Job ID = 1292376 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 22,331,954 reads read : 44,663,908 reads written : 22,331,954 reads 0-length : 22,331,954 spots read : 15,421,996 reads read : 30,843,992 reads written : 15,421,996 reads 0-length : 15,421,996 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: 00:07:43 37753950 reads; of these: 37753950 (100.00%) were unpaired; of these: 8989759 (23.81%) aligned 0 times 23987580 (63.54%) aligned exactly 1 time 4776611 (12.65%) aligned >1 times 76.19% overall alignment rate Time searching: 00:07:43 Overall time: 00:07:43 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 12 files... [bam_rmdupse_core] 4178098 / 28764191 = 0.1453 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 18:37:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3883435/SRX3883435.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3883435/SRX3883435.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3883435/SRX3883435.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3883435/SRX3883435.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 18:37:43: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:37:43: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:37:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3883435/SRX3883435.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3883435/SRX3883435.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3883435/SRX3883435.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3883435/SRX3883435.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 18:37:43: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:37:43: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:37:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3883435/SRX3883435.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3883435/SRX3883435.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3883435/SRX3883435.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3883435/SRX3883435.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 18:37:44: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:37:44: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:37:51: 1000000 INFO @ Sun, 02 Jun 2019 18:37:52: 1000000 INFO @ Sun, 02 Jun 2019 18:37:52: 1000000 INFO @ Sun, 02 Jun 2019 18:37:58: 2000000 INFO @ Sun, 02 Jun 2019 18:37:59: 2000000 INFO @ Sun, 02 Jun 2019 18:38:01: 2000000 INFO @ Sun, 02 Jun 2019 18:38:05: 3000000 INFO @ Sun, 02 Jun 2019 18:38:07: 3000000 INFO @ Sun, 02 Jun 2019 18:38:09: 3000000 INFO @ Sun, 02 Jun 2019 18:38:12: 4000000 INFO @ Sun, 02 Jun 2019 18:38:14: 4000000 INFO @ Sun, 02 Jun 2019 18:38:17: 4000000 INFO @ Sun, 02 Jun 2019 18:38:19: 5000000 INFO @ Sun, 02 Jun 2019 18:38:21: 5000000 INFO @ Sun, 02 Jun 2019 18:38:25: 5000000 INFO @ Sun, 02 Jun 2019 18:38:26: 6000000 INFO @ Sun, 02 Jun 2019 18:38:28: 6000000 INFO @ Sun, 02 Jun 2019 18:38:33: 7000000 INFO @ Sun, 02 Jun 2019 18:38:34: 6000000 INFO @ Sun, 02 Jun 2019 18:38:35: 7000000 INFO @ Sun, 02 Jun 2019 18:38:40: 8000000 INFO @ Sun, 02 Jun 2019 18:38:42: 7000000 INFO @ Sun, 02 Jun 2019 18:38:42: 8000000 INFO @ Sun, 02 Jun 2019 18:38:47: 9000000 INFO @ Sun, 02 Jun 2019 18:38:49: 9000000 INFO @ Sun, 02 Jun 2019 18:38:50: 8000000 INFO @ Sun, 02 Jun 2019 18:38:54: 10000000 INFO @ Sun, 02 Jun 2019 18:38:56: 10000000 INFO @ Sun, 02 Jun 2019 18:38:58: 9000000 INFO @ Sun, 02 Jun 2019 18:39:01: 11000000 INFO @ Sun, 02 Jun 2019 18:39:04: 11000000 INFO @ Sun, 02 Jun 2019 18:39:06: 10000000 INFO @ Sun, 02 Jun 2019 18:39:08: 12000000 INFO @ Sun, 02 Jun 2019 18:39:11: 12000000 INFO @ Sun, 02 Jun 2019 18:39:14: 11000000 INFO @ Sun, 02 Jun 2019 18:39:15: 13000000 INFO @ Sun, 02 Jun 2019 18:39:18: 13000000 INFO @ Sun, 02 Jun 2019 18:39:21: 14000000 INFO @ Sun, 02 Jun 2019 18:39:22: 12000000 INFO @ Sun, 02 Jun 2019 18:39:24: 14000000 INFO @ Sun, 02 Jun 2019 18:39:28: 15000000 INFO @ Sun, 02 Jun 2019 18:39:30: 13000000 INFO @ Sun, 02 Jun 2019 18:39:31: 15000000 INFO @ Sun, 02 Jun 2019 18:39:35: 16000000 INFO @ Sun, 02 Jun 2019 18:39:38: 14000000 INFO @ Sun, 02 Jun 2019 18:39:38: 16000000 INFO @ Sun, 02 Jun 2019 18:39:42: 17000000 INFO @ Sun, 02 Jun 2019 18:39:45: 17000000 INFO @ Sun, 02 Jun 2019 18:39:46: 15000000 INFO @ Sun, 02 Jun 2019 18:39:49: 18000000 INFO @ Sun, 02 Jun 2019 18:39:52: 18000000 INFO @ Sun, 02 Jun 2019 18:39:54: 16000000 INFO @ Sun, 02 Jun 2019 18:39:56: 19000000 INFO @ Sun, 02 Jun 2019 18:40:00: 19000000 INFO @ Sun, 02 Jun 2019 18:40:02: 17000000 INFO @ Sun, 02 Jun 2019 18:40:03: 20000000 INFO @ Sun, 02 Jun 2019 18:40:07: 20000000 INFO @ Sun, 02 Jun 2019 18:40:10: 21000000 INFO @ Sun, 02 Jun 2019 18:40:10: 18000000 INFO @ Sun, 02 Jun 2019 18:40:14: 21000000 INFO @ Sun, 02 Jun 2019 18:40:17: 22000000 INFO @ Sun, 02 Jun 2019 18:40:18: 19000000 INFO @ Sun, 02 Jun 2019 18:40:21: 22000000 INFO @ Sun, 02 Jun 2019 18:40:23: 23000000 INFO @ Sun, 02 Jun 2019 18:40:26: 20000000 INFO @ Sun, 02 Jun 2019 18:40:28: 23000000 INFO @ Sun, 02 Jun 2019 18:40:30: 24000000 INFO @ Sun, 02 Jun 2019 18:40:34: 21000000 INFO @ Sun, 02 Jun 2019 18:40:35: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 18:40:35: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 18:40:35: #1 total tags in treatment: 24586093 INFO @ Sun, 02 Jun 2019 18:40:35: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:40:35: #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 18:40:35: 24000000 INFO @ Sun, 02 Jun 2019 18:40:35: #1 tags after filtering in treatment: 24586093 INFO @ Sun, 02 Jun 2019 18:40:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:40:35: #1 