Job ID = 1293635 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T16:09:33 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 ) 2019-06-02T16:09:33 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 ) 2019-06-02T16:15:33 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 ) 2019-06-02T16:15:33 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 : 32,069,449 reads read : 32,069,449 reads written : 32,069,449 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:11:59 32069449 reads; of these: 32069449 (100.00%) were unpaired; of these: 1104817 (3.45%) aligned 0 times 24062900 (75.03%) aligned exactly 1 time 6901732 (21.52%) aligned >1 times 96.55% overall alignment rate Time searching: 00:11:59 Overall time: 00:11:59 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 8555405 / 30964632 = 0.2763 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 @ Mon, 03 Jun 2019 01:40:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1032410/SRX1032410.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1032410/SRX1032410.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1032410/SRX1032410.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1032410/SRX1032410.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 01:40:52: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:40:52: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:40:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1032410/SRX1032410.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1032410/SRX1032410.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1032410/SRX1032410.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1032410/SRX1032410.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 01:40:52: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:40:52: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:40:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1032410/SRX1032410.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1032410/SRX1032410.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1032410/SRX1032410.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1032410/SRX1032410.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 01:40:52: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:40:52: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:41:00: 1000000 INFO @ Mon, 03 Jun 2019 01:41:00: 1000000 INFO @ Mon, 03 Jun 2019 01:41:01: 1000000 INFO @ Mon, 03 Jun 2019 01:41:07: 2000000 INFO @ Mon, 03 Jun 2019 01:41:08: 2000000 INFO @ Mon, 03 Jun 2019 01:41:09: 2000000 INFO @ Mon, 03 Jun 2019 01:41:15: 3000000 INFO @ Mon, 03 Jun 2019 01:41:15: 3000000 INFO @ Mon, 03 Jun 2019 01:41:17: 3000000 INFO @ Mon, 03 Jun 2019 01:41:22: 4000000 INFO @ Mon, 03 Jun 2019 01:41:22: 4000000 INFO @ Mon, 03 Jun 2019 01:41:25: 4000000 INFO @ Mon, 03 Jun 2019 01:41:29: 5000000 INFO @ Mon, 03 Jun 2019 01:41:29: 5000000 INFO @ Mon, 03 Jun 2019 01:41:33: 5000000 INFO @ Mon, 03 Jun 2019 01:41:36: 6000000 INFO @ Mon, 03 Jun 2019 01:41:36: 6000000 INFO @ Mon, 03 Jun 2019 01:41:40: 6000000 INFO @ Mon, 03 Jun 2019 01:41:43: 7000000 INFO @ Mon, 03 Jun 2019 01:41:44: 7000000 INFO @ Mon, 03 Jun 2019 01:41:48: 7000000 INFO @ Mon, 03 Jun 2019 01:41:50: 8000000 INFO @ Mon, 03 Jun 2019 01:41:51: 8000000 INFO @ Mon, 03 Jun 2019 01:41:56: 8000000 INFO @ Mon, 03 Jun 2019 01:41:57: 9000000 INFO @ Mon, 03 Jun 2019 01:41:58: 9000000 INFO @ Mon, 03 Jun 2019 01:42:04: 10000000 INFO @ Mon, 03 Jun 2019 01:42:04: 9000000 INFO @ Mon, 03 Jun 2019 01:42:05: 10000000 INFO @ Mon, 03 Jun 2019 01:42:11: 11000000 INFO @ Mon, 03 Jun 2019 01:42:12: 10000000 INFO @ Mon, 03 Jun 2019 01:42:12: 11000000 INFO @ Mon, 03 Jun 2019 01:42:17: 12000000 INFO @ Mon, 03 Jun 2019 01:42:19: 12000000 INFO @ Mon, 03 Jun 2019 01:42:19: 11000000 INFO @ Mon, 03 Jun 2019 01:42:24: 13000000 INFO @ Mon, 03 Jun 2019 01:42:26: 13000000 INFO @ Mon, 03 Jun 2019 01:42:27: 12000000 INFO @ Mon, 03 Jun 2019 01:42:31: 14000000 INFO @ Mon, 03 Jun 2019 01:42:32: 14000000 INFO @ Mon, 03 Jun 2019 01:42:35: 13000000 INFO @ Mon, 03 Jun 2019 01:42:38: 15000000 INFO @ Mon, 03 Jun 2019 01:42:40: 15000000 INFO @ Mon, 03 Jun 2019 01:42:42: 14000000 INFO @ Mon, 03 Jun 2019 01:42:45: 16000000 INFO @ Mon, 03 Jun 2019 01:42:47: 16000000 INFO @ Mon, 03 Jun 2019 01:42:50: 15000000 INFO @ Mon, 03 Jun 2019 01:42:52: 17000000 INFO @ Mon, 03 Jun 2019 01:42:54: 17000000 INFO @ Mon, 03 Jun 2019 01:42:58: 16000000 INFO @ Mon, 03 Jun 2019 01:42:59: 18000000 INFO @ Mon, 03 Jun 2019 01:43:01: 18000000 INFO @ Mon, 03 Jun 2019 01:43:05: 17000000 INFO @ Mon, 03 Jun 2019 01:43:06: 19000000 INFO @ Mon, 03 Jun 2019 01:43:08: 19000000 INFO @ Mon, 03 Jun 2019 01:43:13: 20000000 INFO @ Mon, 03 Jun 2019 01:43:13: 18000000 INFO @ Mon, 03 Jun 2019 01:43:15: 20000000 INFO @ Mon, 03 Jun 2019 01:43:20: 21000000 INFO @ Mon, 03 Jun 2019 01:43:21: 19000000 INFO @ Mon, 03 Jun 2019 01:43:22: 21000000 INFO @ Mon, 03 Jun 2019 01:43:27: 22000000 INFO @ Mon, 03 Jun 2019 01:43:29: 20000000 INFO @ Mon, 03 Jun 2019 01:43:29: 22000000 INFO @ Mon, 03 Jun 2019 01:43:30: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 01:43:30: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 01:43:30: #1 total tags in treatment: 22409227 INFO @ Mon, 03 Jun 2019 01:43:30: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:43:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 