Job ID = 1294178 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T20:18:27 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 : 15,982,455 reads read : 15,982,455 reads written : 15,982,455 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: 00:02:34 15982455 reads; of these: 15982455 (100.00%) were unpaired; of these: 7255018 (45.39%) aligned 0 times 8275785 (51.78%) aligned exactly 1 time 451652 (2.83%) aligned >1 times 54.61% overall alignment rate Time searching: 00:02:34 Overall time: 00:02:34 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] 5473396 / 8727437 = 0.6271 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 05:23:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX197566/SRX197566.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX197566/SRX197566.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX197566/SRX197566.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX197566/SRX197566.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 05:23:18: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:23:18: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:23:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX197566/SRX197566.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX197566/SRX197566.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX197566/SRX197566.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX197566/SRX197566.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 05:23:18: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:23:18: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:23:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX197566/SRX197566.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX197566/SRX197566.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX197566/SRX197566.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX197566/SRX197566.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 05:23:18: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:23:18: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:23:27: 1000000 INFO @ Mon, 03 Jun 2019 05:23:27: 1000000 INFO @ Mon, 03 Jun 2019 05:23:29: 1000000 INFO @ Mon, 03 Jun 2019 05:23:36: 2000000 INFO @ Mon, 03 Jun 2019 05:23:36: 2000000 INFO @ Mon, 03 Jun 2019 05:23:40: 2000000 INFO @ Mon, 03 Jun 2019 05:23:45: 3000000 INFO @ Mon, 03 Jun 2019 05:23:45: 3000000 INFO @ Mon, 03 Jun 2019 05:23:47: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 05:23:47: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 05:23:47: #1 total tags in treatment: 3254041 INFO @ Mon, 03 Jun 2019 05:23:47: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:23:47: #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 05:23:47: #1 tags after filtering in treatment: 3254041 INFO @ Mon, 03 Jun 2019 05:23:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:23:47: #1 finished! INFO @ Mon, 03 Jun 2019 05:23:47: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:23:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:23:47: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 05:23:47: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 05:23:47: #1 total tags in treatment: 3254041 INFO @ Mon, 03 Jun 2019 05:23:47: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:23:47: #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 05:23:47: #1 tags after filtering in treatment: 3254041 INFO @ Mon, 03 Jun 2019 05:23:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:23:47: #1 finished! INFO @ Mon, 03 Jun 2019 05:23:47: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:23:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:23:48: #2 number of paired peaks: 6839 INFO @ Mon, 03 Jun 2019 05:23:48: start model_add_line... INFO @ Mon, 03 Jun 2019 05:23:48: start X-correlation... INFO @ Mon, 03 Jun 2019 05:23:48: end of X-cor INFO @ Mon, 03 Jun 2019 05:23:48: #2 finished! INFO @ Mon, 03 Jun 2019 05:23:48: #2 predicted fragment length is 124 bps INFO @ Mon, 03 Jun 2019 05:23:48: #2 alternative fragment length(s) may be 124 bps INFO @ Mon, 03 Jun 2019 05:23:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX197566/SRX197566.10_model.r INFO @ Mon, 03 Jun 2019 05:23:48: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:23:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:23:48: #2 number of paired peaks: 6839 INFO @ Mon, 03 Jun 2019 05:23:48: start model_add_line... INFO @ Mon, 03 Jun 2019 05:23:48: start X-correlation... INFO @ Mon, 03 Jun 2019 05:23:48: end of X-cor INFO @ Mon, 03 Jun 2019 05:23:48: #2 finished! INFO @ Mon, 03 Jun 2019 05:23:48: #2 predicted fragment length is 124 bps INFO @ Mon, 03 Jun 2019 05:23:48: #2 alternative fragment length(s) may be 124 bps INFO @ Mon, 03 Jun 2019 05:23:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX197566/SRX197566.05_model.r INFO @ Mon, 03 Jun 2019 05:23:48: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:23:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:23:50: 3000000 INFO @ Mon, 03 Jun 2019 05:23:52: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 05:23:52: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 05:23:52: #1 total tags in treatment: 3254041 INFO @ Mon, 03 Jun 2019 05:23:52: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:23:52: #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 05:23:52: #1 tags after filtering in treatment: 3254041 INFO @ Mon, 03 Jun 2019 05:23:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:23:52: #1 finished! INFO @ Mon, 03 Jun 2019 05:23:52: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:23:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:23:53: #2 number of paired peaks: 6839 INFO @ Mon, 03 Jun 2019 05:23:53: start model_add_line... INFO @ Mon, 03 Jun 2019 05:23:53: start X-correlation... INFO @ Mon, 03 Jun 2019 05:23:53: end of X-cor INFO @ Mon, 03 Jun 2019 05:23:53: #2 finished! INFO @ Mon, 03 Jun 2019 05:23:53: #2 predicted fragment length is 124 bps INFO @ Mon, 03 Jun 2019 05:23:53: #2 alternative fragment length(s) may be 124 bps INFO @ Mon, 03 Jun 2019 05:23:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX197566/SRX197566.20_model.r INFO @ Mon, 03 Jun 2019 05:23:53: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:23:53: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 05:23:59: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:24:00: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Mon, 03 Jun 2019 05:24:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX197566/SRX197566.10_peaks.xls INFO @ Mon, 03 Jun 2019 05:24:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX197566/SRX197566.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:24:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX197566/SRX197566.10_summits.bed INFO @ Mon, 03 Jun 2019 05:24:04: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (5267 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:24:05: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:24:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX197566/SRX197566.05_peaks.xls INFO @ Mon, 03 Jun 2019 05:24:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX197566/SRX197566.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:24:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX197566/SRX197566.05_summits.bed INFO @ Mon, 03 Jun 2019 05:24:05: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (6067 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:24:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX197566/SRX197566.20_peaks.xls INFO @ Mon, 03 Jun 2019 05:24:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX197566/SRX197566.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:24:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX197566/SRX197566.20_summits.bed INFO @ Mon, 03 Jun 2019 05:24:10: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4469 records, 4 fields): 8 millis CompletedMACS2peakCalling