Job ID = 2590232 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,842,184 reads read : 19,842,184 reads written : 19,842,184 rm: cannot remove ‘[DSE]RR*’: 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: 00:04:38 19842184 reads; of these: 19842184 (100.00%) were unpaired; of these: 8851209 (44.61%) aligned 0 times 9622303 (48.49%) aligned exactly 1 time 1368672 (6.90%) aligned >1 times 55.39% overall alignment rate Time searching: 00:04:38 Overall time: 00:04:38 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1413057 / 10990975 = 0.1286 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, 12 Aug 2019 20:34:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5985666/SRX5985666.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5985666/SRX5985666.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5985666/SRX5985666.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5985666/SRX5985666.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 12 Aug 2019 20:34:35: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:34:35: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:34:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5985666/SRX5985666.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5985666/SRX5985666.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5985666/SRX5985666.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5985666/SRX5985666.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 12 Aug 2019 20:34:36: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:34:36: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:34:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5985666/SRX5985666.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5985666/SRX5985666.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5985666/SRX5985666.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5985666/SRX5985666.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 12 Aug 2019 20:34:37: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:34:37: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:34:44: 1000000 INFO @ Mon, 12 Aug 2019 20:34:46: 1000000 INFO @ Mon, 12 Aug 2019 20:34:49: 1000000 INFO @ Mon, 12 Aug 2019 20:34:53: 2000000 INFO @ Mon, 12 Aug 2019 20:34:55: 2000000 INFO @ Mon, 12 Aug 2019 20:35:01: 3000000 INFO @ Mon, 12 Aug 2019 20:35:02: 2000000 INFO @ Mon, 12 Aug 2019 20:35:05: 3000000 INFO @ Mon, 12 Aug 2019 20:35:10: 4000000 INFO @ Mon, 12 Aug 2019 20:35:13: 3000000 INFO @ Mon, 12 Aug 2019 20:35:15: 4000000 INFO @ Mon, 12 Aug 2019 20:35:18: 5000000 INFO @ Mon, 12 Aug 2019 20:35:24: 5000000 INFO @ Mon, 12 Aug 2019 20:35:25: 4000000 INFO @ Mon, 12 Aug 2019 20:35:27: 6000000 INFO @ Mon, 12 Aug 2019 20:35:34: 6000000 INFO @ Mon, 12 Aug 2019 20:35:36: 7000000 INFO @ Mon, 12 Aug 2019 20:35:37: 5000000 INFO @ Mon, 12 Aug 2019 20:35:43: 7000000 INFO @ Mon, 12 Aug 2019 20:35:44: 8000000 INFO @ Mon, 12 Aug 2019 20:35:48: 6000000 INFO @ Mon, 12 Aug 2019 20:35:53: 8000000 INFO @ Mon, 12 Aug 2019 20:35:53: 9000000 INFO @ Mon, 12 Aug 2019 20:35:58: #1 tag size is determined as 76 bps INFO @ Mon, 12 Aug 2019 20:35:58: #1 tag size = 76 INFO @ Mon, 12 Aug 2019 20:35:58: #1 total tags in treatment: 9577918 INFO @ Mon, 12 Aug 2019 20:35:58: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:35:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:35:58: #1 tags after filtering in treatment: 9577918 INFO @ Mon, 12 Aug 2019 20:35:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:35:58: #1 finished! INFO @ Mon, 12 Aug 2019 20:35:58: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:35:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:35:59: #2 number of paired peaks: 1699 INFO @ Mon, 12 Aug 2019 20:35:59: start model_add_line... INFO @ Mon, 12 Aug 2019 20:35:59: start X-correlation... INFO @ Mon, 12 Aug 2019 20:35:59: end of X-cor INFO @ Mon, 12 Aug 2019 20:35:59: #2 finished! INFO @ Mon, 12 Aug 2019 20:35:59: #2 predicted fragment length is 193 bps INFO @ Mon, 12 Aug 2019 20:35:59: #2 alternative fragment length(s) may be 193 bps INFO @ Mon, 12 Aug 2019 20:35:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5985666/SRX5985666.05_model.r INFO @ Mon, 12 Aug 2019 20:35:59: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:35:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:36:00: 7000000 