Job ID = 2002140 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T01:36:48 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 ) 2019-07-05T01:38:47 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 ) 2019-07-05T01:38:47 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 ) 2019-07-05T01:49:22 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 : 113,372,120 reads read : 113,372,120 reads written : 113,372,120 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: 01:00:38 113372120 reads; of these: 113372120 (100.00%) were unpaired; of these: 2073792 (1.83%) aligned 0 times 100024855 (88.23%) aligned exactly 1 time 11273473 (9.94%) aligned >1 times 98.17% overall alignment rate Time searching: 01:00:39 Overall time: 01:00:39 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 48 files... [bam_rmdupse_core] 77098071 / 111298328 = 0.6927 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 12:51:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102040/ERX102040.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102040/ERX102040.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102040/ERX102040.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102040/ERX102040.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 12:51:19: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:51:19: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:51:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102040/ERX102040.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102040/ERX102040.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102040/ERX102040.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102040/ERX102040.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 12:51:20: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:51:20: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:51:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102040/ERX102040.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102040/ERX102040.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102040/ERX102040.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102040/ERX102040.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 12:51:21: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:51:21: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:51:27: 1000000 INFO @ Fri, 05 Jul 2019 12:51:28: 1000000 INFO @ Fri, 05 Jul 2019 12:51:29: 1000000 INFO @ Fri, 05 Jul 2019 12:51:35: 2000000 INFO @ Fri, 05 Jul 2019 12:51:36: 2000000 INFO @ Fri, 05 Jul 2019 12:51:37: 2000000 INFO @ Fri, 05 Jul 2019 12:51:43: 3000000 INFO @ Fri, 05 Jul 2019 12:51:44: 3000000 INFO @ Fri, 05 Jul 2019 12:51:45: 3000000 INFO @ Fri, 05 Jul 2019 12:51:51: 4000000 INFO @ Fri, 05 Jul 2019 12:51:52: 4000000 INFO @ Fri, 05 Jul 2019 12:51:53: 4000000 INFO @ Fri, 05 Jul 2019 12:52:00: 5000000 INFO @ Fri, 05 Jul 2019 12:52:00: 5000000 INFO @ Fri, 05 Jul 2019 12:52:01: 5000000 INFO @ Fri, 05 Jul 2019 12:52:08: 6000000 INFO @ Fri, 05 Jul 2019 12:52:08: 6000000 INFO @ Fri, 05 Jul 2019 12:52:08: 6000000 INFO @ Fri, 05 Jul 2019 12:52:15: 7000000 INFO @ Fri, 05 Jul 2019 12:52:16: 7000000 INFO @ Fri, 05 Jul 2019 12:52:16: 7000000 INFO @ Fri, 05 Jul 2019 12:52:23: 8000000 INFO @ Fri, 05 Jul 2019 12:52:24: 8000000 INFO @ Fri, 05 Jul 2019 12:52:24: 8000000 INFO @ Fri, 05 Jul 2019 12:52:31: 9000000 INFO @ Fri, 05 Jul 2019 12:52:32: 9000000 INFO @ Fri, 05 Jul 2019 12:52:32: 9000000 INFO @ Fri, 05 Jul 2019 12:52:39: 10000000 INFO @ Fri, 05 Jul 2019 12:52:40: 10000000 INFO @ Fri, 05 Jul 2019 12:52:40: 10000000 INFO @ Fri, 05 Jul 2019 12:52:46: 11000000 INFO @ Fri, 05 Jul 2019 12:52:47: 11000000 INFO @ Fri, 05 Jul 2019 12:52:48: 11000000 INFO @ Fri, 05 Jul 2019 12:52:54: 12000000 INFO @ Fri, 05 Jul 2019 12:52:55: 12000000 INFO @ Fri, 05 Jul 2019 12:52:56: 12000000 INFO @ Fri, 05 Jul 2019 12:53:02: 13000000 INFO @ Fri, 05 Jul 2019 12:53:02: 13000000 INFO @ Fri, 05 Jul 2019 12:53:04: 13000000 INFO @ Fri, 05 Jul 2019 12:53:09: 14000000 INFO @ Fri, 05 Jul 2019 12:53:10: 14000000 INFO @ Fri, 05 Jul 2019 12:53:12: 14000000 INFO @ Fri, 05 Jul 2019 12:53:17: 15000000 INFO @ Fri, 