finished! INFO @ Sun, 02 Jun 2019 18:40:35: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:40:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:40:37: #2 number of paired peaks: 192 WARNING @ Sun, 02 Jun 2019 18:40:37: Fewer paired peaks (192) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 192 pairs to build model! INFO @ Sun, 02 Jun 2019 18:40:37: start model_add_line... INFO @ Sun, 02 Jun 2019 18:40:37: start X-correlation... INFO @ Sun, 02 Jun 2019 18:40:37: end of X-cor INFO @ Sun, 02 Jun 2019 18:40:37: #2 finished! INFO @ Sun, 02 Jun 2019 18:40:37: #2 predicted fragment length is 177 bps INFO @ Sun, 02 Jun 2019 18:40:37: #2 alternative fragment length(s) may be 2,78,177 bps INFO @ Sun, 02 Jun 2019 18:40:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3883435/SRX3883435.05_model.r INFO @ Sun, 02 Jun 2019 18:40:37: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:40:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:40:39: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 18:40:39: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 18:40:39: #1 total tags in treatment: 24586093 INFO @ Sun, 02 Jun 2019 18:40:39: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:40:39: #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 18:40:40: #1 tags after filtering in treatment: 24586093 INFO @ Sun, 02 Jun 2019 18:40:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:40:40: #1 finished! INFO @ Sun, 02 Jun 2019 18:40:40: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:40:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:40:42: 22000000 INFO @ Sun, 02 Jun 2019 18:40:42: #2 number of paired peaks: 192 WARNING @ Sun, 02 Jun 2019 18:40:42: Fewer paired peaks (192) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 192 pairs to build model! INFO @ Sun, 02 Jun 2019 18:40:42: start model_add_line... INFO @ Sun, 02 Jun 2019 18:40:42: start X-correlation... INFO @ Sun, 02 Jun 2019 18:40:42: end of X-cor INFO @ Sun, 02 Jun 2019 18:40:42: #2 finished! INFO @ Sun, 02 Jun 2019 18:40:42: #2 predicted fragment length is 177 bps INFO @ Sun, 02 Jun 2019 18:40:42: #2 alternative fragment length(s) may be 2,78,177 bps INFO @ Sun, 02 Jun 2019 18:40:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3883435/SRX3883435.20_model.r INFO @ Sun, 02 Jun 2019 18:40:42: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:40:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:40:49: 23000000 INFO @ Sun, 02 Jun 2019 18:40:57: 24000000 INFO @ Sun, 02 Jun 2019 18:41:01: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 18:41:01: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 18:41:01: #1 total tags in treatment: 24586093 INFO @ Sun, 02 Jun 2019 18:41:01: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:41:01: #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 18:41:02: #1 tags after filtering in treatment: 24586093 INFO @ Sun, 02 Jun 2019 18:41:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:41:02: #1 finished! INFO @ Sun, 02 Jun 2019 18:41:02: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:41:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:41:04: #2 number of paired peaks: 192 WARNING @ Sun, 02 Jun 2019 18:41:04: Fewer paired peaks (192) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 192 pairs to build model! INFO @ Sun, 02 Jun 2019 18:41:04: start model_add_line... INFO @ Sun, 02 Jun 2019 18:41:04: start X-correlation... INFO @ Sun, 02 Jun 2019 18:41:04: end of X-cor INFO @ Sun, 02 Jun 2019 18:41:04: #2 finished! INFO @ Sun, 02 Jun 2019 18:41:04: #2 predicted fragment length is 177 bps INFO @ Sun, 02 Jun 2019 18:41:04: #2 alternative fragment length(s) may be 2,78,177 bps INFO @ Sun, 02 Jun 2019 18:41:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3883435/SRX3883435.10_model.r INFO @ Sun, 02 Jun 2019 18:41:04: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:41:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:41:42: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:41:46: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:42:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3883435/SRX3883435.05_peaks.xls INFO @ Sun, 02 Jun 2019 18:42:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3883435/SRX3883435.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:42:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3883435/SRX3883435.05_summits.bed INFO @ Sun, 02 Jun 2019 18:42:09: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1875 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:42:09: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:42:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3883435/SRX3883435.20_peaks.xls INFO @ Sun, 02 Jun 2019 18:42:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3883435/SRX3883435.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:42:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3883435/SRX3883435.20_summits.bed INFO @ Sun, 02 Jun 2019 18:42:13: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (305 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:42:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3883435/SRX3883435.10_peaks.xls INFO @ Sun, 02 Jun 2019 18:42:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3883435/SRX3883435.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:42:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3883435/SRX3883435.10_summits.bed INFO @ Sun, 02 Jun 2019 18:42:36: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (840 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。