INFO @ Mon, 12 Aug 2019 20:36:03: 9000000 INFO @ Mon, 12 Aug 2019 20:36:08: #1 tag size is determined as 76 bps INFO @ Mon, 12 Aug 2019 20:36:08: #1 tag size = 76 INFO @ Mon, 12 Aug 2019 20:36:08: #1 total tags in treatment: 9577918 INFO @ Mon, 12 Aug 2019 20:36:08: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:36:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:36:08: #1 tags after filtering in treatment: 9577918 INFO @ Mon, 12 Aug 2019 20:36:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:36:08: #1 finished! INFO @ Mon, 12 Aug 2019 20:36:08: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:36:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:36:09: #2 number of paired peaks: 1699 INFO @ Mon, 12 Aug 2019 20:36:09: start model_add_line... INFO @ Mon, 12 Aug 2019 20:36:10: start X-correlation... INFO @ Mon, 12 Aug 2019 20:36:10: end of X-cor INFO @ Mon, 12 Aug 2019 20:36:10: #2 finished! INFO @ Mon, 12 Aug 2019 20:36:10: #2 predicted fragment length is 193 bps INFO @ Mon, 12 Aug 2019 20:36:10: #2 alternative fragment length(s) may be 193 bps INFO @ Mon, 12 Aug 2019 20:36:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5985666/SRX5985666.10_model.r INFO @ Mon, 12 Aug 2019 20:36:10: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:36:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:36:11: 8000000 INFO @ Mon, 12 Aug 2019 20:36:23: 9000000 INFO @ Mon, 12 Aug 2019 20:36:29: #1 tag size is determined as 76 bps INFO @ Mon, 12 Aug 2019 20:36:29: #1 tag size = 76 INFO @ Mon, 12 Aug 2019 20:36:29: #1 total tags in treatment: 9577918 INFO @ Mon, 12 Aug 2019 20:36:29: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:36:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:36:29: #1 tags after filtering in treatment: 9577918 INFO @ Mon, 12 Aug 2019 20:36:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:36:29: #1 finished! INFO @ Mon, 12 Aug 2019 20:36:29: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:36:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:36:30: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:36:30: #2 number of paired peaks: 1699 INFO @ Mon, 12 Aug 2019 20:36:30: start model_add_line... INFO @ Mon, 12 Aug 2019 20:36:31: start X-correlation... INFO @ Mon, 12 Aug 2019 20:36:31: end of X-cor INFO @ Mon, 12 Aug 2019 20:36:31: #2 finished! INFO @ Mon, 12 Aug 2019 20:36:31: #2 predicted fragment length is 193 bps INFO @ Mon, 12 Aug 2019 20:36:31: #2 alternative fragment length(s) may be 193 bps INFO @ Mon, 12 Aug 2019 20:36:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5985666/SRX5985666.20_model.r INFO @ Mon, 12 Aug 2019 20:36:31: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:36:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:36:40: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:36:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5985666/SRX5985666.05_peaks.xls INFO @ Mon, 12 Aug 2019 20:36:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5985666/SRX5985666.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:36:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5985666/SRX5985666.05_summits.bed INFO @ Mon, 12 Aug 2019 20:36:43: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (3650 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:36:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5985666/SRX5985666.10_peaks.xls INFO @ Mon, 12 Aug 2019 20:36:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5985666/SRX5985666.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:36:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5985666/SRX5985666.10_summits.bed INFO @ Mon, 12 Aug 2019 20:36:54: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2498 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:37:01: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:37:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5985666/SRX5985666.20_peaks.xls INFO @ Mon, 12 Aug 2019 20:37:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5985666/SRX5985666.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:37:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5985666/SRX5985666.20_summits.bed INFO @ Mon, 12 Aug 2019 20:37:15: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (1383 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。