Job ID = 1294815 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T01:11:53 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 : 10,650,843 reads read : 10,650,843 reads written : 10,650,843 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: 00:03:37 10650843 reads; of these: 10650843 (100.00%) were unpaired; of these: 2352268 (22.09%) aligned 0 times 5605460 (52.63%) aligned exactly 1 time 2693115 (25.29%) aligned >1 times 77.91% overall alignment rate Time searching: 00:03:37 Overall time: 00:03:37 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] 533342 / 8298575 = 0.0643 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 10:20:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287914/SRX287914.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287914/SRX287914.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287914/SRX287914.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287914/SRX287914.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 10:20:26: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:20:26: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:20:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287914/SRX287914.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287914/SRX287914.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287914/SRX287914.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287914/SRX287914.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 10:20:26: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:20:26: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:20:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287914/SRX287914.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287914/SRX287914.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287914/SRX287914.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287914/SRX287914.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 10:20:26: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:20:26: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:20:33: 1000000 INFO @ Mon, 03 Jun 2019 10:20:34: 1000000 INFO @ Mon, 03 Jun 2019 10:20:34: 1000000 INFO @ Mon, 03 Jun 2019 10:20:39: 2000000 INFO @ Mon, 03 Jun 2019 10:20:42: 2000000 INFO @ Mon, 03 Jun 2019 10:20:42: 2000000 INFO @ Mon, 03 Jun 2019 10:20:46: 3000000 INFO @ Mon, 03 Jun 2019 10:20:49: 3000000 INFO @ Mon, 03 Jun 2019 10:20:50: 3000000 INFO @ Mon, 03 Jun 2019 10:20:53: 4000000 INFO @ Mon, 03 Jun 2019 10:20:56: 4000000 INFO @ Mon, 03 Jun 2019 10:20:58: 4000000 INFO @ Mon, 03 Jun 2019 10:21:00: 5000000 INFO @ Mon, 03 Jun 2019 10:21:03: 5000000 INFO @ Mon, 03 Jun 2019 10:21:06: 5000000 INFO @ Mon, 03 Jun 2019 10:21:06: 6000000 INFO @ Mon, 03 Jun 2019 10:21:10: 6000000 INFO @ Mon, 03 Jun 2019 10:21:13: 7000000 INFO @ Mon, 03 Jun 2019 10:21:14: 6000000 INFO @ Mon, 03 Jun 2019 10:21:18: 7000000 INFO @ Mon, 03 Jun 2019 10:21:18: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 10:21:18: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 10:21:18: #1 total tags in treatment: 7765233 INFO @ Mon, 03 Jun 2019 10:21:18: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:21:18: #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 10:21:18: #1 tags after filtering in treatment: 7765233 INFO @ Mon, 03 Jun 2019 10:21:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:21:18: #1 finished! INFO @ Mon, 03 Jun 2019 10:21:18: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:21:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:21:19: #2 number of paired peaks: 416 WARNING @ Mon, 03 Jun 2019 10:21:19: Fewer paired peaks (416) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 416 pairs to build model! INFO @ Mon, 03 Jun 2019 10:21:19: start model_add_line... INFO @ Mon, 03 Jun 2019 10:21:19: start X-correlation... INFO @ Mon, 03 Jun 2019 10:21:19: end of X-cor INFO @ Mon, 03 Jun 2019 10:21:19: #2 finished! INFO @ Mon, 03 Jun 2019 10:21:19: #2 predicted fragment length is 35 bps INFO @ Mon, 03 Jun 2019 10:21:19: #2 alternative fragment length(s) may be 35 bps INFO @ Mon, 03 Jun 2019 10:21:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287914/SRX287914.20_model.r WARNING @ Mon, 03 Jun 2019 10:21:19: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:21:19: #2 You may need to consider one of the other alternative d(s): 35 WARNING @ Mon, 03 Jun 2019 10:21:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 10:21:19: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:21:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:21:21: 7000000 INFO @ Mon, 03 Jun 2019 10:21:23: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 10:21:23: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 10:21:23: #1 total tags in treatment: 7765233 INFO @ Mon, 03 