Job ID = 10480733 sra ファイルのダウンロード中... Completed: 462034K bytes transferred in 16 seconds (233403K 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 15653947 spots for /home/okishinya/chipatlas/results/dm3/SRX3380792/SRR6278155.sra Written 15653947 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: 00:06:17 15653947 reads; of these: 15653947 (100.00%) were unpaired; of these: 509846 (3.26%) aligned 0 times 11067926 (70.70%) aligned exactly 1 time 4076175 (26.04%) aligned >1 times 96.74% overall alignment rate Time searching: 00:06:17 Overall time: 00:06:17 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1340266 / 15144101 = 0.0885 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 @ Fri, 16 Mar 2018 07:56:11: # Command line: callpeak -t SRX3380792.bam -f BAM -g dm -n SRX3380792.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3380792.10 # format = BAM # ChIP-seq file = ['SRX3380792.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Fri, 16 Mar 2018 07:56:11: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:56:11: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:56:11: # Command line: callpeak -t SRX3380792.bam -f BAM -g dm -n SRX3380792.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3380792.20 # format = BAM # ChIP-seq file = ['SRX3380792.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Fri, 16 Mar 2018 07:56:11: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:56:11: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:56:11: # Command line: callpeak -t SRX3380792.bam -f BAM -g dm -n SRX3380792.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3380792.05 # format = BAM # ChIP-seq file = ['SRX3380792.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Fri, 16 Mar 2018 07:56:11: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:56:11: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:56:17: 1000000 INFO @ Fri, 16 Mar 2018 07:56:17: 1000000 INFO @ Fri, 16 Mar 2018 07:56:17: 1000000 INFO @ Fri, 16 Mar 2018 07:56:23: 2000000 INFO @ Fri, 16 Mar 2018 07:56:23: 2000000 INFO @ Fri, 16 Mar 2018 07:56:23: 2000000 INFO @ Fri, 16 Mar 2018 07:56:28: 3000000 INFO @ Fri, 16 Mar 2018 07:56:29: 3000000 INFO @ Fri, 16 Mar 2018 07:56:29: 3000000 INFO @ Fri, 16 Mar 2018 07:56:34: 4000000 INFO @ Fri, 16 Mar 2018 07:56:35: 4000000 INFO @ Fri, 16 Mar 2018 07:56:36: 4000000 INFO @ Fri, 16 Mar 2018 07:56:40: 5000000 INFO @ Fri, 16 Mar 2018 07:56:42: 5000000 INFO @ Fri, 16 Mar 2018 07:56:43: 5000000 INFO @ Fri, 16 Mar 2018 07:56:46: 6000000 INFO @ Fri, 16 Mar 2018 07:56:48: 6000000 INFO @ Fri, 16 Mar 2018 07:56:49: 6000000 INFO @ Fri, 16 Mar 2018 07:56:52: 7000000 INFO @ Fri, 16 Mar 2018 07:56:54: 7000000 INFO @ Fri, 16 Mar 2018 07:56:55: 7000000 INFO @ Fri, 16 Mar 2018 07:56:58: 8000000 INFO @ Fri, 16 Mar 2018 07:57:00: 8000000 INFO @ Fri, 16 Mar 2018 07:57:02: 8000000 INFO @ Fri, 16 Mar 2018 07:57:04: 9000000 INFO @ Fri, 16 Mar 2018 07:57:07: 9000000 INFO @ Fri, 16 Mar 2018 07:57:08: 9000000 INFO @ Fri, 16 Mar 2018 07:57:10: 10000000 INFO @ Fri, 16 Mar 2018 07:57:13: 10000000 INFO @ Fri, 16 Mar 2018 07:57:15: 10000000 INFO @ Fri, 16 Mar 2018 07:57:15: 11000000 INFO @ Fri, 16 Mar 2018 07:57:19: 11000000 INFO @ Fri, 16 Mar 2018 07:57:21: 12000000 INFO @ Fri, 16 Mar 2018 07:57:22: 11000000 INFO @ Fri, 16 Mar 2018 07:57:25: 12000000 INFO @ Fri, 16 Mar 2018 07:57:27: 13000000 INFO @ Fri, 16 Mar 2018 07:57:28: 12000000 INFO @ Fri, 16 Mar 2018 07:57:32: 13000000 INFO @ Fri, 16 Mar 2018 07:57:32: #1 tag size is determined as 50 bps INFO @ Fri, 16 Mar 2018 07:57:32: #1 tag size = 50 INFO @ Fri, 16 Mar 2018 07:57:32: #1 total tags in treatment: 13803835 INFO @ Fri, 16 Mar 2018 07:57:32: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:57:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:57:32: #1 tags after filtering in treatment: 13803835 INFO @ Fri, 16 Mar 2018 07:57:32: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:57:32: #1 finished! INFO @ Fri, 16 Mar 2018 07:57:32: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:57:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:57:34: #2 number of paired peaks: 141 WARNING @ Fri, 16 Mar 2018 07:57:34: Fewer paired peaks (141) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 141 pairs to build model! INFO @ Fri, 16 Mar 2018 07:57:34: start model_add_line... INFO @ Fri, 16 Mar 2018 07:57:34: start X-correlation... INFO @ Fri, 16 Mar 2018 07:57:34: end of X-cor INFO @ Fri, 16 Mar 2018 07:57:34: #2 finished! INFO @ Fri, 16 Mar 2018 07:57:34: #2 predicted fragment length is 47 bps INFO @ Fri, 16 Mar 2018 07:57:34: #2 alternative fragment length(s) may be 47 bps INFO @ Fri, 16 Mar 2018 07:57:34: #2.2 Generate R script for model : SRX3380792.10_model.r WARNING @ Fri, 16 Mar 2018 07:57:34: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Mar 2018 07:57:34: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Fri, 