Job ID = 1294374 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T22:00:43 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 ) 2019-06-02T22:00:43 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 : 10,008,743 reads read : 10,008,743 reads written : 10,008,743 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 10008743 reads; of these: 10008743 (100.00%) were unpaired; of these: 545180 (5.45%) aligned 0 times 6953047 (69.47%) aligned exactly 1 time 2510516 (25.08%) aligned >1 times 94.55% 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_rmdupse_core] 3922954 / 9463563 = 0.4145 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 07:08:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX273674/SRX273674.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX273674/SRX273674.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX273674/SRX273674.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX273674/SRX273674.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 07:08:42: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:08:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX273674/SRX273674.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX273674/SRX273674.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX273674/SRX273674.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX273674/SRX273674.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 07:08:42: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:08:42: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:08:42: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:08:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX273674/SRX273674.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX273674/SRX273674.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX273674/SRX273674.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX273674/SRX273674.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 07:08:42: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:08:42: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:08:51: 1000000 INFO @ Mon, 03 Jun 2019 07:08:54: 1000000 INFO @ Mon, 03 Jun 2019 07:08:54: 1000000 INFO @ Mon, 03 Jun 2019 07:09:01: 2000000 INFO @ Mon, 03 Jun 2019 07:09:05: 2000000 INFO @ Mon, 03 Jun 2019 07:09:06: 2000000 INFO @ Mon, 03 Jun 2019 07:09:10: 3000000 INFO @ Mon, 03 Jun 2019 07:09:16: 3000000 INFO @ Mon, 03 Jun 2019 07:09:17: 3000000 INFO @ Mon, 03 Jun 2019 07:09:19: 4000000 INFO @ Mon, 03 Jun 2019 07:09:27: 4000000 INFO @ Mon, 03 Jun 2019 07:09:28: 4000000 INFO @ Mon, 03 Jun 2019 07:09:28: 5000000 INFO @ Mon, 03 Jun 2019 07:09:33: #1 tag size is determined as 71 bps INFO @ Mon, 03 Jun 2019 07:09:33: #1 tag size = 71 INFO @ Mon, 03 Jun 2019 07:09:33: #1 total tags in treatment: 5540609 INFO @ Mon, 03 Jun 2019 07:09:33: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:09:33: #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 07:09:33: #1 tags after filtering in treatment: 5540609 INFO @ Mon, 03 Jun 2019 07:09:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 07:09:33: #1 finished! INFO @ Mon, 03 Jun 2019 07:09:33: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:09:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:09:34: #2 number of paired peaks: 4304 INFO @ Mon, 03 Jun 2019 07:09:34: start model_add_line... INFO @ Mon, 03 Jun 2019 07:09:34: start X-correlation... INFO @ Mon, 03 Jun 2019 07:09:34: end of X-cor INFO @ Mon, 03 Jun 2019 07:09:34: #2 finished! INFO @ Mon, 03 Jun 2019 07:09:34: #2 predicted fragment length is 229 bps INFO @ Mon, 03 Jun 2019 07:09:34: #2 alternative fragment length(s) may be 229 bps INFO @ Mon, 03 Jun 2019 07:09:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX273674/SRX273674.05_model.r INFO @ Mon, 03 Jun 2019 07:09:34: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:09:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:09:39: 5000000 INFO @ Mon, 03 Jun 2019 07:09:39: 5000000 INFO @ Mon, 03 Jun 2019 07:09:44: #1 tag size is determined as 71 bps INFO @ Mon, 03 Jun 2019 07:09:44: #1 tag size = 71 INFO @ Mon, 03 Jun 2019 07:09:44: #1 total tags in treatment: 5540609 INFO @ Mon, 03 Jun 2019 07:09:44: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:09:44: #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 07:09:45: #1 tags after filtering in treatment: 5540609 INFO @ Mon, 03 Jun 2019 07:09:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 07:09:45: #1 finished! INFO @ Mon, 03 Jun 2019 07:09:45: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:09:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:09:45: #1 tag size is determined as 71 bps INFO @ Mon, 03 Jun 2019 07:09:45: #1 tag size = 71 INFO @ Mon, 03 Jun 2019 07:09:45: #1 total tags in treatment: 5540609 INFO @ Mon, 03 Jun 2019 07:09:45: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:09:45: #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 07:09:45: #1 tags after filtering in treatment: 5540609 INFO @ Mon, 03 Jun 2019 07:09:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 07:09:45: #1 finished! INFO @ Mon, 03 Jun 2019 07:09:45: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:09:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:09:45: #2 number of paired peaks: 4304 INFO @ Mon, 03 Jun 2019 07:09:45: start model_add_line... INFO @ Mon, 03 Jun 2019 07:09:46: start X-correlation... INFO @ Mon, 03 Jun 2019 07:09:46: end of X-cor INFO @ Mon, 03 Jun 2019 07:09:46: #2 finished! INFO @ Mon, 03 Jun 2019 07:09:46: #2 predicted fragment length is 229 bps INFO @ Mon, 03 Jun 2019 07:09:46: #2 alternative fragment length(s) may be 229 bps INFO @ Mon, 03 Jun 2019 07:09:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX273674/SRX273674.10_model.r INFO @ Mon, 03 Jun 2019 07:09:46: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:09:46: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:09:46: #2 number of paired peaks: 4304 INFO @ Mon, 03 Jun 2019 07:09:46: start model_add_line... INFO @ Mon, 03 Jun 2019 07:09:46: start X-correlation... INFO @ Mon, 03 Jun 2019 07:09:46: end of X-cor INFO @ Mon, 03 Jun 2019 07:09:46: #2 finished! INFO @ Mon, 03 Jun 2019 07:09:46: #2 predicted fragment length is 229 bps INFO @ Mon, 03 Jun 2019 07:09:46: #2 alternative fragment length(s) may be 229 bps INFO @ Mon, 03 Jun 2019 07:09:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX273674/SRX273674.20_model.r INFO @ Mon, 03 Jun 2019 07:09:46: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:09:46: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:09:55: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:10:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX273674/SRX273674.05_peaks.xls INFO @ Mon, 03 Jun 2019 07:10:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX273674/SRX273674.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:10:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX273674/SRX273674.05_summits.bed INFO @ Mon, 03 Jun 2019 07:10:04: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7557 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 07:10:06: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:10:07: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:10:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX273674/SRX273674.10_peaks.xls INFO @ Mon, 03 Jun 2019 07:10:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX273674/SRX273674.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:10:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX273674/SRX273674.10_summits.bed INFO @ Mon, 03 Jun 2019 07:10:15: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (5814 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 07:10:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX273674/SRX273674.20_peaks.xls INFO @ Mon, 03 Jun 2019 07:10:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX273674/SRX273674.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:10:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX273674/SRX273674.20_summits.bed INFO @ Mon, 03 Jun 2019 07:10:17: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (4248 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。