Job ID = 1293856 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 15,391,190 reads read : 15,391,190 reads written : 15,391,190 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: 00:07:20 15391190 reads; of these: 15391190 (100.00%) were unpaired; of these: 4578610 (29.75%) aligned 0 times 4972576 (32.31%) aligned exactly 1 time 5840004 (37.94%) aligned >1 times 70.25% overall alignment rate Time searching: 00:07:20 Overall time: 00:07:20 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] 3608904 / 10812580 = 0.3338 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 02:59:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1299935/SRX1299935.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1299935/SRX1299935.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1299935/SRX1299935.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1299935/SRX1299935.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 02:59:07: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:59:07: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:59:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1299935/SRX1299935.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1299935/SRX1299935.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1299935/SRX1299935.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1299935/SRX1299935.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 02:59:07: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:59:07: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:59:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1299935/SRX1299935.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1299935/SRX1299935.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1299935/SRX1299935.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1299935/SRX1299935.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 02:59:07: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:59:07: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:59:14: 1000000 INFO @ Mon, 03 Jun 2019 02:59:14: 1000000 INFO @ Mon, 03 Jun 2019 02:59:14: 1000000 INFO @ Mon, 03 Jun 2019 02:59:20: 2000000 INFO @ Mon, 03 Jun 2019 02:59:20: 2000000 INFO @ Mon, 03 Jun 2019 02:59:21: 2000000 INFO @ Mon, 03 Jun 2019 02:59:27: 3000000 INFO @ Mon, 03 Jun 2019 02:59:27: 3000000 INFO @ Mon, 03 Jun 2019 02:59:29: 3000000 INFO @ Mon, 03 Jun 2019 02:59:34: 4000000 INFO @ Mon, 03 Jun 2019 02:59:34: 4000000 INFO @ Mon, 03 Jun 2019 02:59:36: 4000000 INFO @ Mon, 03 Jun 2019 02:59:41: 5000000 INFO @ Mon, 03 Jun 2019 02:59:41: 5000000 INFO @ Mon, 03 Jun 2019 02:59:43: 5000000 INFO @ Mon, 03 Jun 2019 02:59:47: 6000000 INFO @ Mon, 03 Jun 2019 02:59:47: 6000000 INFO @ Mon, 03 Jun 2019 02:59:50: 6000000 INFO @ Mon, 03 Jun 2019 02:59:54: 7000000 INFO @ Mon, 03 Jun 2019 02:59:54: 7000000 INFO @ Mon, 03 Jun 2019 02:59:55: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 02:59:55: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 02:59:55: #1 total tags in treatment: 7203676 INFO @ Mon, 03 Jun 2019 02:59:55: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:59:55: #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 02:59:55: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 02:59:55: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 02:59:55: #1 total tags in treatment: 7203676 INFO @ Mon, 03 Jun 2019 02:59:55: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:59:55: #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 02:59:55: #1 tags after filtering in treatment: 7203676 INFO @ Mon, 03 Jun 2019 02:59:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:59:55: #1 finished! INFO @ Mon, 03 Jun 2019 02:59:55: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:59:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:59:55: #1 tags after filtering in treatment: 7203676 INFO @ Mon, 03 Jun 2019 02:59:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:59:55: #1 finished! INFO @ Mon, 03 Jun 2019 02:59:55: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:59:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:59:56: #2 number of paired peaks: 1242 INFO @ Mon, 03 Jun 2019 02:59:56: start model_add_line... INFO @ Mon, 03 Jun 2019 02:59:56: #2 number of paired peaks: 1242 INFO @ Mon, 03 Jun 2019 02:59:56: start model_add_line... INFO @ Mon, 03 Jun 2019 02:59:56: start X-correlation... INFO @ Mon, 03 Jun 2019 02:59:56: end of X-cor INFO @ Mon, 03 Jun 2019 02:59:56: #2 finished! INFO @ Mon, 03 Jun 2019 02:59:56: #2 predicted fragment length is 68 bps INFO @ Mon, 03 Jun 2019 02:59:56: #2 alternative fragment length(s) may be 68 bps INFO @ Mon, 03 Jun 2019 02:59:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1299935/SRX1299935.05_model.r WARNING @ Mon, 03 Jun 2019 02:59:56: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:59:56: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Mon, 03 Jun 2019 02:59:56: #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 02:59:56: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:59:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:59:56: start X-correlation... INFO @ Mon, 03 Jun 2019 02:59:56: end of X-cor INFO @ Mon, 03 Jun 2019 02:59:56: #2 finished! INFO @ Mon, 03 Jun 2019 02:59:56: #2 predicted fragment length is 68 bps INFO @ Mon, 03 Jun 2019 02:59:56: #2 alternative fragment length(s) may be 68 bps INFO @ Mon, 03 Jun 2019 02:59:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1299935/SRX1299935.10_model.r WARNING @ Mon, 03 Jun 2019 02:59:56: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:59:56: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Mon, 03 Jun 2019 02:59:56: #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 02:59:56: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:59:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:59:57: 7000000 INFO @ Mon, 03 Jun 2019 02:59:58: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 02:59:58: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 02:59:58: #1 total tags in treatment: 7203676 INFO @ Mon, 03 Jun 2019 02:59:58: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:59:58: #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 02:59:58: #1 tags after filtering in treatment: 7203676 INFO @ Mon, 03 Jun 2019 02:59:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:59:58: #1 finished! INFO @ Mon, 03 Jun 2019 02:59:58: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:59:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:59:59: #2 number of paired peaks: 1242 INFO @ Mon, 03 Jun 2019 02:59:59: start model_add_line... INFO @ Mon, 03 Jun 2019 02:59:59: start X-correlation... INFO @ Mon, 03 Jun 2019 02:59:59: end of X-cor INFO @ Mon, 03 Jun 2019 02:59:59: #2 finished! INFO @ Mon, 03 Jun 2019 02:59:59: #2 predicted fragment length is 68 bps INFO @ Mon, 03 Jun 2019 02:59:59: #2 alternative fragment length(s) may be 68 bps INFO @ Mon, 03 Jun 2019 02:59:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1299935/SRX1299935.20_model.r WARNING @ Mon, 03 Jun 2019 02:59:59: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:59:59: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Mon, 03 Jun 2019 02:59:59: #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 02:59:59: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:59:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:00:18: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:00:18: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:00:20: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:00:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1299935/SRX1299935.05_peaks.xls INFO @ Mon, 03 Jun 2019 03:00:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1299935/SRX1299935.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:00:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1299935/SRX1299935.05_summits.bed INFO @ Mon, 03 Jun 2019 03:00:28: Done! INFO @ Mon, 03 Jun 2019 03:00:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1299935/SRX1299935.10_peaks.xls INFO @ Mon, 03 Jun 2019 03:00:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1299935/SRX1299935.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:00:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1299935/SRX1299935.10_summits.bed pass1 - making usageList (14 chroms): 1 millis INFO @ Mon, 03 Jun 2019 03:00:28: Done! pass2 - checking and writing primary data (2479 records, 4 fields): 5 millis CompletedMACS2peakCalling pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (1443 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:00:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1299935/SRX1299935.20_peaks.xls INFO @ Mon, 03 Jun 2019 03:00:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1299935/SRX1299935.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:00:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1299935/SRX1299935.20_summits.bed INFO @ Mon, 03 Jun 2019 03:00:31: Done! pass1 - making usageList (10 chroms): 2 millis pass2 - checking and writing primary data (907 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。