01:43:30: #1 tags after filtering in treatment: 22409227 INFO @ Mon, 03 Jun 2019 01:43:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:43:30: #1 finished! INFO @ Mon, 03 Jun 2019 01:43:30: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:43:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:43:32: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 01:43:32: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 01:43:32: #1 total tags in treatment: 22409227 INFO @ Mon, 03 Jun 2019 01:43:32: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:43:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 01:43:32: #1 tags after filtering in treatment: 22409227 INFO @ Mon, 03 Jun 2019 01:43:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:43:32: #1 finished! INFO @ Mon, 03 Jun 2019 01:43:32: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:43:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:43:33: #2 number of paired peaks: 4397 INFO @ Mon, 03 Jun 2019 01:43:33: start model_add_line... INFO @ Mon, 03 Jun 2019 01:43:33: start X-correlation... INFO @ Mon, 03 Jun 2019 01:43:33: end of X-cor INFO @ Mon, 03 Jun 2019 01:43:33: #2 finished! INFO @ Mon, 03 Jun 2019 01:43:33: #2 predicted fragment length is 138 bps INFO @ Mon, 03 Jun 2019 01:43:33: #2 alternative fragment length(s) may be 4,138 bps INFO @ Mon, 03 Jun 2019 01:43:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1032410/SRX1032410.10_model.r INFO @ Mon, 03 Jun 2019 01:43:33: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:43:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:43:35: #2 number of paired peaks: 4397 INFO @ Mon, 03 Jun 2019 01:43:35: start model_add_line... INFO @ Mon, 03 Jun 2019 01:43:35: start X-correlation... INFO @ Mon, 03 Jun 2019 01:43:35: end of X-cor INFO @ Mon, 03 Jun 2019 01:43:35: #2 finished! INFO @ Mon, 03 Jun 2019 01:43:35: #2 predicted fragment length is 138 bps INFO @ Mon, 03 Jun 2019 01:43:35: #2 alternative fragment length(s) may be 4,138 bps INFO @ Mon, 03 Jun 2019 01:43:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1032410/SRX1032410.20_model.r INFO @ Mon, 03 Jun 2019 01:43:35: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:43:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:43:36: 21000000 INFO @ Mon, 03 Jun 2019 01:43:44: 22000000 INFO @ Mon, 03 Jun 2019 01:43:47: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 01:43:47: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 01:43:47: #1 total tags in treatment: 22409227 INFO @ Mon, 03 Jun 2019 01:43:47: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:43:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 01:43:47: #1 tags after filtering in treatment: 22409227 INFO @ Mon, 03 Jun 2019 01:43:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:43:47: #1 finished! INFO @ Mon, 03 Jun 2019 01:43:47: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:43:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:43:50: #2 number of paired peaks: 4397 INFO @ Mon, 03 Jun 2019 01:43:50: start model_add_line... INFO @ Mon, 03 Jun 2019 01:43:50: start X-correlation... INFO @ Mon, 03 Jun 2019 01:43:50: end of X-cor INFO @ Mon, 03 Jun 2019 01:43:50: #2 finished! INFO @ Mon, 03 Jun 2019 01:43:50: #2 predicted fragment length is 138 bps INFO @ Mon, 03 Jun 2019 01:43:50: #2 alternative fragment length(s) may be 4,138 bps INFO @ Mon, 03 Jun 2019 01:43:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1032410/SRX1032410.05_model.r INFO @ Mon, 03 Jun 2019 01:43:50: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:43:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:44:41: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:44:43: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:44:58: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:45:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1032410/SRX1032410.10_peaks.xls INFO @ Mon, 03 Jun 2019 01:45:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1032410/SRX1032410.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:45:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1032410/SRX1032410.10_summits.bed INFO @ Mon, 03 Jun 2019 01:45:06: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (2301 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:45:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1032410/SRX1032410.20_peaks.xls INFO @ Mon, 03 Jun 2019 01:45:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1032410/SRX1032410.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:45:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1032410/SRX1032410.20_summits.bed INFO @ Mon, 03 Jun 2019 01:45:09: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (990 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:45:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1032410/SRX1032410.05_peaks.xls INFO @ Mon, 03 Jun 2019 01:45:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1032410/SRX1032410.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:45:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1032410/SRX1032410.05_summits.bed INFO @ Mon, 03 Jun 2019 01:45:23: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5748 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。