Job ID = 4288944 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T03:49:06 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 : 22,494,791 reads read : 44,989,582 reads written : 22,494,791 reads 0-length : 22,494,791 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: 00:20:32 22494791 reads; of these: 22494791 (100.00%) were unpaired; of these: 1718897 (7.64%) aligned 0 times 17875535 (79.47%) aligned exactly 1 time 2900359 (12.89%) aligned >1 times 92.36% overall alignment rate Time searching: 00:20:33 Overall time: 00:20:33 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] 2493537 / 20775894 = 0.1200 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 13:42:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460573/SRX5460573.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460573/SRX5460573.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460573/SRX5460573.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460573/SRX5460573.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 @ Tue, 10 Dec 2019 13:42:06: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:42:06: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:42:15: 1000000 INFO @ Tue, 10 Dec 2019 13:42:24: 2000000 INFO @ Tue, 10 Dec 2019 13:42:32: 3000000 INFO @ Tue, 10 Dec 2019 13:42:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460573/SRX5460573.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460573/SRX5460573.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460573/SRX5460573.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460573/SRX5460573.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 @ Tue, 10 Dec 2019 13:42:36: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:42:36: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:42:40: 4000000 INFO @ Tue, 10 Dec 2019 13:42:48: 5000000 INFO @ Tue, 10 Dec 2019 13:42:48: 1000000 INFO @ Tue, 10 Dec 2019 13:42:56: 6000000 INFO @ Tue, 10 Dec 2019 13:43:00: 2000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 13:43:05: 7000000 INFO @ Tue, 10 Dec 2019 13:43:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460573/SRX5460573.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460573/SRX5460573.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460573/SRX5460573.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460573/SRX5460573.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 @ Tue, 10 Dec 2019 13:43:06: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:43:06: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:43:10: 3000000 INFO @ Tue, 10 Dec 2019 13:43:13: 8000000 INFO @ Tue, 10 Dec 2019 13:43:15: 1000000 INFO @ Tue, 10 Dec 2019 13:43:20: 4000000 INFO @ Tue, 10 Dec 2019 13:43:21: 9000000 INFO @ Tue, 10 Dec 2019 13:43:25: 2000000 INFO @ Tue, 10 Dec 2019 13:43:30: 5000000 INFO @ Tue, 10 Dec 2019 13:43:30: 10000000 INFO @ Tue, 10 Dec 2019 13:43:33: 3000000 INFO @ Tue, 10 Dec 2019 13:43:38: 11000000 INFO @ Tue, 10 Dec 2019 13:43:39: 6000000 INFO @ Tue, 10 Dec 2019 13:43:42: 4000000 INFO @ Tue, 10 Dec 2019 13:43:46: 12000000 INFO @ Tue, 10 Dec 2019 13:43:49: 7000000 INFO @ Tue, 10 Dec 2019 13:43:50: 5000000 INFO @ Tue, 10 Dec 2019 13:43:54: 13000000 INFO @ Tue, 10 Dec 2019 13:43:58: 6000000 INFO @ Tue, 10 Dec 2019 13:44:01: 8000000 INFO @ Tue, 10 Dec 2019 13:44:03: 14000000 INFO @ Tue, 10 Dec 2019 13:44:07: 7000000 INFO @ Tue, 10 Dec 2019 13:44:12: 15000000 INFO @ Tue, 10 Dec 2019 13:44:13: 9000000 INFO @ Tue, 10 Dec 2019 13:44:16: 8000000 INFO @ Tue, 10 Dec 2019 13:44:21: 16000000 INFO @ Tue, 10 Dec 2019 13:44:24: 10000000 INFO @ Tue, 10 Dec 2019 13:44:25: 9000000 INFO @ Tue, 10 Dec 2019 13:44:30: 17000000 INFO @ Tue, 10 Dec 2019 13:44:34: 10000000 INFO @ Tue, 10 Dec 2019 13:44:36: 11000000 INFO @ Tue, 10 Dec 2019 13:44:39: 18000000 INFO @ Tue, 10 Dec 2019 13:44:42: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 13:44:42: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 13:44:42: #1 total tags in treatment: 18282357 INFO @ Tue, 10 Dec 2019 13:44:42: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:44:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:44:42: #1 tags after filtering in treatment: 18282159 INFO @ Tue, 10 Dec 2019 13:44:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:44:42: #1 finished! INFO @ Tue, 10 Dec 2019 13:44:42: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:44:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:44:43: 11000000 INFO @ Tue, 10 Dec 2019 13:44:47: #2 number of paired peaks: 83132 INFO @ Tue, 10 Dec 2019 13:44:47: start model_add_line... INFO @ Tue, 10 Dec 2019 13:44:47: start X-correlation... INFO @ Tue, 10 Dec 2019 13:44:48: end of X-cor INFO @ Tue, 10 Dec 2019 13:44:48: #2 finished! INFO @ Tue, 10 Dec 2019 13:44:48: #2 predicted fragment length is 179 bps INFO @ Tue, 10 Dec 2019 13:44:48: #2 alternative fragment length(s) may be 179 bps INFO @ Tue, 10 Dec 2019 13:44:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460573/SRX5460573.05_model.r INFO @ Tue, 10 Dec 2019 