Job ID = 1292880 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 16,829,782 reads read : 33,659,564 reads written : 33,659,564 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: 00:20:39 16829782 reads; of these: 16829782 (100.00%) were paired; of these: 1040147 (6.18%) aligned concordantly 0 times 13261718 (78.80%) aligned concordantly exactly 1 time 2527917 (15.02%) aligned concordantly >1 times ---- 1040147 pairs aligned concordantly 0 times; of these: 413620 (39.77%) aligned discordantly 1 time ---- 626527 pairs aligned 0 times concordantly or discordantly; of these: 1253054 mates make up the pairs; of these: 914078 (72.95%) aligned 0 times 196943 (15.72%) aligned exactly 1 time 142033 (11.33%) aligned >1 times 97.28% overall alignment rate Time searching: 00:20:39 Overall time: 00:20:39 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 16 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 5724853 / 16195974 = 0.3535 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 @ Sun, 02 Jun 2019 21:34:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4996810/SRX4996810.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4996810/SRX4996810.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4996810/SRX4996810.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4996810/SRX4996810.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 @ Sun, 02 Jun 2019 21:34:17: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:34:17: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:34:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4996810/SRX4996810.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4996810/SRX4996810.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4996810/SRX4996810.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4996810/SRX4996810.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 @ Sun, 02 Jun 2019 21:34:17: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:34:17: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:34:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4996810/SRX4996810.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4996810/SRX4996810.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4996810/SRX4996810.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4996810/SRX4996810.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 @ Sun, 02 Jun 2019 21:34:17: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:34:17: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:34:24: 1000000 INFO @ Sun, 02 Jun 2019 21:34:24: 1000000 INFO @ Sun, 02 Jun 2019 21:34:24: 1000000 INFO @ Sun, 02 Jun 2019 21:34:31: 2000000 INFO @ Sun, 02 Jun 2019 21:34:32: 2000000 INFO @ Sun, 02 Jun 2019 21:34:32: 2000000 INFO @ Sun, 02 Jun 2019 21:34:39: 3000000 INFO @ Sun, 02 Jun 2019 21:34:40: 3000000 INFO @ Sun, 02 Jun 2019 21:34:40: 3000000 INFO @ Sun, 02 Jun 2019 21:34:46: 4000000 INFO @ Sun, 02 Jun 2019 21:34:47: 4000000 INFO @ Sun, 02 Jun 2019 21:34:47: 4000000 INFO @ Sun, 02 Jun 2019 21:34:54: 5000000 INFO @ Sun, 02 Jun 2019 21:34:55: 5000000 INFO @ Sun, 02 Jun 2019 21:34:55: 5000000 INFO @ Sun, 02 Jun 2019 21:35:02: 6000000 INFO @ Sun, 02 Jun 2019 21:35:03: 6000000 INFO @ Sun, 02 Jun 2019 21:35:03: 6000000 INFO @ Sun, 02 Jun 2019 21:35:09: 7000000 INFO @ Sun, 02 Jun 2019 21:35:11: 7000000 INFO @ Sun, 02 Jun 2019 21:35:11: 7000000 INFO @ Sun, 02 Jun 2019 21:35:17: 8000000 INFO @ Sun, 02 Jun 2019 21:35:18: 8000000 INFO @ Sun, 02 Jun 2019 21:35:19: 8000000 INFO @ Sun, 02 Jun 2019 21:35:25: 9000000 INFO @ Sun, 02 Jun 2019 21:35:25: 9000000 INFO @ Sun, 02 Jun 2019 21:35:27: 9000000 INFO @ Sun, 02 Jun 2019 21:35:32: 10000000 INFO @ Sun, 02 Jun 2019 21:35:32: 10000000 INFO @ Sun, 02 Jun 2019 21:35:35: 10000000 INFO @ Sun, 02 Jun 2019 21:35:39: 11000000 INFO @ Sun, 02 Jun 2019 21:35:40: 11000000 INFO @ Sun, 02 Jun 2019 21:35:42: 11000000 INFO @ Sun, 02 Jun 2019 21:35:46: 12000000 INFO @ Sun, 02 Jun 2019 21:35:47: 12000000 INFO @ Sun, 02 Jun 2019 21:35:49: 12000000 INFO @ Sun, 02 Jun 2019 21:35:53: 13000000 INFO @ Sun, 02 Jun 2019 21:35:54: 13000000 INFO @ Sun, 02 Jun 2019 21:35:56: 13000000 INFO @ Sun, 02 Jun 2019 21:36:00: 14000000 INFO @ Sun, 02 Jun 2019 21:36:01: 14000000 INFO @ Sun, 02 Jun 2019 21:36:03: 14000000 INFO @ Sun, 02 Jun 2019 21:36:07: 15000000 INFO @ Sun, 02 Jun 2019 21:36:08: 15000000 INFO @ Sun, 02 Jun 2019 21:36:11: 15000000 INFO @ Sun, 02 Jun 2019 21:36:14: 16000000 INFO @ Sun, 02 Jun 2019 21:36:16: 16000000 INFO @ Sun, 02 Jun 2019 21:36:18: 16000000 INFO @ Sun, 02 Jun 2019 21:36:21: 17000000 INFO @ Sun, 02 Jun 2019 21:36:23: 17000000 INFO @ Sun, 02 Jun 2019 21:36:25: 17000000 INFO @ Sun, 02 Jun 2019 21:36:28: 18000000 INFO @ Sun, 02 Jun 2019 21:36:30: 18000000 INFO @ Sun, 02 Jun 2019 21:36:32: 18000000 INFO @ Sun, 02 Jun 2019 21:36:35: 19000000 INFO @ Sun, 02 Jun 2019 21:36:37: 19000000 INFO @ Sun, 02 Jun 2019 21:36:39: 19000000 INFO @ Sun, 02 Jun 2019 21:36:42: 20000000 INFO @ Sun, 02 Jun 2019 21:36:43: 20000000 INFO @ Sun, 02 Jun 2019 21:36:46: 20000000 INFO @ Sun, 02 Jun 2019 21:36:49: 21000000 INFO @ Sun, 02 Jun 2019 21:36:50: 21000000 INFO @ Sun, 02 Jun 2019 21:36:51: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 21:36:51: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 21:36:51: #1 total tags in treatment: 10136199 INFO @ Sun, 02 Jun 2019 21:36:51: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:36:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 21:36:52: #1 tags after filtering in treatment: 9319258 INFO @ Sun, 02 Jun 2019 21:36:52: #1 Redundant rate of treatment: 0.08 