Job ID = 1294970 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T01:57:38 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 : 14,103,697 reads read : 14,103,697 reads written : 14,103,697 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: 00:06:02 14103697 reads; of these: 14103697 (100.00%) were unpaired; of these: 977644 (6.93%) aligned 0 times 8973840 (63.63%) aligned exactly 1 time 4152213 (29.44%) aligned >1 times 93.07% overall alignment rate Time searching: 00:06:02 Overall time: 00:06:02 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] 3523244 / 13126053 = 0.2684 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 11:14:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288029/SRX288029.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288029/SRX288029.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288029/SRX288029.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288029/SRX288029.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 11:14:58: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:14:58: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:14:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288029/SRX288029.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288029/SRX288029.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288029/SRX288029.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288029/SRX288029.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 11:14:58: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:14:58: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:14:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288029/SRX288029.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288029/SRX288029.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288029/SRX288029.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288029/SRX288029.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 11:14:58: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:14:58: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:15:05: 1000000 INFO @ Mon, 03 Jun 2019 11:15:07: 1000000 INFO @ Mon, 03 Jun 2019 11:15:07: 1000000 INFO @ Mon, 03 Jun 2019 11:15:12: 2000000 INFO @ Mon, 03 Jun 2019 11:15:15: 2000000 INFO @ Mon, 03 Jun 2019 11:15:16: 2000000 INFO @ Mon, 03 Jun 2019 11:15:19: 3000000 INFO @ Mon, 03 Jun 2019 11:15:24: 3000000 INFO @ Mon, 03 Jun 2019 11:15:25: 3000000 INFO @ Mon, 03 Jun 2019 11:15:26: 4000000 INFO @ Mon, 03 Jun 2019 11:15:32: 4000000 INFO @ Mon, 03 Jun 2019 11:15:33: 5000000 INFO @ Mon, 03 Jun 2019 11:15:33: 4000000 INFO @ Mon, 03 Jun 2019 11:15:40: 6000000 INFO @ Mon, 03 Jun 2019 11:15:40: 5000000 INFO @ Mon, 03 Jun 2019 11:15:42: 5000000 INFO @ Mon, 03 Jun 2019 11:15:46: 7000000 INFO @ Mon, 03 Jun 2019 11:15:48: 6000000 INFO @ Mon, 03 Jun 2019 11:15:51: 6000000 INFO @ Mon, 03 Jun 2019 11:15:53: 8000000 INFO @ Mon, 03 Jun 2019 11:15:57: 7000000 INFO @ Mon, 03 Jun 2019 11:16:00: 7000000 INFO @ Mon, 03 Jun 2019 11:16:00: 9000000 INFO @ Mon, 03 Jun 2019 11:16:04: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:16:04: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:16:04: #1 total tags in treatment: 9602809 INFO @ Mon, 03 Jun 2019 11:16:04: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:16:04: #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 11:16:04: #1 tags after filtering in treatment: 9602809 INFO @ Mon, 03 Jun 2019 11:16:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:16:04: #1 finished! INFO @ Mon, 03 Jun 2019 11:16:04: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:16:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:16:05: 8000000 INFO @ Mon, 03 Jun 2019 11:16:05: #2 number of paired peaks: 1197 INFO @ Mon, 03 Jun 2019 11:16:05: start model_add_line... INFO @ Mon, 03 Jun 2019 11:16:05: start X-correlation... INFO @ Mon, 03 Jun 2019 11:16:05: end of X-cor INFO @ Mon, 03 Jun 2019 11:16:05: #2 finished! INFO @ Mon, 03 Jun 2019 11:16:05: #2 predicted fragment length is 120 bps INFO @ Mon, 03 Jun 2019 11:16:05: #2 alternative fragment length(s) may be 120 bps INFO @ Mon, 03 Jun 2019 11:16:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288029/SRX288029.20_model.r INFO @ Mon, 03 Jun 2019 11:16:05: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:16:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:16:08: 8000000 INFO @ Mon, 03 Jun 2019 11:16:13: 9000000 INFO @ Mon, 03 Jun 2019 11:16:17: 9000000 INFO @ Mon, 03 Jun 2019 11:16:18: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:16:18: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:16:18: #1 total tags in treatment: 9602809 INFO @ Mon, 03 Jun 2019 11:16:18: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:16:18: #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 11:16:19: #1 tags after filtering in treatment: 9602809 INFO @ Mon, 03 Jun 2019 11:16:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:16:19: #1 finished! INFO @ Mon, 03 Jun 2019 11:16:19: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:16:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:16:20: #2 number of paired peaks: 1197 INFO @ Mon, 03 Jun 2019 11:16:20: start model_add_line... INFO @ Mon, 03 Jun 2019 11:16:20: start X-correlation... INFO @ Mon, 03 Jun 2019 11:16:20: end of X-cor INFO @ Mon, 03 Jun 2019 11:16:20: #2 finished! INFO @ Mon, 03 Jun 2019 11:16:20: #2 predicted fragment length is 120 bps INFO @ Mon, 03 Jun 2019 11:16:20: #2 alternative fragment length(s) may be 120 bps INFO @ Mon, 03 Jun 2019 11:16:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288029/SRX288029.05_model.r INFO @ Mon, 03 Jun 2019 11:16:20: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:16:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:16:22: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:16:22: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:16:22: #1 total tags in treatment: 9602809 INFO @ Mon, 03 Jun 2019 11:16:22: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:16:22: #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 11:16:22: #1 tags after filtering in treatment: 9602809 INFO @ Mon, 03 Jun 2019 11:16:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:16:22: #1 finished! INFO @ Mon, 03 Jun 2019 11:16:22: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:16:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:16:23: #2 number of paired peaks: 1197 INFO @ Mon, 03 Jun 2019 11:16:23: start model_add_line... INFO @ Mon, 03 Jun 2019 11:16:23: start X-correlation... INFO @ Mon, 03 Jun 2019 11:16:23: end of X-cor INFO @ Mon, 03 Jun 2019 11:16:23: #2 finished! INFO @ Mon, 03 Jun 2019 11:16:23: #2 predicted fragment length is 120 bps INFO @ Mon, 03 Jun 2019 11:16:23: #2 alternative fragment length(s) may be 120 bps INFO @ Mon, 03 Jun 2019 11:16:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288029/SRX288029.10_model.r INFO @ Mon, 03 Jun 2019 11:16:23: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:16:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:16:34: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:16:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288029/SRX288029.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:16:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288029/SRX288029.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:16:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288029/SRX288029.20_summits.bed INFO @ Mon, 03 Jun 2019 11:16:48: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2760 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:16:49: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:16:52: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:17:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288029/SRX288029.05_peaks.xls INFO @ Mon, 03 Jun 2019 11:17:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288029/SRX288029.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:17:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288029/SRX288029.05_summits.bed INFO @ Mon, 03 Jun 2019 11:17:04: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6896 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:17:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288029/SRX288029.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:17:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288029/SRX288029.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:17:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288029/SRX288029.10_summits.bed INFO @ Mon, 03 Jun 2019 11:17:06: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4582 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。