13:44:48: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:44:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:44:48: 12000000 INFO @ Tue, 10 Dec 2019 13:44:51: 12000000 INFO @ Tue, 10 Dec 2019 13:44:59: 13000000 INFO @ Tue, 10 Dec 2019 13:44:59: 13000000 INFO @ Tue, 10 Dec 2019 13:45:07: 14000000 INFO @ Tue, 10 Dec 2019 13:45:10: 14000000 INFO @ Tue, 10 Dec 2019 13:45:16: 15000000 INFO @ Tue, 10 Dec 2019 13:45:20: 15000000 INFO @ Tue, 10 Dec 2019 13:45:24: 16000000 INFO @ Tue, 10 Dec 2019 13:45:31: 16000000 INFO @ Tue, 10 Dec 2019 13:45:32: 17000000 INFO @ Tue, 10 Dec 2019 13:45:40: 18000000 INFO @ Tue, 10 Dec 2019 13:45:42: 17000000 INFO @ Tue, 10 Dec 2019 13:45:43: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 13:45:43: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 13:45:43: #1 total tags in treatment: 18282357 INFO @ Tue, 10 Dec 2019 13:45:43: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:45:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:45:43: #1 tags after filtering in treatment: 18282159 INFO @ Tue, 10 Dec 2019 13:45:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:45:43: #1 finished! INFO @ Tue, 10 Dec 2019 13:45:43: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:45:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:45:48: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:45:48: #2 number of paired peaks: 83132 INFO @ Tue, 10 Dec 2019 13:45:48: start model_add_line... INFO @ Tue, 10 Dec 2019 13:45:49: start X-correlation... INFO @ Tue, 10 Dec 2019 13:45:49: end of X-cor INFO @ Tue, 10 Dec 2019 13:45:49: #2 finished! INFO @ Tue, 10 Dec 2019 13:45:49: #2 predicted fragment length is 179 bps INFO @ Tue, 10 Dec 2019 13:45:49: #2 alternative fragment length(s) may be 179 bps INFO @ Tue, 10 Dec 2019 13:45:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460573/SRX5460573.20_model.r INFO @ Tue, 10 Dec 2019 13:45:49: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:45:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:45:52: 18000000 INFO @ Tue, 10 Dec 2019 13:45:55: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 13:45:55: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 13:45:55: #1 total tags in treatment: 18282357 INFO @ Tue, 10 Dec 2019 13:45:55: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:45:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:45:56: #1 tags after filtering in treatment: 18282159 INFO @ Tue, 10 Dec 2019 13:45:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:45:56: #1 finished! INFO @ Tue, 10 Dec 2019 13:45:56: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:45:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:46:01: #2 number of paired peaks: 83132 INFO @ Tue, 10 Dec 2019 13:46:01: start model_add_line... INFO @ Tue, 10 Dec 2019 13:46:01: start X-correlation... INFO @ Tue, 10 Dec 2019 13:46:01: end of X-cor INFO @ Tue, 10 Dec 2019 13:46:01: #2 finished! INFO @ Tue, 10 Dec 2019 13:46:01: #2 predicted fragment length is 179 bps INFO @ Tue, 10 Dec 2019 13:46:01: #2 alternative fragment length(s) may be 179 bps INFO @ Tue, 10 Dec 2019 13:46:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460573/SRX5460573.10_model.r INFO @ Tue, 10 Dec 2019 13:46:02: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:46:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:46:20: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460573/SRX5460573.05_peaks.xls INFO @ Tue, 10 Dec 2019 13:46:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460573/SRX5460573.05_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:46:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460573/SRX5460573.05_summits.bed INFO @ Tue, 10 Dec 2019 13:46:22: Done! pass1 - making usageList (127 chroms): 21 millis pass2 - checking and writing primary data (75547 records, 4 fields): 101 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:46:48: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:47:09: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:47:20: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460573/SRX5460573.20_peaks.xls INFO @ Tue, 10 Dec 2019 13:47:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460573/SRX5460573.20_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:47:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460573/SRX5460573.20_summits.bed INFO @ Tue, 10 Dec 2019 13:47:20: Done! pass1 - making usageList (56 chroms): 9 millis pass2 - checking and writing primary data (20812 records, 4 fields): 38 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:47:43: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460573/SRX5460573.10_peaks.xls INFO @ Tue, 10 Dec 2019 13:47:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460573/SRX5460573.10_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:47:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460573/SRX5460573.10_summits.bed INFO @ Tue, 10 Dec 2019 13:47:44: Done! pass1 - making usageList (88 chroms): 14 millis pass2 - checking and writing primary data (44108 records, 4 fields): 61 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。