Jun 2019 10:21:23: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:21:23: #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 10:21:23: #1 tags after filtering in treatment: 7765233 INFO @ Mon, 03 Jun 2019 10:21:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:21:23: #1 finished! INFO @ Mon, 03 Jun 2019 10:21:23: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:21:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:21:24: #2 number of paired peaks: 416 WARNING @ Mon, 03 Jun 2019 10:21:24: Fewer paired peaks (416) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 416 pairs to build model! INFO @ Mon, 03 Jun 2019 10:21:24: start model_add_line... INFO @ Mon, 03 Jun 2019 10:21:24: start X-correlation... INFO @ Mon, 03 Jun 2019 10:21:24: end of X-cor INFO @ Mon, 03 Jun 2019 10:21:24: #2 finished! INFO @ Mon, 03 Jun 2019 10:21:24: #2 predicted fragment length is 35 bps INFO @ Mon, 03 Jun 2019 10:21:24: #2 alternative fragment length(s) may be 35 bps INFO @ Mon, 03 Jun 2019 10:21:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287914/SRX287914.05_model.r WARNING @ Mon, 03 Jun 2019 10:21:24: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:21:24: #2 You may need to consider one of the other alternative d(s): 35 WARNING @ Mon, 03 Jun 2019 10:21:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 10:21:24: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:21:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:21:27: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 10:21:27: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 10:21:27: #1 total tags in treatment: 7765233 INFO @ Mon, 03 Jun 2019 10:21:27: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:21:27: #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 10:21:27: #1 tags after filtering in treatment: 7765233 INFO @ Mon, 03 Jun 2019 10:21:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:21:27: #1 finished! INFO @ Mon, 03 Jun 2019 10:21:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:21:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:21:28: #2 number of paired peaks: 416 WARNING @ Mon, 03 Jun 2019 10:21:28: Fewer paired peaks (416) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 416 pairs to build model! INFO @ Mon, 03 Jun 2019 10:21:28: start model_add_line... INFO @ Mon, 03 Jun 2019 10:21:28: start X-correlation... INFO @ Mon, 03 Jun 2019 10:21:28: end of X-cor INFO @ Mon, 03 Jun 2019 10:21:28: #2 finished! INFO @ Mon, 03 Jun 2019 10:21:28: #2 predicted fragment length is 35 bps INFO @ Mon, 03 Jun 2019 10:21:28: #2 alternative fragment length(s) may be 35 bps INFO @ Mon, 03 Jun 2019 10:21:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287914/SRX287914.10_model.r WARNING @ Mon, 03 Jun 2019 10:21:28: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:21:28: #2 You may need to consider one of the other alternative d(s): 35 WARNING @ Mon, 03 Jun 2019 10:21:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 10:21:28: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:21:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:21:41: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:21:47: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:21:51: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:21:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287914/SRX287914.20_peaks.xls INFO @ Mon, 03 Jun 2019 10:21:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287914/SRX287914.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:21:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287914/SRX287914.20_summits.bed INFO @ Mon, 03 Jun 2019 10:21:52: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (848 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:21:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287914/SRX287914.05_peaks.xls INFO @ Mon, 03 Jun 2019 10:21:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287914/SRX287914.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:21:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287914/SRX287914.05_summits.bed INFO @ Mon, 03 Jun 2019 10:21:57: Done! pass1 - making usageList (10 chroms): 2 millis pass2 - checking and writing primary data (1726 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:22:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287914/SRX287914.10_peaks.xls INFO @ Mon, 03 Jun 2019 10:22:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287914/SRX287914.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:22:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287914/SRX287914.10_summits.bed INFO @ Mon, 03 Jun 2019 10:22:01: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (1387 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。