Job ID = 10320318 sra ファイルのダウンロード中... Completed: 325952K bytes transferred in 46 seconds (57803K 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... Written 11528619 spots for /home/okishinya/chipatlas/results/ce10/SRX3043409/SRR5875893.sra Written 11528619 spots total 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: 00:04:07 11528619 reads; of these: 11528619 (100.00%) were unpaired; of these: 123565 (1.07%) aligned 0 times 9685634 (84.01%) aligned exactly 1 time 1719420 (14.91%) aligned >1 times 98.93% overall alignment rate Time searching: 00:04:07 Overall time: 00:04:07 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] 1063656 / 11405054 = 0.0933 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 @ Thu, 11 Jan 2018 02:12:46: # Command line: callpeak -t SRX3043409.bam -f BAM -g ce -n SRX3043409.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3043409.10 # format = BAM # ChIP-seq file = ['SRX3043409.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, 11 Jan 2018 02:12:46: # Command line: callpeak -t SRX3043409.bam -f BAM -g ce -n SRX3043409.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3043409.20 # format = BAM # ChIP-seq file = ['SRX3043409.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, 11 Jan 2018 02:12:46: # Command line: callpeak -t SRX3043409.bam -f BAM -g ce -n SRX3043409.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3043409.05 # format = BAM # ChIP-seq file = ['SRX3043409.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, 11 Jan 2018 02:12:46: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:12:46: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:12:46: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:12:46: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:12:46: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:12:46: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:12:53: 1000000 INFO @ Thu, 11 Jan 2018 02:12:53: 1000000 INFO @ Thu, 11 Jan 2018 02:12:53: 1000000 INFO @ Thu, 11 Jan 2018 02:13:00: 2000000 INFO @ Thu, 11 Jan 2018 02:13:00: 2000000 INFO @ Thu, 11 Jan 2018 02:13:00: 2000000 INFO @ Thu, 11 Jan 2018 02:13:07: 3000000 INFO @ Thu, 11 Jan 2018 02:13:07: 3000000 INFO @ Thu, 11 Jan 2018 02:13:07: 3000000 INFO @ Thu, 11 Jan 2018 02:13:14: 4000000 INFO @ Thu, 11 Jan 2018 02:13:14: 4000000 INFO @ Thu, 11 Jan 2018 02:13:14: 4000000 INFO @ Thu, 11 Jan 2018 02:13:21: 5000000 INFO @ Thu, 11 Jan 2018 02:13:21: 5000000 INFO @ Thu, 11 Jan 2018 02:13:22: 5000000 INFO @ Thu, 11 Jan 2018 02:13:27: 6000000 INFO @ Thu, 11 Jan 2018 02:13:28: 6000000 INFO @ Thu, 11 Jan 2018 02:13:29: 6000000 INFO @ Thu, 11 Jan 2018 02:13:34: 7000000 INFO @ Thu, 11 Jan 2018 02:13:35: 7000000 INFO @ Thu, 11 Jan 2018 02:13:37: 7000000 INFO @ Thu, 11 Jan 2018 02:13:41: 8000000 INFO @ Thu, 11 Jan 2018 02:13:42: 8000000 INFO @ Thu, 11 Jan 2018 02:13:44: 8000000 INFO @ Thu, 11 Jan 2018 02:13:48: 9000000 INFO @ Thu, 11 Jan 2018 02:13:50: 9000000 INFO @ Thu, 11 Jan 2018 02:13:51: 9000000 INFO @ Thu, 11 Jan 2018 02:13:55: 10000000 INFO @ Thu, 11 Jan 2018 02:13:57: 10000000 INFO @ Thu, 11 Jan 2018 02:13:57: #1 tag size is determined as 50 bps INFO @ Thu, 11 Jan 2018 02:13:57: #1 tag size = 50 INFO @ Thu, 11 Jan 2018 02:13:57: #1 total tags in treatment: 10341398 INFO @ Thu, 11 Jan 2018 02:13:57: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:13:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 11 Jan 2018 02:13:57: #1 tags after filtering in treatment: 10341398 INFO @ Thu, 11 Jan 2018 02:13:57: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 11 Jan 2018 02:13:57: #1 finished! INFO @ Thu, 11 Jan 2018 02:13:57: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:13:57: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:13:58: #2 number of paired peaks: 181 WARNING @ Thu, 11 Jan 2018 02:13:58: Fewer paired peaks (181) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 181 pairs to build model! INFO @ Thu, 11 Jan 2018 02:13:58: start model_add_line... INFO @ Thu, 11 Jan 2018 02:13:58: start X-correlation... INFO @ Thu, 11 Jan 2018 02:13:58: end of X-cor INFO @ Thu, 11 Jan 2018 02:13:58: #2 finished! INFO @ Thu, 11 Jan 2018 02:13:58: #2 predicted fragment length is 51 bps INFO @ Thu, 11 Jan 2018 02:13:58: #2 alternative fragment length(s) may be 2,51,537,583 bps INFO @ Thu, 11 Jan 2018 02:13:58: #2.2 Generate R script for model : SRX3043409.20_model.r WARNING @ Thu, 11 Jan 2018 02:13:58: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 11 Jan 2018 02:13:58: #2 You may need to consider one of the other alternative d(s): 2,51,537,583 WARNING @ Thu, 11 Jan 2018 02:13:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 11 Jan 2018 02:13:58: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:13:58: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 02:13:59: 10000000 INFO @ Thu, 11 Jan 2018 02:13:59: #1 tag size