Job ID = 1295056 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T02:27:10 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 ) 2019-06-03T02:27:10 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 : 7,760,856 reads read : 7,760,856 reads written : 7,760,856 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: 00:03:10 7760856 reads; of these: 7760856 (100.00%) were unpaired; of these: 806761 (10.40%) aligned 0 times 4955442 (63.85%) aligned exactly 1 time 1998653 (25.75%) aligned >1 times 89.60% overall alignment rate Time searching: 00:03:10 Overall time: 00:03:10 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] 1954278 / 6954095 = 0.2810 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 11:35:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3167250/SRX3167250.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3167250/SRX3167250.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3167250/SRX3167250.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3167250/SRX3167250.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 11:35:07: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:35:07: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:35:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3167250/SRX3167250.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3167250/SRX3167250.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3167250/SRX3167250.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3167250/SRX3167250.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 11:35:07: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:35:07: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:35:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3167250/SRX3167250.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3167250/SRX3167250.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3167250/SRX3167250.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3167250/SRX3167250.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 11:35:07: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:35:07: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:35:17: 1000000 INFO @ Mon, 03 Jun 2019 11:35:17: 1000000 INFO @ Mon, 03 Jun 2019 11:35:19: 1000000 INFO @ Mon, 03 Jun 2019 11:35:27: 2000000 INFO @ Mon, 03 Jun 2019 11:35:28: 2000000 INFO @ Mon, 03 Jun 2019 11:35:31: 2000000 INFO @ Mon, 03 Jun 2019 11:35:37: 3000000 INFO @ Mon, 03 Jun 2019 11:35:38: 3000000 INFO @ Mon, 03 Jun 2019 11:35:43: 3000000 INFO @ Mon, 03 Jun 2019 11:35:46: 4000000 INFO @ Mon, 03 Jun 2019 11:35:48: 4000000 INFO @ Mon, 03 Jun 2019 11:35:55: 4000000 INFO @ Mon, 03 Jun 2019 11:35:56: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 11:35:56: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 11:35:56: #1 total tags in treatment: 4999817 INFO @ Mon, 03 Jun 2019 11:35:56: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:35:56: #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 11:35:56: #1 tags after filtering in treatment: 4999817 INFO @ Mon, 03 Jun 2019 11:35:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:35:56: #1 finished! INFO @ Mon, 03 Jun 2019 11:35:56: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:35:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:35:56: #2 number of paired peaks: 2727 INFO @ Mon, 03 Jun 2019 11:35:56: start model_add_line... INFO @ Mon, 03 Jun 2019 11:35:56: start X-correlation... INFO @ Mon, 03 Jun 2019 11:35:56: end of X-cor INFO @ Mon, 03 Jun 2019 11:35:56: #2 finished! INFO @ Mon, 03 Jun 2019 11:35:56: #2 predicted fragment length is 303 bps INFO @ Mon, 03 Jun 2019 11:35:56: #2 alternative fragment length(s) may be 303 bps INFO @ Mon, 03 Jun 2019 11:35:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3167250/SRX3167250.05_model.r INFO @ Mon, 03 Jun 2019 11:35:56: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:35:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:35:58: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 11:35:58: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 11:35:58: #1 total tags in treatment: 4999817 INFO @ Mon, 03 Jun 2019 11:35:58: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:35:58: #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 11:35:58: #1 tags after filtering in treatment: 4999817 INFO @ Mon, 03 Jun 2019 11:35:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:35:58: #1 finished! INFO @ Mon, 03 Jun 2019 11:35:58: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:35:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:35:58: #2 number of paired peaks: 2727 INFO @ Mon, 03 Jun 2019 11:35:58: start model_add_line... INFO @ Mon, 03 Jun 2019 11:35:59: start X-correlation... INFO @ Mon, 03 Jun 2019 11:35:59: end of X-cor INFO @ Mon, 03 Jun 2019 11:35:59: #2 finished! INFO @ Mon, 03 Jun 2019 11:35:59: #2 predicted fragment length is 303 bps INFO @ Mon, 03 Jun 2019 11:35:59: #2 alternative fragment length(s) may be 303 bps INFO @ Mon, 03 Jun 2019 11:35:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3167250/SRX3167250.10_model.r INFO @ Mon, 03 Jun 2019 11:35:59: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:35:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:36:06: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 11:36:06: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 11:36:06: #1 total tags in treatment: 4999817 INFO @ Mon, 03 Jun 2019 11:36:06: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:36:06: #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 11:36:06: #1 tags after filtering in treatment: 4999817 INFO @ Mon, 03 Jun 2019 11:36:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:36:06: #1 finished! INFO @ Mon, 03 Jun 2019 11:36:06: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:36:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:36:07: #2 number of paired peaks: 2727 INFO @ Mon, 03 Jun 2019 11:36:07: start model_add_line... INFO @ Mon, 03 Jun 2019 11:36:07: start X-correlation... INFO @ Mon, 03 Jun 2019 11:36:07: end of X-cor INFO @ Mon, 03 Jun 2019 11:36:07: #2 finished! INFO @ Mon, 03 Jun 2019 11:36:07: #2 predicted fragment length is 303 bps INFO @ Mon, 03 Jun 2019 11:36:07: #2 alternative fragment length(s) may be 303 bps INFO @ Mon, 03 Jun 2019 11:36:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3167250/SRX3167250.20_model.r INFO @ Mon, 03 Jun 2019 11:36:07: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:36:07: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:36:15: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:36:18: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:36:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3167250/SRX3167250.05_peaks.xls INFO @ Mon, 03 Jun 2019 11:36:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3167250/SRX3167250.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:36:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3167250/SRX3167250.05_summits.bed INFO @ Mon, 03 Jun 2019 11:36:24: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3743 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:36:26: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:36:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3167250/SRX3167250.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:36:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3167250/SRX3167250.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:36:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3167250/SRX3167250.10_summits.bed INFO @ Mon, 03 Jun 2019 11:36:26: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2700 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:36:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3167250/SRX3167250.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:36:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3167250/SRX3167250.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:36:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3167250/SRX3167250.20_summits.bed INFO @ Mon, 03 Jun 2019 11:36:35: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1863 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。