Job ID = 1294806 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 : 12,148,753 reads read : 12,148,753 reads written : 12,148,753 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:54 12148753 reads; of these: 12148753 (100.00%) were unpaired; of these: 599977 (4.94%) aligned 0 times 7690843 (63.31%) aligned exactly 1 time 3857933 (31.76%) aligned >1 times 95.06% overall alignment rate Time searching: 00:05:55 Overall time: 00:05:55 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] 1809117 / 11548776 = 0.1567 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 10:22:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287890/SRX287890.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287890/SRX287890.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287890/SRX287890.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287890/SRX287890.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 10:22:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:22:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:22:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287890/SRX287890.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287890/SRX287890.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287890/SRX287890.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287890/SRX287890.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 10:22:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:22:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:22:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287890/SRX287890.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287890/SRX287890.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287890/SRX287890.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287890/SRX287890.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 10:22:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:22:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:22:16: 1000000 INFO @ Mon, 03 Jun 2019 10:22:17: 1000000 INFO @ Mon, 03 Jun 2019 10:22:17: 1000000 INFO @ Mon, 03 Jun 2019 10:22:23: 2000000 INFO @ Mon, 03 Jun 2019 10:22:24: 2000000 INFO @ Mon, 03 Jun 2019 10:22:26: 2000000 INFO @ Mon, 03 Jun 2019 10:22:29: 3000000 INFO @ Mon, 03 Jun 2019 10:22:31: 3000000 INFO @ Mon, 03 Jun 2019 10:22:35: 3000000 INFO @ Mon, 03 Jun 2019 10:22:37: 4000000 INFO @ Mon, 03 Jun 2019 10:22:38: 4000000 INFO @ Mon, 03 Jun 2019 10:22:43: 4000000 INFO @ Mon, 03 Jun 2019 10:22:44: 5000000 INFO @ Mon, 03 Jun 2019 10:22:46: 5000000 INFO @ Mon, 03 Jun 2019 10:22:51: 6000000 INFO @ Mon, 03 Jun 2019 10:22:52: 5000000 INFO @ Mon, 03 Jun 2019 10:22:53: 6000000 INFO @ Mon, 03 Jun 2019 10:22:58: 7000000 INFO @ Mon, 03 Jun 2019 10:23:00: 6000000 INFO @ Mon, 03 Jun 2019 10:23:00: 7000000 INFO @ Mon, 03 Jun 2019 10:23:04: 8000000 INFO @ Mon, 03 Jun 2019 10:23:07: 8000000 INFO @ Mon, 03 Jun 2019 10:23:08: 7000000 INFO @ Mon, 03 Jun 2019 10:23:11: 9000000 INFO @ Mon, 03 Jun 2019 10:23:14: 9000000 INFO @ Mon, 03 Jun 2019 10:23:16: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:23:16: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:23:16: #1 total tags in treatment: 9739659 INFO @ Mon, 03 Jun 2019 10:23:16: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:23:16: #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 10:23:16: #1 tags after filtering in treatment: 9739659 INFO @ Mon, 03 Jun 2019 10:23:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:23:16: #1 finished! INFO @ Mon, 03 Jun 2019 10:23:16: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:23:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:23:16: 8000000 INFO @ Mon, 03 Jun 2019 10:23:17: #2 number of paired peaks: 494 WARNING @ Mon, 03 Jun 2019 10:23:17: Fewer paired peaks (494) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 494 pairs to build model! INFO @ Mon, 03 Jun 2019 10:23:17: start model_add_line... INFO @ Mon, 03 Jun 2019 10:23:17: start X-correlation... INFO @ Mon, 03 Jun 2019 10:23:17: end of X-cor INFO @ Mon, 03 Jun 2019 10:23:17: #2 finished! INFO @ Mon, 03 Jun 2019 10:23:17: #2 predicted fragment length is 47 bps INFO @ Mon, 03 Jun 2019 10:23:17: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 03 Jun 2019 10:23:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287890/SRX287890.05_model.r WARNING @ Mon, 03 Jun 2019 10:23:17: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:23:17: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 03 Jun 2019 10:23:17: #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 10:23:17: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:23:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:23:20: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:23:20: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:23:20: #1 total tags in treatment: 9739659 INFO @ Mon, 03 Jun 2019 10:23:20: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:23:20: #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 10:23:20: #1 tags after filtering in treatment: 9739659 INFO @ Mon, 03 Jun 2019 10:23:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:23:20: #1 finished! INFO @ Mon, 03 Jun 2019 10:23:20: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:23:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:23:21: #2 number of paired peaks: 494 WARNING @ Mon, 03 Jun 2019 10:23:21: Fewer paired peaks (494) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 494 pairs to build model! INFO @ Mon, 03 Jun 2019 10:23:21: start model_add_line... INFO @ Mon, 03 Jun 2019 10:23:21: start X-correlation... INFO @ Mon, 03 Jun 2019 10:23:21: end of X-cor INFO @ Mon, 03 Jun 2019 10:23:21: #2 finished! INFO @ Mon, 03 Jun 2019 10:23:21: #2 predicted fragment length is 47 bps INFO @ Mon, 03 Jun 2019 10:23:21: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 03 Jun 2019 10:23:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287890/SRX287890.10_model.r WARNING @ Mon, 03 Jun 2019 10:23:21: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:23:21: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 03 Jun 2019 10:23:21: #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 10:23:21: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:23:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:23:25: 9000000 INFO @ Mon, 03 Jun 2019 10:23:31: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:23:31: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:23:31: #1 total tags in treatment: 9739659 INFO @ Mon, 03 Jun 2019 10:23:31: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:23:31: #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 10:23:31: #1 tags after filtering in treatment: 9739659 INFO @ Mon, 03 Jun 2019 10:23:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:23:31: #1 finished! INFO @ Mon, 03 Jun 2019 10:23:31: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:23:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:23:32: #2 number of paired peaks: 494 WARNING @ Mon, 03 Jun 2019 10:23:32: Fewer paired peaks (494) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 494 pairs to build model! INFO @ Mon, 03 Jun 2019 10:23:32: start model_add_line... INFO @ Mon, 03 Jun 2019 10:23:32: start X-correlation... INFO @ Mon, 03 Jun 2019 10:23:32: end of X-cor INFO @ Mon, 03 Jun 2019 10:23:32: #2 finished! INFO @ Mon, 03 Jun 2019 10:23:32: #2 predicted fragment length is 47 bps INFO @ Mon, 03 Jun 2019 10:23:32: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 03 Jun 2019 10:23:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287890/SRX287890.20_model.r WARNING @ Mon, 03 Jun 2019 10:23:32: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:23:32: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 03 Jun 2019 10:23:32: #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 10:23:32: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:23:32: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:23:45: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:23:48: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:23:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287890/SRX287890.05_peaks.xls INFO @ Mon, 03 Jun 2019 10:23:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287890/SRX287890.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:23:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287890/SRX287890.05_summits.bed INFO @ Mon, 03 Jun 2019 10:23:58: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1983 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:24:00: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:24:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287890/SRX287890.10_peaks.xls INFO @ Mon, 03 Jun 2019 10:24:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287890/SRX287890.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:24:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287890/SRX287890.10_summits.bed INFO @ Mon, 03 Jun 2019 10:24:02: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1729 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:24:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287890/SRX287890.20_peaks.xls INFO @ Mon, 03 Jun 2019 10:24:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287890/SRX287890.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:24:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287890/SRX287890.20_summits.bed INFO @ Mon, 03 Jun 2019 10:24:13: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1292 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。