is determined as 50 bps INFO @ Thu, 11 Jan 2018 02:13:59: #1 tag size = 50 INFO @ Thu, 11 Jan 2018 02:13:59: #1 total tags in treatment: 10341398 INFO @ Thu, 11 Jan 2018 02:13:59: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:13:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 11 Jan 2018 02:13:59: #1 tags after filtering in treatment: 10341398 INFO @ Thu, 11 Jan 2018 02:13:59: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 11 Jan 2018 02:13:59: #1 finished! INFO @ Thu, 11 Jan 2018 02:13:59: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:13:59: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:14:00: #2 number of paired peaks: 181 WARNING @ Thu, 11 Jan 2018 02:14:00: Fewer paired peaks (181) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 181 pairs to build model! INFO @ Thu, 11 Jan 2018 02:14:00: start model_add_line... INFO @ Thu, 11 Jan 2018 02:14:00: start X-correlation... INFO @ Thu, 11 Jan 2018 02:14:00: end of X-cor INFO @ Thu, 11 Jan 2018 02:14:00: #2 finished! INFO @ Thu, 11 Jan 2018 02:14:00: #2 predicted fragment length is 51 bps INFO @ Thu, 11 Jan 2018 02:14:00: #2 alternative fragment length(s) may be 2,51,537,583 bps INFO @ Thu, 11 Jan 2018 02:14:00: #2.2 Generate R script for model : SRX3043409.10_model.r WARNING @ Thu, 11 Jan 2018 02:14:00: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 11 Jan 2018 02:14:00: #2 You may need to consider one of the other alternative d(s): 2,51,537,583 WARNING @ Thu, 11 Jan 2018 02:14:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 11 Jan 2018 02:14:00: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:14:00: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 02:14:01: #1 tag size is determined as 50 bps INFO @ Thu, 11 Jan 2018 02:14:01: #1 tag size = 50 INFO @ Thu, 11 Jan 2018 02:14:01: #1 total tags in treatment: 10341398 INFO @ Thu, 11 Jan 2018 02:14:01: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:14:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 11 Jan 2018 02:14:01: #1 tags after filtering in treatment: 10341398 INFO @ Thu, 11 Jan 2018 02:14:01: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 11 Jan 2018 02:14:01: #1 finished! INFO @ Thu, 11 Jan 2018 02:14:01: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:14:01: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:14:02: #2 number of paired peaks: 181 WARNING @ Thu, 11 Jan 2018 02:14:02: Fewer paired peaks (181) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 181 pairs to build model! INFO @ Thu, 11 Jan 2018 02:14:02: start model_add_line... INFO @ Thu, 11 Jan 2018 02:14:02: start X-correlation... INFO @ Thu, 11 Jan 2018 02:14:02: end of X-cor INFO @ Thu, 11 Jan 2018 02:14:02: #2 finished! INFO @ Thu, 11 Jan 2018 02:14:02: #2 predicted fragment length is 51 bps INFO @ Thu, 11 Jan 2018 02:14:02: #2 alternative fragment length(s) may be 2,51,537,583 bps INFO @ Thu, 11 Jan 2018 02:14:02: #2.2 Generate R script for model : SRX3043409.05_model.r WARNING @ Thu, 11 Jan 2018 02:14:02: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 11 Jan 2018 02:14:02: #2 You may need to consider one of the other alternative d(s): 2,51,537,583 WARNING @ Thu, 11 Jan 2018 02:14:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 11 Jan 2018 02:14:02: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:14:02: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 02:14:21: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 02:14:21: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 02:14:24: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 02:14:32: #4 Write output xls file... SRX3043409.20_peaks.xls INFO @ Thu, 11 Jan 2018 02:14:32: #4 Write peak in narrowPeak format file... SRX3043409.20_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 02:14:32: #4 Write output xls file... SRX3043409.10_peaks.xls INFO @ Thu, 11 Jan 2018 02:14:32: #4 Write peak in narrowPeak format file... SRX3043409.10_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 02:14:32: #4 Write summits bed file... SRX3043409.10_summits.bed INFO @ Thu, 11 Jan 2018 02:14:32: Done! INFO @ Thu, 11 Jan 2018 02:14:32: #4 Write summits bed file... SRX3043409.20_summits.bed INFO @ Thu, 11 Jan 2018 02:14:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (97 records, 4 fields): 2 millis CompletedMACS2peakCalling pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (287 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 11 Jan 2018 02:14:36: #4 Write output xls file... SRX3043409.05_peaks.xls INFO @ Thu, 11 Jan 2018 02:14:36: #4 Write peak in narrowPeak format file... SRX3043409.05_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 02:14:36: #4 Write summits bed file... SRX3043409.05_summits.bed INFO @ Thu, 11 Jan 2018 02:14:36: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (517 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。