Job ID = 2002150 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T01:36:54 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 ) 2019-07-05T01:36:54 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 : 49,620,794 reads read : 49,620,794 reads written : 49,620,794 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: 00:31:15 49620794 reads; of these: 49620794 (100.00%) were unpaired; of these: 1175049 (2.37%) aligned 0 times 43358688 (87.38%) aligned exactly 1 time 5087057 (10.25%) aligned >1 times 97.63% overall alignment rate Time searching: 00:31:16 Overall time: 00:31:16 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 20 files... [bam_rmdupse_core] 28274290 / 48445745 = 0.5836 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 11:37:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102045/ERX102045.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102045/ERX102045.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102045/ERX102045.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102045/ERX102045.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 11:37:54: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:37:54: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:37:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102045/ERX102045.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102045/ERX102045.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102045/ERX102045.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102045/ERX102045.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 11:37:55: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:37:55: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:37:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102045/ERX102045.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102045/ERX102045.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102045/ERX102045.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102045/ERX102045.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 11:37:56: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:37:56: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:38:04: 1000000 INFO @ Fri, 05 Jul 2019 11:38:05: 1000000 INFO @ Fri, 05 Jul 2019 11:38:06: 1000000 INFO @ Fri, 05 Jul 2019 11:38:11: 2000000 INFO @ Fri, 05 Jul 2019 11:38:15: 2000000 INFO @ Fri, 05 Jul 2019 11:38:16: 2000000 INFO @ Fri, 05 Jul 2019 11:38:18: 3000000 INFO @ Fri, 05 Jul 2019 11:38:25: 4000000 INFO @ Fri, 05 Jul 2019 11:38:25: 3000000 INFO @ Fri, 05 Jul 2019 11:38:26: 3000000 INFO @ Fri, 05 Jul 2019 11:38:32: 5000000 INFO @ Fri, 05 Jul 2019 11:38:35: 4000000 INFO @ Fri, 05 Jul 2019 11:38:36: 4000000 INFO @ Fri, 05 Jul 2019 11:38:40: 6000000 INFO @ Fri, 05 Jul 2019 11:38:45: 5000000 INFO @ Fri, 05 Jul 2019 11:38:46: 5000000 INFO @ Fri, 05 Jul 2019 11:38:48: 7000000 INFO @ Fri, 05 Jul 2019 11:38:55: 8000000 INFO @ Fri, 05 Jul 2019 11:38:56: 6000000 INFO @ Fri, 05 Jul 2019 11:38:58: 6000000 INFO @ Fri, 05 Jul 2019 11:39:02: 9000000 INFO @ Fri, 05 Jul 2019 11:39:08: 7000000 INFO @ Fri, 05 Jul 2019 11:39:09: 7000000 INFO @ Fri, 05 Jul 2019 11:39:09: 10000000 INFO @ Fri, 05 Jul 2019 11:39:17: 11000000 INFO @ Fri, 05 Jul 2019 11:39:18: 8000000 INFO @ Fri, 05 Jul 2019 11:39:20: 8000000 INFO @ Fri, 05 Jul 2019 11:39:24: 12000000 INFO @ Fri, 05 Jul 2019 11:39:28: 9000000 INFO @ Fri, 05 Jul 2019 11:39:30: 9000000 INFO @ Fri, 05 Jul 2019 11:39:32: 13000000 INFO @ Fri, 05 Jul 2019 11:39:38: 10000000 INFO @ Fri, 05 Jul 2019 11:39:39: 14000000 INFO @ Fri, 05 Jul 2019 11:39:40: 10000000 INFO @ Fri, 05 Jul 2019 11:39:46: 15000000 INFO @ Fri, 05 Jul 2019 11:39:48: 11000000 INFO @ Fri, 05 Jul 2019 11:39:50: 11000000 INFO @ Fri, 05 Jul 2019 11:39:54: 16000000 INFO @ Fri, 05 Jul 2019 11:39:58: 12000000 INFO @ Fri, 05 Jul 2019 11:40:00: 12000000 INFO @ Fri, 05 Jul 2019 11:40:01: 17000000 INFO @ Fri, 05 Jul 2019 11:40:08: 18000000 INFO @ Fri, 05 Jul 2019 11:40:09: 13000000 INFO @ Fri, 05 Jul 2019 11:40:10: 13000000 INFO @ Fri, 05 Jul 2019 11:40:15: 19000000 INFO @ Fri, 05 Jul 2019 11:40:18: 14000000 INFO @ Fri, 05 Jul 2019 11:40:19: 14000000 INFO @ Fri, 05 Jul 2019 11:40:23: 20000000 INFO @ Fri, 05 Jul 2019 11:40:24: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 11:40:24: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 11:40:24: #1 total tags in treatment: 20171455 INFO @ Fri, 05 Jul 2019 11:40:24: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:40:24: #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 11:40:25: #1 tags after filtering in treatment: 20171214 INFO @ Fri, 05 Jul 2019 11:40:25: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:40:25: #1 finished! INFO @ Fri, 05 Jul 2019 11:40:25: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:40:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:40:28: 15000000 INFO @ Fri, 05 Jul 2019 11:40:29: 15000000 INFO @ Fri, 05 Jul 2019 11:40:29: #2 number of paired peaks: 56172 INFO @ Fri, 05 Jul 2019 11:40:29: start model_add_line... INFO @ Fri, 05 Jul 2019 11:40:30: start X-correlation... INFO @ Fri, 05 Jul 2019 11:40:30: end of X-cor INFO @ Fri, 05 Jul 2019 11:40:30: #2 finished! INFO @ Fri, 05 Jul 2019 11:40:30: #2 