05 Jul 2019 12:53:18: 15000000 INFO @ Fri, 05 Jul 2019 12:53:20: 15000000 INFO @ Fri, 05 Jul 2019 12:53:24: 16000000 INFO @ Fri, 05 Jul 2019 12:53:25: 16000000 INFO @ Fri, 05 Jul 2019 12:53:28: 16000000 INFO @ Fri, 05 Jul 2019 12:53:32: 17000000 INFO @ Fri, 05 Jul 2019 12:53:33: 17000000 INFO @ Fri, 05 Jul 2019 12:53:35: 17000000 INFO @ Fri, 05 Jul 2019 12:53:40: 18000000 INFO @ Fri, 05 Jul 2019 12:53:40: 18000000 INFO @ Fri, 05 Jul 2019 12:53:43: 18000000 INFO @ Fri, 05 Jul 2019 12:53:47: 19000000 INFO @ Fri, 05 Jul 2019 12:53:48: 19000000 INFO @ Fri, 05 Jul 2019 12:53:51: 19000000 INFO @ Fri, 05 Jul 2019 12:53:55: 20000000 INFO @ Fri, 05 Jul 2019 12:53:55: 20000000 INFO @ Fri, 05 Jul 2019 12:53:59: 20000000 INFO @ Fri, 05 Jul 2019 12:54:02: 21000000 INFO @ Fri, 05 Jul 2019 12:54:03: 21000000 INFO @ Fri, 05 Jul 2019 12:54:06: 21000000 INFO @ Fri, 05 Jul 2019 12:54:10: 22000000 INFO @ Fri, 05 Jul 2019 12:54:10: 22000000 INFO @ Fri, 05 Jul 2019 12:54:14: 22000000 INFO @ Fri, 05 Jul 2019 12:54:17: 23000000 INFO @ Fri, 05 Jul 2019 12:54:17: 23000000 INFO @ Fri, 05 Jul 2019 12:54:21: 23000000 INFO @ Fri, 05 Jul 2019 12:54:24: 24000000 INFO @ Fri, 05 Jul 2019 12:54:25: 24000000 INFO @ Fri, 05 Jul 2019 12:54:29: 24000000 INFO @ Fri, 05 Jul 2019 12:54:32: 25000000 INFO @ Fri, 05 Jul 2019 12:54:32: 25000000 INFO @ Fri, 05 Jul 2019 12:54:37: 25000000 INFO @ Fri, 05 Jul 2019 12:54:39: 26000000 INFO @ Fri, 05 Jul 2019 12:54:40: 26000000 INFO @ Fri, 05 Jul 2019 12:54:44: 26000000 INFO @ Fri, 05 Jul 2019 12:54:47: 27000000 INFO @ Fri, 05 Jul 2019 12:54:47: 27000000 INFO @ Fri, 05 Jul 2019 12:54:52: 27000000 INFO @ Fri, 05 Jul 2019 12:54:54: 28000000 INFO @ Fri, 05 Jul 2019 12:54:55: 28000000 INFO @ Fri, 05 Jul 2019 12:55:00: 28000000 INFO @ Fri, 05 Jul 2019 12:55:02: 29000000 INFO @ Fri, 05 Jul 2019 12:55:02: 29000000 INFO @ Fri, 05 Jul 2019 12:55:07: 29000000 INFO @ Fri, 05 Jul 2019 12:55:09: 30000000 INFO @ Fri, 05 Jul 2019 12:55:10: 30000000 INFO @ Fri, 05 Jul 2019 12:55:15: 30000000 INFO @ Fri, 05 Jul 2019 12:55:17: 31000000 INFO @ Fri, 05 Jul 2019 12:55:17: 31000000 INFO @ Fri, 05 Jul 2019 12:55:23: 31000000 INFO @ Fri, 05 Jul 2019 12:55:24: 32000000 INFO @ Fri, 05 Jul 2019 12:55:25: 32000000 INFO @ Fri, 05 Jul 2019 12:55:30: 32000000 INFO @ Fri, 05 Jul 2019 12:55:32: 33000000 INFO @ Fri, 05 Jul 2019 12:55:32: 33000000 INFO @ Fri, 05 Jul 2019 12:55:38: 33000000 INFO @ Fri, 05 Jul 2019 12:55:40: 34000000 INFO @ Fri, 05 Jul 2019 12:55:40: 34000000 INFO @ Fri, 05 Jul 2019 12:55:42: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 12:55:42: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 12:55:42: #1 total tags in treatment: 34200257 INFO @ Fri, 05 Jul 2019 12:55:42: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:55:42: #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 12:55:42: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 12:55:42: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 12:55:42: #1 total tags in treatment: 34200257 INFO @ Fri, 05 Jul 2019 12:55:42: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:55:42: #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 12:55:42: #1 tags after filtering in treatment: 34200053 INFO @ Fri, 05 Jul 2019 12:55:42: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:55:42: #1 finished! INFO @ Fri, 05 Jul 2019 12:55:42: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:55:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:55:43: #1 tags after filtering in treatment: 34200053 INFO @ Fri, 05 Jul 2019 12:55:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:55:43: #1 finished! INFO @ Fri, 05 Jul 2019 12:55:43: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:55:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:55:46: 34000000 INFO @ Fri, 05 Jul 2019 12:55:48: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 12:55:48: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 12:55:48: #1 total tags in treatment: 34200257 INFO @ Fri, 05 Jul 2019 12:55:48: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:55:48: #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 