Job ID = 1294760 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T00:55:21 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 ) 2019-06-03T00:55:21 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 ) 2019-06-03T00:55:21 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 ) 2019-06-03T00:56:51 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 ) 2019-06-03T01:00:55 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 13,658,367 reads read : 13,658,367 reads written : 13,658,367 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: 00:04:02 13658367 reads; of these: 13658367 (100.00%) were unpaired; of these: 584244 (4.28%) aligned 0 times 11143258 (81.59%) aligned exactly 1 time 1930865 (14.14%) aligned >1 times 95.72% overall alignment rate Time searching: 00:04:02 Overall time: 00:04:02 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 8 files... [bam_rmdupse_core] 1510844 / 13074123 = 0.1156 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 10:09:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287863/SRX287863.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287863/SRX287863.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287863/SRX287863.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287863/SRX287863.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 10:09:42: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:09:42: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:09:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287863/SRX287863.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287863/SRX287863.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287863/SRX287863.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287863/SRX287863.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 10:09:42: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:09:42: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:09:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287863/SRX287863.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287863/SRX287863.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287863/SRX287863.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287863/SRX287863.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 10:09:42: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:09:42: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:09:50: 1000000 INFO @ Mon, 03 Jun 2019 10:09:51: 1000000 INFO @ Mon, 03 Jun 2019 10:09:52: 1000000 INFO @ Mon, 03 Jun 2019 10:09:59: 2000000 INFO @ Mon, 03 Jun 2019 10:09:59: 2000000 INFO @ Mon, 03 Jun 2019 10:10:01: 2000000 INFO @ Mon, 03 Jun 2019 10:10:07: 3000000 INFO @ Mon, 03 Jun 2019 10:10:08: 3000000 INFO @ Mon, 03 Jun 2019 10:10:11: 3000000 INFO @ Mon, 03 Jun 2019 10:10:15: 4000000 INFO @ Mon, 03 Jun 2019 10:10:16: 4000000 INFO @ Mon, 03 Jun 2019 10:10:20: 4000000 INFO @ Mon, 03 Jun 2019 10:10:24: 5000000 INFO @ Mon, 03 Jun 2019 10:10:24: 5000000 INFO @ Mon, 03 Jun 2019 10:10:30: 5000000 INFO @ Mon, 03 Jun 2019 10:10:32: 6000000 INFO @ Mon, 03 Jun 2019 10:10:33: 6000000 INFO @ Mon, 03 Jun 2019 10:10:39: 6000000 INFO @ Mon, 03 Jun 2019 10:10:40: 7000000 INFO @ Mon, 03 Jun 2019 10:10:41: 7000000 INFO @ Mon, 03 Jun 2019 10:10:48: 8000000 INFO @ Mon, 03 Jun 2019 10:10:49: 7000000 INFO @ Mon, 03 Jun 2019 10:10:50: 8000000 INFO @ Mon, 03 Jun 2019 10:10:56: 9000000 INFO @ Mon, 03 Jun 2019 10:10:58: 9000000 INFO @ Mon, 03 Jun 2019 10:10:58: 8000000 INFO @ Mon, 03 Jun 2019 10:11:04: 10000000 INFO @ Mon, 03 Jun 2019 10:11:06: 10000000 INFO @ Mon, 03 Jun 2019 10:11:07: 9000000 INFO @ Mon, 03 Jun 2019 10:11:12: 11000000 INFO @ Mon, 03 Jun 2019 10:11:14: 11000000 INFO @ Mon, 03 Jun 2019 10:11:16: 10000000 INFO @ Mon, 03 Jun 2019 10:11:17: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:11:17: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:11:17: #1 total tags in treatment: 11563279 INFO @ Mon, 03 Jun 2019 10:11:17: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:11:17: #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 10:11:17: #1 tags after filtering in treatment: 11563279 INFO @ Mon, 03 Jun 2019 10:11:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:11:17: #1 finished! INFO @ Mon, 03 Jun 2019 10:11:17: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:11:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:11:19: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:11:19: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:11:19: #1 total tags in treatment: 11563279 INFO @ Mon, 03 Jun 2019 10:11:19: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:11:19: #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 10:11:19: #2 number of paired peaks: 3623 INFO @ Mon, 03 Jun 2019 10:11:19: start model_add_line... INFO @ Mon, 03 Jun 2019 10:11:19: #1 tags after filtering in treatment: 11563279 INFO @ Mon, 03 Jun 2019 10:11:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:11:19: #1 finished! INFO @ Mon, 03 Jun 2019 10:11:19: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:11:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:11:19: start X-correlation... INFO @ Mon, 03 Jun 2019 10:11:19: end of X-cor INFO @ Mon, 03 Jun 2019 10:11:19: #2 finished! INFO @ Mon, 03 Jun 2019 10:11:19: #2 predicted fragment length is 218 bps INFO @ Mon, 03 Jun 2019 10:11:19: #2 alternative fragment length(s) may be 2,200,218 bps INFO @ Mon, 03 Jun 2019 10:11:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287863/SRX287863.10_model.r INFO @ Mon, 03 Jun 2019 10:11:19: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:11:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:11:20: #2 number of paired peaks: 3623 INFO @ Mon, 03 Jun 2019 10:11:20: start model_add_line... INFO @ Mon, 03 Jun 2019 10:11:20: start X-correlation... INFO @ Mon, 03 Jun 2019 10:11:20: end of X-cor INFO @ Mon, 03 Jun 2019 10:11:20: #2 finished! INFO @ Mon, 03 Jun 2019 10:11:20: #2 predicted fragment length is 218 bps INFO @ Mon, 03 Jun 2019 10:11:20: #2 alternative fragment length(s) may be 2,200,218 bps INFO @ Mon, 03 Jun 2019 10:11:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287863/SRX287863.05_model.r INFO @ Mon, 03 Jun 2019 10:11:20: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:11:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:11:25: 11000000 INFO @ Mon, 03 Jun 2019 10:11:31: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:11:31: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:11:31: #1 total tags in treatment: 11563279 INFO @ Mon, 03 Jun 2019 10:11:31: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:11:31: #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 10:11:31: #1 tags after filtering in treatment: 11563279 INFO @ Mon, 03 Jun 2019 10:11:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:11:31: #1 finished! INFO @ Mon, 03 Jun 2019 10:11:31: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:11:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:11:32: #2 number of paired peaks: 3623 INFO @ Mon, 03 Jun 2019 10:11:32: start model_add_line... INFO @ Mon, 03 Jun 2019 10:11:32: start X-correlation... INFO @ Mon, 03 Jun 2019 10:11:32: end of X-cor INFO @ Mon, 03 Jun 2019 10:11:32: #2 finished! INFO @ Mon, 03 Jun 2019 10:11:32: #2 predicted fragment length is 218 bps INFO @ Mon, 03 Jun 2019 10:11:32: #2 alternative fragment length(s) may be 2,200,218 bps INFO @ Mon, 03 Jun 2019 10:11:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287863/SRX287863.20_model.r INFO @ Mon, 03 Jun 2019 10:11:32: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:11:32: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:11:57: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:11:57: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:12:09: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:12:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287863/SRX287863.10_peaks.xls INFO @ Mon, 03 Jun 2019 10:12:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287863/SRX287863.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:12:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287863/SRX287863.10_summits.bed INFO @ Mon, 03 Jun 2019 10:12:14: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2948 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:12:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287863/SRX287863.05_peaks.xls INFO @ Mon, 03 Jun 2019 10:12:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287863/SRX287863.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:12:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287863/SRX287863.05_summits.bed INFO @ Mon, 03 Jun 2019 10:12:14: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (5520 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:12:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287863/SRX287863.20_peaks.xls INFO @ Mon, 03 Jun 2019 10:12:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287863/SRX287863.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:12:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287863/SRX287863.20_summits.bed INFO @ Mon, 03 Jun 2019 10:12:26: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1063 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。