INFO @ Sun, 02 Jun 2019 21:36:52: #1 finished! INFO @ Sun, 02 Jun 2019 21:36:52: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:36:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:36:52: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 21:36:52: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 21:36:52: #1 total tags in treatment: 10136199 INFO @ Sun, 02 Jun 2019 21:36:52: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:36:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 21:36:52: #1 tags after filtering in treatment: 9319258 INFO @ Sun, 02 Jun 2019 21:36:52: #1 Redundant rate of treatment: 0.08 INFO @ Sun, 02 Jun 2019 21:36:52: #1 finished! INFO @ Sun, 02 Jun 2019 21:36:52: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:36:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:36:52: #2 number of paired peaks: 542 WARNING @ Sun, 02 Jun 2019 21:36:52: Fewer paired peaks (542) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 542 pairs to build model! INFO @ Sun, 02 Jun 2019 21:36:52: start model_add_line... INFO @ Sun, 02 Jun 2019 21:36:53: start X-correlation... INFO @ Sun, 02 Jun 2019 21:36:53: end of X-cor INFO @ Sun, 02 Jun 2019 21:36:53: #2 finished! INFO @ Sun, 02 Jun 2019 21:36:53: #2 predicted fragment length is 150 bps INFO @ Sun, 02 Jun 2019 21:36:53: #2 alternative fragment length(s) may be 4,150 bps INFO @ Sun, 02 Jun 2019 21:36:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4996810/SRX4996810.05_model.r INFO @ Sun, 02 Jun 2019 21:36:53: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:36:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:36:53: 21000000 INFO @ Sun, 02 Jun 2019 21:36:53: #2 number of paired peaks: 542 WARNING @ Sun, 02 Jun 2019 21:36:53: Fewer paired peaks (542) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 542 pairs to build model! INFO @ Sun, 02 Jun 2019 21:36:53: start model_add_line... INFO @ Sun, 02 Jun 2019 21:36:53: start X-correlation... INFO @ Sun, 02 Jun 2019 21:36:53: end of X-cor INFO @ Sun, 02 Jun 2019 21:36:53: #2 finished! INFO @ Sun, 02 Jun 2019 21:36:53: #2 predicted fragment length is 150 bps INFO @ Sun, 02 Jun 2019 21:36:53: #2 alternative fragment length(s) may be 4,150 bps INFO @ Sun, 02 Jun 2019 21:36:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4996810/SRX4996810.10_model.r INFO @ Sun, 02 Jun 2019 21:36:53: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:36:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:36:55: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 21:36:55: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 21:36:55: #1 total tags in treatment: 10136199 INFO @ Sun, 02 Jun 2019 21:36:55: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:36:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 21:36:55: #1 tags after filtering in treatment: 9319258 INFO @ Sun, 02 Jun 2019 21:36:55: #1 Redundant rate of treatment: 0.08 INFO @ Sun, 02 Jun 2019 21:36:55: #1 finished! INFO @ Sun, 02 Jun 2019 21:36:55: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:36:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:36:56: #2 number of paired peaks: 542 WARNING @ Sun, 02 Jun 2019 21:36:56: Fewer paired peaks (542) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 542 pairs to build model! INFO @ Sun, 02 Jun 2019 21:36:56: start model_add_line... INFO @ Sun, 02 Jun 2019 21:36:56: start X-correlation... INFO @ Sun, 02 Jun 2019 21:36:56: end of X-cor INFO @ Sun, 02 Jun 2019 21:36:56: #2 finished! INFO @ Sun, 02 Jun 2019 21:36:56: #2 predicted fragment length is 150 bps INFO @ Sun, 02 Jun 2019 21:36:56: #2 alternative fragment length(s) may be 4,150 bps INFO @ Sun, 02 Jun 2019 21:36:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4996810/SRX4996810.20_model.r INFO @ Sun, 02 Jun 2019 21:36:56: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:36:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:37:22: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:37:22: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:37:26: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:37:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4996810/SRX4996810.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:37:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4996810/SRX4996810.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:37:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4996810/SRX4996810.10_summits.bed INFO @ Sun, 02 Jun 2019 21:37:35: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (336 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:37:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4996810/SRX4996810.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:37:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4996810/SRX4996810.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:37:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4996810/SRX4996810.05_summits.bed INFO @ Sun, 02 Jun 2019 21:37:36: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (432 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:37:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4996810/SRX4996810.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:37:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4996810/SRX4996810.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:37:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4996810/SRX4996810.20_summits.bed INFO @ Sun, 02 Jun 2019 21:37:39: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (221 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。