16 Mar 2018 07:57:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 16 Mar 2018 07:57:34: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:57:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:57:35: 13000000 INFO @ Fri, 16 Mar 2018 07:57:37: #1 tag size is determined as 50 bps INFO @ Fri, 16 Mar 2018 07:57:37: #1 tag size = 50 INFO @ Fri, 16 Mar 2018 07:57:37: #1 total tags in treatment: 13803835 INFO @ Fri, 16 Mar 2018 07:57:37: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:57:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:57:37: #1 tags after filtering in treatment: 13803835 INFO @ Fri, 16 Mar 2018 07:57:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:57:37: #1 finished! INFO @ Fri, 16 Mar 2018 07:57:37: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:57:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:57:38: #2 number of paired peaks: 141 WARNING @ Fri, 16 Mar 2018 07:57:38: Fewer paired peaks (141) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 141 pairs to build model! INFO @ Fri, 16 Mar 2018 07:57:38: start model_add_line... INFO @ Fri, 16 Mar 2018 07:57:38: start X-correlation... INFO @ Fri, 16 Mar 2018 07:57:38: end of X-cor INFO @ Fri, 16 Mar 2018 07:57:38: #2 finished! INFO @ Fri, 16 Mar 2018 07:57:38: #2 predicted fragment length is 47 bps INFO @ Fri, 16 Mar 2018 07:57:38: #2 alternative fragment length(s) may be 47 bps INFO @ Fri, 16 Mar 2018 07:57:38: #2.2 Generate R script for model : SRX3380792.20_model.r WARNING @ Fri, 16 Mar 2018 07:57:38: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Mar 2018 07:57:38: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Fri, 16 Mar 2018 07:57:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 16 Mar 2018 07:57:38: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:57:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:57:40: #1 tag size is determined as 50 bps INFO @ Fri, 16 Mar 2018 07:57:40: #1 tag size = 50 INFO @ Fri, 16 Mar 2018 07:57:40: #1 total tags in treatment: 13803835 INFO @ Fri, 16 Mar 2018 07:57:40: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:57:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:57:40: #1 tags after filtering in treatment: 13803835 INFO @ Fri, 16 Mar 2018 07:57:40: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:57:40: #1 finished! INFO @ Fri, 16 Mar 2018 07:57:40: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:57:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:57:41: #2 number of paired peaks: 141 WARNING @ Fri, 16 Mar 2018 07:57:41: Fewer paired peaks (141) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 141 pairs to build model! INFO @ Fri, 16 Mar 2018 07:57:41: start model_add_line... INFO @ Fri, 16 Mar 2018 07:57:41: start X-correlation... INFO @ Fri, 16 Mar 2018 07:57:41: end of X-cor INFO @ Fri, 16 Mar 2018 07:57:41: #2 finished! INFO @ Fri, 16 Mar 2018 07:57:41: #2 predicted fragment length is 47 bps INFO @ Fri, 16 Mar 2018 07:57:41: #2 alternative fragment length(s) may be 47 bps INFO @ Fri, 16 Mar 2018 07:57:41: #2.2 Generate R script for model : SRX3380792.05_model.r WARNING @ Fri, 16 Mar 2018 07:57:41: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Mar 2018 07:57:41: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Fri, 16 Mar 2018 07:57:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 16 Mar 2018 07:57:41: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:57:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:58:01: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:58:08: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:58:09: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:58:15: #4 Write output xls file... SRX3380792.10_peaks.xls INFO @ Fri, 16 Mar 2018 07:58:15: #4 Write peak in narrowPeak format file... SRX3380792.10_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:58:15: #4 Write summits bed file... SRX3380792.10_summits.bed INFO @ Fri, 16 Mar 2018 07:58:15: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1275 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:58:23: #4 Write output xls file... SRX3380792.20_peaks.xls INFO @ Fri, 16 Mar 2018 07:58:23: #4 Write peak in narrowPeak format file... SRX3380792.20_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:58:23: #4 Write summits bed file... SRX3380792.20_summits.bed INFO @ Fri, 16 Mar 2018 07:58:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (938 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:58:24: #4 Write output xls file... SRX3380792.05_peaks.xls INFO @ Fri, 16 Mar 2018 07:58:24: #4 Write peak in narrowPeak format file... SRX3380792.05_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:58:24: #4 Write summits bed file... SRX3380792.05_summits.bed INFO @ Fri, 16 Mar 2018 07:58:24: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1527 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。