Job ID = 4303033 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 16,533,626 reads read : 16,533,626 reads written : 16,533,626 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1163596.sra.cache’: 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: 00:04:46 16533626 reads; of these: 16533626 (100.00%) were unpaired; of these: 944360 (5.71%) aligned 0 times 10276776 (62.16%) aligned exactly 1 time 5312490 (32.13%) aligned >1 times 94.29% overall alignment rate Time searching: 00:04:46 Overall time: 00:04:46 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_rmdupse_core] 8245361 / 15589266 = 0.5289 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 12 Dec 2019 00:41:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466530/SRX466530.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466530/SRX466530.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466530/SRX466530.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466530/SRX466530.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 @ Thu, 12 Dec 2019 00:41:32: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:41:32: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:41:40: 1000000 INFO @ Thu, 12 Dec 2019 00:41:48: 2000000 INFO @ Thu, 12 Dec 2019 00:41:56: 3000000 INFO @ Thu, 12 Dec 2019 00:42:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466530/SRX466530.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466530/SRX466530.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466530/SRX466530.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466530/SRX466530.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 @ Thu, 12 Dec 2019 00:42:01: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:42:01: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:42:06: 4000000 INFO @ Thu, 12 Dec 2019 00:42:14: 1000000 INFO @ Thu, 12 Dec 2019 00:42:16: 5000000 INFO @ Thu, 12 Dec 2019 00:42:26: 6000000 INFO @ Thu, 12 Dec 2019 00:42:27: 2000000 BedGraph に変換中... INFO @ Thu, 12 Dec 2019 00:42:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466530/SRX466530.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466530/SRX466530.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466530/SRX466530.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466530/SRX466530.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 @ Thu, 12 Dec 2019 00:42:31: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:42:31: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:42:36: 7000000 INFO @ Thu, 12 Dec 2019 00:42:40: #1 tag size is determined as 42 bps INFO @ Thu, 12 Dec 2019 00:42:40: #1 tag size = 42 INFO @ Thu, 12 Dec 2019 00:42:40: #1 total tags in treatment: 7343905 INFO @ Thu, 12 Dec 2019 00:42:40: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:42:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:42:40: #1 tags after filtering in treatment: 7343905 INFO @ Thu, 12 Dec 2019 00:42:40: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:42:40: #1 finished! INFO @ Thu, 12 Dec 2019 00:42:40: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:42:40: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:42:40: 3000000 INFO @ Thu, 12 Dec 2019 00:42:41: #2 number of paired peaks: 3633 INFO @ Thu, 12 Dec 2019 00:42:41: start model_add_line... INFO @ Thu, 12 Dec 2019 00:42:41: start X-correlation... INFO @ Thu, 12 Dec 2019 00:42:41: end of X-cor INFO @ Thu, 12 Dec 2019 00:42:41: #2 finished! INFO @ Thu, 12 Dec 2019 00:42:41: #2 predicted fragment length is 185 bps INFO @ Thu, 12 Dec 2019 00:42:41: #2 alternative fragment length(s) may be 185 bps INFO @ Thu, 12 Dec 2019 00:42:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466530/SRX466530.05_model.r INFO @ Thu, 12 Dec 2019 00:42:41: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:42:41: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:42:44: 1000000 INFO @ Thu, 12 Dec 2019 00:42:53: 4000000 INFO @ Thu, 12 Dec 2019 00:42:58: 2000000 INFO @ Thu, 12 Dec 2019 00:43:08: 5000000 INFO @ Thu, 12 Dec 2019 00:43:13: 3000000 INFO @ Thu, 12 Dec 2019 00:43:15: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:43:22: 6000000 INFO @ Thu, 12 Dec 2019 00:43:25: 4000000 INFO @ Thu, 12 Dec 2019 00:43:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466530/SRX466530.05_peaks.xls INFO @ Thu, 12 Dec 2019 00:43:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466530/SRX466530.05_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:43:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466530/SRX466530.05_summits.bed INFO @ Thu, 12 Dec 2019 00:43:29: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (5331 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 00:43:35: 7000000 INFO @ Thu, 12 Dec 2019 00:43:38: 5000000 INFO @ Thu, 12 Dec 2019 00:43:39: #1 tag size is determined as 42 bps INFO @ Thu, 12 Dec 2019 00:43:39: #1 tag size = 42 INFO @ Thu, 12 Dec 2019 00:43:39: #1 total tags in treatment: 7343905 INFO @ Thu, 12 Dec 2019 00:43:39: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:43:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:43:39: #1 tags after filtering in treatment: 7343905 INFO @ Thu, 12 Dec 2019 00:43:39: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:43:39: #1 finished! INFO @ Thu, 12 Dec 2019 00:43:39: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:43:39: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:43:40: #2 number of paired peaks: 3633 INFO @ Thu, 12 Dec 2019 00:43:40: start model_add_line... INFO @ Thu, 12 Dec 2019 00:43:40: start X-correlation... INFO @ Thu, 12 Dec 2019 00:43:40: end of X-cor INFO @ Thu, 12 Dec 2019 00:43:40: #2 finished! INFO @ Thu, 12 Dec 2019 00:43:40: #2 predicted fragment length is 185 bps INFO @ Thu, 12 Dec 2019 00:43:40: #2 alternative fragment length(s) may be 185 bps INFO @ Thu, 12 Dec 2019 00:43:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466530/SRX466530.10_model.r INFO @ Thu, 12 Dec 2019 00:43:40: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:43:40: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:43:49: 6000000 INFO @ Thu, 12 Dec 2019 00:44:00: 7000000 INFO @ Thu, 12 Dec 2019 00:44:04: #1 tag size is determined as 42 bps INFO @ Thu, 12 Dec 2019 00:44:04: #1 tag size = 42 INFO @ Thu, 12 Dec 2019 00:44:04: #1 total tags in treatment: 7343905 INFO @ Thu, 12 Dec 2019 00:44:04: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:44:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:44:04: #1 tags after filtering in treatment: 7343905 INFO @ Thu, 12 Dec 2019 00:44:04: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:44:04: #1 finished! INFO @ Thu, 12 Dec 2019 00:44:04: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:44:04: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:44:05: #2 number of paired peaks: 3633 INFO @ Thu, 12 Dec 2019 00:44:05: start model_add_line... INFO @ Thu, 12 Dec 2019 00:44:05: start X-correlation... INFO @ Thu, 12 Dec 2019 00:44:05: end of X-cor INFO @ Thu, 12 Dec 2019 00:44:05: #2 finished! INFO @ Thu, 12 Dec 2019 00:44:05: #2 predicted fragment length is 185 bps INFO @ Thu, 12 Dec 2019 00:44:05: #2 alternative fragment length(s) may be 185 bps INFO @ Thu, 12 Dec 2019 00:44:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466530/SRX466530.20_model.r INFO @ Thu, 12 Dec 2019 00:44:05: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:44:05: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:44:10: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:44:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466530/SRX466530.10_peaks.xls INFO @ Thu, 12 Dec 2019 00:44:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466530/SRX466530.10_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:44:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466530/SRX466530.10_summits.bed INFO @ Thu, 12 Dec 2019 00:44:23: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (3539 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 00:44:35: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 12 Dec 2019 00:44:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466530/SRX466530.20_peaks.xls INFO @ Thu, 12 Dec 2019 00:44:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466530/SRX466530.20_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:44:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466530/SRX466530.20_summits.bed INFO @ Thu, 12 Dec 2019 00:44:47: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1813 records, 4 fields): 23 millis CompletedMACS2peakCalling BigWig に変換しました。