, 05 Jul 2019 05:55:19: 12000000 INFO @ Fri, 05 Jul 2019 05:55:24: 15000000 INFO @ Fri, 05 Jul 2019 05:55:24: 15000000 INFO @ Fri, 05 Jul 2019 05:55:29: 13000000 INFO @ Fri, 05 Jul 2019 05:55:34: 16000000 INFO @ Fri, 05 Jul 2019 05:55:36: 16000000 INFO @ Fri, 05 Jul 2019 05:55:42: 14000000 INFO @ Fri, 05 Jul 2019 05:55:44: 17000000 INFO @ Fri, 05 Jul 2019 05:55:45: 17000000 INFO @ Fri, 05 Jul 2019 05:55:54: 18000000 INFO @ Fri, 05 Jul 2019 05:55:54: 15000000 INFO @ Fri, 05 Jul 2019 05:55:57: 18000000 INFO @ Fri, 05 Jul 2019 05:56:04: 19000000 INFO @ Fri, 05 Jul 2019 05:56:07: 16000000 INFO @ Fri, 05 Jul 2019 05:56:08: 19000000 INFO @ Fri, 05 Jul 2019 05:56:13: 20000000 INFO @ Fri, 05 Jul 2019 05:56:18: 20000000 INFO @ Fri, 05 Jul 2019 05:56:19: 17000000 INFO @ Fri, 05 Jul 2019 05:56:23: 21000000 INFO @ Fri, 05 Jul 2019 05:56:28: 21000000 INFO @ Fri, 05 Jul 2019 05:56:31: 18000000 INFO @ Fri, 05 Jul 2019 05:56:33: 22000000 INFO @ Fri, 05 Jul 2019 05:56:37: 22000000 INFO @ Fri, 05 Jul 2019 05:56:42: 23000000 INFO @ Fri, 05 Jul 2019 05:56:43: 19000000 INFO @ Fri, 05 Jul 2019 05:56:46: 23000000 INFO @ Fri, 05 Jul 2019 05:56:51: 24000000 INFO @ Fri, 05 Jul 2019 05:56:55: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 05:56:55: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 05:56:55: #1 total tags in treatment: 24339304 INFO @ Fri, 05 Jul 2019 05:56:55: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:56:55: #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 05:56:55: 20000000 INFO @ Fri, 05 Jul 2019 05:56:55: #1 tags after filtering in treatment: 24339078 INFO @ Fri, 05 Jul 2019 05:56:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:56:55: #1 finished! INFO @ Fri, 05 Jul 2019 05:56:55: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:56:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:56:55: 24000000 INFO @ Fri, 05 Jul 2019 05:56:58: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 05:56:58: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 05:56:58: #1 total tags in treatment: 24339304 INFO @ Fri, 05 Jul 2019 05:56:58: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:56:58: #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 05:56:59: #1 tags after filtering in treatment: 24339078 INFO @ Fri, 05 Jul 2019 05:56:59: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:56:59: #1 finished! INFO @ Fri, 05 Jul 2019 05:56:59: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:56:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:57:01: #2 number of paired peaks: 59164 INFO @ Fri, 05 Jul 2019 05:57:01: start model_add_line... INFO @ Fri, 05 Jul 2019 05:57:01: start X-correlation... INFO @ Fri, 05 Jul 2019 05:57:02: end of X-cor INFO @ Fri, 05 Jul 2019 05:57:02: #2 finished! INFO @ Fri, 05 Jul 2019 05:57:02: #2 predicted fragment length is 119 bps INFO @ Fri, 05 Jul 2019 05:57:02: #2 alternative fragment length(s) may be 119 bps INFO @ Fri, 05 Jul 2019 05:57:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101891/ERX101891.10_model.r INFO @ Fri, 05 Jul 2019 05:57:02: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:57:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:57:05: #2 number of paired peaks: 59164 INFO @ Fri, 05 Jul 2019 05:57:05: start model_add_line... INFO @ Fri, 05 Jul 2019 05:57:05: start X-correlation... INFO @ Fri, 05 Jul 2019 05:57:05: end of X-cor INFO @ Fri, 05 Jul 2019 05:57:05: #2 finished! INFO @ Fri, 05 Jul 2019 05:57:05: #2 predicted fragment length is 119 bps INFO @ Fri, 05 Jul 2019 05:57:05: #2 alternative fragment length(s) may be 119 bps INFO @ Fri, 05 Jul 2019 05:57:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101891/ERX101891.20_model.r INFO @ Fri, 05 Jul 2019 05:57:05: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:57:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:57:06: 21000000 INFO @ Fri, 05 Jul 2019 05:57:17: 22000000 INFO @ Fri, 05 Jul 2019 05:57:28: 23000000 INFO @ Fri, 05 Jul 2019 05:57:39: 24000000 INFO @ Fri, 05 Jul 2019 05:57:43: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 05:57:43: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 05:57:43: #1 total tags in treatment: 24339304 INFO @ Fri, 05 Jul 2019 05:57:43: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:57:43: #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 05:57:43: #1 tags after filtering in treatment: 24339078 INFO @ Fri, 05 Jul 2019 05:57:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:57:43: #1 finished! INFO @ Fri, 05 Jul 2019 05:57:43: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:57:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:57:49: #2 number of paired peaks: 59164 INFO @ Fri, 05 Jul 2019 05:57:49: start model_add_line... INFO @ Fri, 05 Jul 2019 05:57:50: start X-correlation... INFO @ Fri, 05 Jul 2019 05:57:50: end of X-cor INFO @ Fri, 05 Jul 2019 05:57:50: #2 finished! INFO @ Fri, 05 Jul 2019 05:57:50: #2 predicted fragment length is 119 bps INFO @ Fri, 05 Jul 2019 05:57:50: #2 alternative fragment length(s) may be 119 bps INFO @ Fri, 05 Jul 2019 05:57:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101891/ERX101891.05_model.r INFO @ Fri, 05 Jul 2019 05:57:50: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:57:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:58:18: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 05:58:19: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 05:58:59: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101891/ERX101891.20_peaks.xls INFO @ Fri, 05 Jul 2019 05:58:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101891/ERX101891.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 05:58:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101891/ERX101891.20_summits.bed INFO @ Fri, 05 Jul 2019 05:59:00: Done! pass1 - making usageList (111 chroms): 14 millis pass2 - checking and writing primary data (33012 records, 4 fields): 48 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 05:59:01: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101891/ERX101891.10_peaks.xls INFO @ Fri, 05 Jul 2019 05:59:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101891/ERX101891.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 05:59:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101891/ERX101891.10_summits.bed INFO @ Fri, 05 Jul 2019 05:59:02: Done! pass1 - making usageList (136 chroms): 9 millis pass2 - checking and writing primary data (44907 records, 4 fields): 60 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 05:59:03: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 05:59:45: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101891/ERX101891.05_peaks.xls INFO @ Fri, 05 Jul 2019 05:59:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101891/ERX101891.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 05:59:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101891/ERX101891.05_summits.bed INFO @ Fri, 05 Jul 2019 05:59:46: Done! pass1 - making usageList (162 chroms): 15 millis pass2 - checking and writing primary data (56306 records, 4 fields): 76 millis CompletedMACS2peakCalling