12:55:48: #1 tags after filtering in treatment: 34200053 INFO @ Fri, 05 Jul 2019 12:55:48: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:55:48: #1 finished! INFO @ Fri, 05 Jul 2019 12:55:48: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:55:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:55:50: #2 number of paired peaks: 63112 INFO @ Fri, 05 Jul 2019 12:55:50: start model_add_line... INFO @ Fri, 05 Jul 2019 12:55:50: #2 number of paired peaks: 63112 INFO @ Fri, 05 Jul 2019 12:55:50: start model_add_line... INFO @ Fri, 05 Jul 2019 12:55:51: start X-correlation... INFO @ Fri, 05 Jul 2019 12:55:51: end of X-cor INFO @ Fri, 05 Jul 2019 12:55:51: #2 finished! INFO @ Fri, 05 Jul 2019 12:55:51: #2 predicted fragment length is 135 bps INFO @ Fri, 05 Jul 2019 12:55:51: #2 alternative fragment length(s) may be 4,135 bps INFO @ Fri, 05 Jul 2019 12:55:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102040/ERX102040.10_model.r INFO @ Fri, 05 Jul 2019 12:55:51: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:55:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:55:51: start X-correlation... INFO @ Fri, 05 Jul 2019 12:55:51: end of X-cor INFO @ Fri, 05 Jul 2019 12:55:51: #2 finished! INFO @ Fri, 05 Jul 2019 12:55:51: #2 predicted fragment length is 135 bps INFO @ Fri, 05 Jul 2019 12:55:51: #2 alternative fragment length(s) may be 4,135 bps INFO @ Fri, 05 Jul 2019 12:55:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102040/ERX102040.20_model.r INFO @ Fri, 05 Jul 2019 12:55:51: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:55:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:55:56: #2 number of paired peaks: 63112 INFO @ Fri, 05 Jul 2019 12:55:56: start model_add_line... INFO @ Fri, 05 Jul 2019 12:55:57: start X-correlation... INFO @ Fri, 05 Jul 2019 12:55:57: end of X-cor INFO @ Fri, 05 Jul 2019 12:55:57: #2 finished! INFO @ Fri, 05 Jul 2019 12:55:57: #2 predicted fragment length is 135 bps INFO @ Fri, 05 Jul 2019 12:55:57: #2 alternative fragment length(s) may be 4,135 bps INFO @ Fri, 05 Jul 2019 12:55:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102040/ERX102040.05_model.r INFO @ Fri, 05 Jul 2019 12:55:57: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:55:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:57:30: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:57:30: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:57:35: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:58:22: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102040/ERX102040.10_peaks.xls INFO @ Fri, 05 Jul 2019 12:58:22: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102040/ERX102040.20_peaks.xls INFO @ Fri, 05 Jul 2019 12:58:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102040/ERX102040.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:58:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102040/ERX102040.10_summits.bed INFO @ Fri, 05 Jul 2019 12:58:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102040/ERX102040.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:58:23: Done! INFO @ Fri, 05 Jul 2019 12:58:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102040/ERX102040.20_summits.bed INFO @ Fri, 05 Jul 2019 12:58:23: Done! pass1 - making usageList (144 chroms): 9 millis pass1 - making usageList (127 chroms): 7 millis pass2 - checking and writing primary data (47999 records, 4 fields): 233 millis pass2 - checking and writing primary data (37103 records, 4 fields): 277 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 12:58:27: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102040/ERX102040.05_peaks.xls INFO @ Fri, 05 Jul 2019 12:58:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102040/ERX102040.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:58:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102040/ERX102040.05_summits.bed INFO @ Fri, 05 Jul 2019 12:58:29: Done! pass1 - making usageList (170 chroms): 16 millis pass2 - checking and writing primary data (58768 records, 4 fields): 80 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。