predicted fragment length is 122 bps INFO @ Fri, 05 Jul 2019 11:40:30: #2 alternative fragment length(s) may be 122 bps INFO @ Fri, 05 Jul 2019 11:40:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102045/ERX102045.20_model.r INFO @ Fri, 05 Jul 2019 11:40:30: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:40:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:40:38: 16000000 INFO @ Fri, 05 Jul 2019 11:40:39: 16000000 INFO @ Fri, 05 Jul 2019 11:40:48: 17000000 INFO @ Fri, 05 Jul 2019 11:40:49: 17000000 INFO @ Fri, 05 Jul 2019 11:40:58: 18000000 INFO @ Fri, 05 Jul 2019 11:40:59: 18000000 INFO @ Fri, 05 Jul 2019 11:41:08: 19000000 INFO @ Fri, 05 Jul 2019 11:41:09: 19000000 INFO @ Fri, 05 Jul 2019 11:41:18: 20000000 INFO @ Fri, 05 Jul 2019 11:41:19: 20000000 INFO @ Fri, 05 Jul 2019 11:41:20: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 11:41:20: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 11:41:20: #1 total tags in treatment: 20171455 INFO @ Fri, 05 Jul 2019 11:41:20: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:41:20: #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 11:41:21: #1 tags after filtering in treatment: 20171214 INFO @ Fri, 05 Jul 2019 11:41:21: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:41:21: #1 finished! INFO @ Fri, 05 Jul 2019 11:41:21: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:41:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:41:21: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 11:41:21: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 11:41:21: #1 total tags in treatment: 20171455 INFO @ Fri, 05 Jul 2019 11:41:21: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:41:21: #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 11:41:21: #1 tags after filtering in treatment: 20171214 INFO @ Fri, 05 Jul 2019 11:41:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:41:22: #1 finished! INFO @ Fri, 05 Jul 2019 11:41:22: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:41:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:41:26: #2 number of paired peaks: 56172 INFO @ Fri, 05 Jul 2019 11:41:26: start model_add_line... INFO @ Fri, 05 Jul 2019 11:41:26: start X-correlation... INFO @ Fri, 05 Jul 2019 11:41:26: end of X-cor INFO @ Fri, 05 Jul 2019 11:41:26: #2 finished! INFO @ Fri, 05 Jul 2019 11:41:26: #2 predicted fragment length is 122 bps INFO @ Fri, 05 Jul 2019 11:41:26: #2 alternative fragment length(s) may be 122 bps INFO @ Fri, 05 Jul 2019 11:41:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102045/ERX102045.05_model.r INFO @ Fri, 05 Jul 2019 11:41:26: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:41:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:41:26: #2 number of paired peaks: 56172 INFO @ Fri, 05 Jul 2019 11:41:26: start model_add_line... INFO @ Fri, 05 Jul 2019 11:41:27: start X-correlation... INFO @ Fri, 05 Jul 2019 11:41:27: end of X-cor INFO @ Fri, 05 Jul 2019 11:41:27: #2 finished! INFO @ Fri, 05 Jul 2019 11:41:27: #2 predicted fragment length is 122 bps INFO @ Fri, 05 Jul 2019 11:41:27: #2 alternative fragment length(s) may be 122 bps INFO @ Fri, 05 Jul 2019 11:41:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102045/ERX102045.10_model.r INFO @ Fri, 05 Jul 2019 11:41:27: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:41:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:41:29: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:42:01: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102045/ERX102045.20_peaks.xls INFO @ Fri, 05 Jul 2019 11:42:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102045/ERX102045.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:42:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102045/ERX102045.20_summits.bed INFO @ Fri, 05 Jul 2019 11:42:02: Done! pass1 - making usageList (110 chroms): 10 millis pass2 - checking and writing primary data (30450 records, 4 fields): 43 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 11:42:24: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:42:25: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:42:57: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102045/ERX102045.05_peaks.xls INFO @ Fri, 05 Jul 2019 11:42:57: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102045/ERX102045.10_peaks.xls INFO @ Fri, 05 Jul 2019 11:42:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102045/ERX102045.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:42:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102045/ERX102045.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:42:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102045/ERX102045.05_summits.bed INFO @ Fri, 05 Jul 2019 11:42:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102045/ERX102045.10_summits.bed INFO @ Fri, 05 Jul 2019 11:42:58: Done! INFO @ Fri, 05 Jul 2019 11:42:58: Done! pass1 - making usageList (133 chroms): 9 millis pass1 - making usageList (161 chroms): 13 millis pass2 - checking and writing primary data (42043 records, 4 fields): 59 millis pass2 - checking and writing primary data (53718 records, 4 fields): 74 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。