Job ID = 10714418 sra ファイルのダウンロード中... Completed: 379044K bytes transferred in 30 seconds (100287K bits/sec), in 1 file. sra ファイルのダウンロードが完了しました。 Read layout: SINGLE fastq に変換中... Read 17374970 spots for /home/okishinya/chipatlas/results/ce10/SRX4082378/SRR7164196.sra Written 17374970 spots for /home/okishinya/chipatlas/results/ce10/SRX4082378/SRR7164196.sra rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません 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: 00:04:39 17374970 reads; of these: 17374970 (100.00%) were unpaired; of these: 521417 (3.00%) aligned 0 times 12894853 (74.22%) aligned exactly 1 time 3958700 (22.78%) aligned >1 times 97.00% overall alignment rate Time searching: 00:04:39 Overall time: 00:04:39 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 8 files... [bam_rmdupse_core] 2934037 / 16853553 = 0.1741 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, 03 Jun 2018 12:39:05: # Command line: callpeak -t SRX4082378.bam -f BAM -g ce -n SRX4082378.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4082378.10 # format = BAM # ChIP-seq file = ['SRX4082378.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, 03 Jun 2018 12:39:05: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:39:05: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:39:05: # Command line: callpeak -t SRX4082378.bam -f BAM -g ce -n SRX4082378.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4082378.05 # format = BAM # ChIP-seq file = ['SRX4082378.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, 03 Jun 2018 12:39:05: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:39:05: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:39:05: # Command line: callpeak -t SRX4082378.bam -f BAM -g ce -n SRX4082378.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4082378.20 # format = BAM # ChIP-seq file = ['SRX4082378.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, 03 Jun 2018 12:39:05: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:39:05: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:39:13: 1000000 INFO @ Sun, 03 Jun 2018 12:39:13: 1000000 INFO @ Sun, 03 Jun 2018 12:39:13: 1000000 INFO @ Sun, 03 Jun 2018 12:39:21: 2000000 INFO @ Sun, 03 Jun 2018 12:39:21: 2000000 INFO @ Sun, 03 Jun 2018 12:39:21: 2000000 INFO @ Sun, 03 Jun 2018 12:39:30: 3000000 INFO @ Sun, 03 Jun 2018 12:39:30: 3000000 INFO @ Sun, 03 Jun 2018 12:39:30: 3000000 INFO @ Sun, 03 Jun 2018 12:39:38: 4000000 INFO @ Sun, 03 Jun 2018 12:39:38: 4000000 INFO @ Sun, 03 Jun 2018 12:39:38: 4000000 INFO @ Sun, 03 Jun 2018 12:39:46: 5000000 INFO @ Sun, 03 Jun 2018 12:39:46: 5000000 INFO @ Sun, 03 Jun 2018 12:39:46: 5000000 INFO @ Sun, 03 Jun 2018 12:39:54: 6000000 INFO @ Sun, 03 Jun 2018 12:39:54: 6000000 INFO @ Sun, 03 Jun 2018 12:39:54: 6000000 INFO @ Sun, 03 Jun 2018 12:40:02: 7000000 INFO @ Sun, 03 Jun 2018 12:40:02: 7000000 INFO @ Sun, 03 Jun 2018 12:40:02: 7000000 INFO @ Sun, 03 Jun 2018 12:40:10: 8000000 INFO @ Sun, 03 Jun 2018 12:40:10: 8000000 INFO @ Sun, 03 Jun 2018 12:40:10: 8000000 INFO @ Sun, 03 Jun 2018 12:40:18: 9000000 INFO @ Sun, 03 Jun 2018 12:40:18: 9000000 INFO @ Sun, 03 Jun 2018 12:40:18: 9000000 INFO @ Sun, 03 Jun 2018 12:40:27: 10000000 INFO @ Sun, 03 Jun 2018 12:40:27: 10000000 INFO @ Sun, 03 Jun 2018 12:40:27: 10000000 INFO @ Sun, 03 Jun 2018 12:40:35: 11000000 INFO @ Sun, 03 Jun 2018 12:40:35: 11000000 INFO @ Sun, 03 Jun 2018 12:40:35: 11000000 INFO @ Sun, 03 Jun 2018 12:40:42: 12000000 INFO @ Sun, 03 Jun 2018 12:40:42: 12000000 INFO @ Sun, 03 Jun 2018 12:40:42: 12000000 INFO @ Sun, 03 Jun 2018 12:40:50: 13000000 INFO @ Sun, 03 Jun 2018 12:40:50: 13000000 INFO @ Sun, 03 Jun 2018 12:40:50: 13000000 INFO @ Sun, 03 Jun 2018 12:40:56: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 12:40:56: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 12:40:56: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 12:40:56: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 12:40:56: #1 total tags in treatment: 13919516 INFO @ Sun, 03 Jun 2018 12:40:56: #1 total tags in treatment: 13919516 INFO @ Sun, 03 Jun 2018 12:40:56: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:40:56: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:40:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 12:40:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 12:40:56: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 12:40:56: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 12:40:56: #1 total tags in treatment: 13919516 INFO @ Sun, 03 Jun 2018 12:40:56: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:40:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 12:40:57: #1 tags after filtering in treatment: 13919516 INFO @ Sun, 03 Jun 2018 12:40:57: #1 tags after filtering in treatment: 13919516 INFO @ Sun, 03 Jun 2018 12:40:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:40:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:40:57: #1 finished! INFO @ Sun, 03 Jun 2018 12:40:57: #1 finished! INFO @ Sun, 03 Jun 2018 12:40:57: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:40:57: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:40:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:40:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:40:57: #1 tags after filtering in treatment: 13919516 INFO @ Sun, 03 Jun 2018 12:40:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:40:57: #1 finished! INFO @ Sun, 03 Jun 2018 12:40:57: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:40:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:40:58: #2 number of paired peaks: 396 WARNING @ Sun, 03 Jun 2018 12:40:58: Fewer paired peaks (396) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 396 pairs to build model! INFO @ Sun, 03 Jun 2018 12:40:58: start model_add_line... INFO @ Sun, 03 Jun 2018 12:40:58: #2 number of paired peaks: 396 WARNING @ Sun, 03 Jun 2018 12:40:58: Fewer paired peaks (396) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 396 pairs to build model! INFO @ Sun, 03 Jun 2018 12:40:58: start model_add_line... INFO @ Sun, 03 Jun 2018 12:40:58: #2 number of paired peaks: 396 WARNING @ Sun, 03 Jun 2018 12:40:58: Fewer paired peaks (396) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 396 pairs to build model! INFO @ Sun, 03 Jun 2018 12:40:58: start model_add_line... INFO @ Sun, 03 Jun 2018 12:40:58: start X-correlation... INFO @ Sun, 03 Jun 2018 12:40:58: end of X-cor INFO @ Sun, 03 Jun 2018 12:40:58: #2 finished! INFO @ Sun, 03 Jun 2018 12:40:58: #2 predicted fragment length is 39 bps INFO @ Sun, 03 Jun 2018 12:40:58: #2 alternative fragment length(s) may be 2,39 bps INFO @ Sun, 03 Jun 2018 12:40:58: #2.2 Generate R script for model : SRX4082378.20_model.r INFO @ Sun, 03 Jun 2018 12:40:58: start X-correlation... WARNING @ Sun, 03 Jun 2018 12:40:58: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 12:40:58: #2 You may need to consider one of the other alternative d(s): 2,39 WARNING @ Sun, 03 Jun 2018 12:40:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 12:40:58: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:40:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:40:58: end of X-cor INFO @ Sun, 03 Jun 2018 12:40:58: #2 finished! INFO @ Sun, 03 Jun 2018 12:40:58: #2 predicted fragment length is 39 bps INFO @ Sun, 03 Jun 2018 12:40:58: #2 alternative fragment length(s) may be 2,39 bps INFO @ Sun, 03 Jun 2018 12:40:58: #2.2 Generate R script for model : SRX4082378.10_model.r WARNING @ Sun, 03 Jun 2018 12:40:58: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 12:40:58: #2 You may need to consider one of the other alternative d(s): 2,39 WARNING @ Sun, 03 Jun 2018 12:40:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 12:40:58: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:40:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:40:58: start X-correlation... INFO @ Sun, 03 Jun 2018 12:40:58: end of X-cor INFO @ Sun, 03 Jun 2018 12:40:58: #2 finished! INFO @ Sun, 03 Jun 2018 12:40:58: #2 predicted fragment length is 39 bps INFO @ Sun, 03 Jun 2018 12:40:58: #2 alternative fragment length(s) may be 2,39 bps INFO @ Sun, 03 Jun 2018 12:40:58: #2.2 Generate R script for model : SRX4082378.05_model.r WARNING @ Sun, 03 Jun 2018 12:40:58: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 12:40:58: #2 You may need to consider one of the other alternative d(s): 2,39 WARNING @ Sun, 03 Jun 2018 12:40:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 12:40:58: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:40:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:41:25: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:41:27: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:41:27: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:41:42: #4 Write output xls file... SRX4082378.20_peaks.xls INFO @ Sun, 03 Jun 2018 12:41:42: #4 Write peak in narrowPeak format file... SRX4082378.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:41:42: #4 Write summits bed file... SRX4082378.20_summits.bed INFO @ Sun, 03 Jun 2018 12:41:42: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (126 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:41:42: #4 Write output xls file... SRX4082378.10_peaks.xls INFO @ Sun, 03 Jun 2018 12:41:42: #4 Write peak in narrowPeak format file... SRX4082378.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:41:42: #4 Write summits bed file... SRX4082378.10_summits.bed INFO @ Sun, 03 Jun 2018 12:41:42: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (431 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:41:44: #4 Write output xls file... SRX4082378.05_peaks.xls INFO @ Sun, 03 Jun 2018 12:41:44: #4 Write peak in narrowPeak format file... SRX4082378.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:41:44: #4 Write summits bed file... SRX4082378.05_summits.bed INFO @ Sun, 03 Jun 2018 12:41:44: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (893 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。