Job ID = 10480674 sra ファイルのダウンロード中... Completed: 508799K bytes transferred in 18 seconds (224373K 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 14778996 spots for /home/okishinya/chipatlas/results/dm3/SRX3009516/SRR5832217.sra Written 14778996 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: 00:05:31 14778996 reads; of these: 14778996 (100.00%) were unpaired; of these: 4813528 (32.57%) aligned 0 times 6689185 (45.26%) aligned exactly 1 time 3276283 (22.17%) aligned >1 times 67.43% overall alignment rate Time searching: 00:05:31 Overall time: 00:05:31 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] 2175800 / 9965468 = 0.2183 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 07:38:40: # Command line: callpeak -t SRX3009516.bam -f BAM -g dm -n SRX3009516.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3009516.20 # format = BAM # ChIP-seq file = ['SRX3009516.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 07:38:40: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:38:40: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:38:40: # Command line: callpeak -t SRX3009516.bam -f BAM -g dm -n SRX3009516.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3009516.05 # format = BAM # ChIP-seq file = ['SRX3009516.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 07:38:40: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:38:40: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:38:40: # Command line: callpeak -t SRX3009516.bam -f BAM -g dm -n SRX3009516.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3009516.10 # format = BAM # ChIP-seq file = ['SRX3009516.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 07:38:40: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:38:40: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:38:46: 1000000 INFO @ Fri, 16 Mar 2018 07:38:46: 1000000 INFO @ Fri, 16 Mar 2018 07:38:47: 1000000 INFO @ Fri, 16 Mar 2018 07:38:53: 2000000 INFO @ Fri, 16 Mar 2018 07:38:53: 2000000 INFO @ Fri, 16 Mar 2018 07:38:53: 2000000 INFO @ Fri, 16 Mar 2018 07:39:00: 3000000 INFO @ Fri, 16 Mar 2018 07:39:00: 3000000 INFO @ Fri, 16 Mar 2018 07:39:01: 3000000 INFO @ Fri, 16 Mar 2018 07:39:06: 4000000 INFO @ Fri, 16 Mar 2018 07:39:07: 4000000 INFO @ Fri, 16 Mar 2018 07:39:08: 4000000 INFO @ Fri, 16 Mar 2018 07:39:13: 5000000 INFO @ Fri, 16 Mar 2018 07:39:14: 5000000 INFO @ Fri, 16 Mar 2018 07:39:15: 5000000 INFO @ Fri, 16 Mar 2018 07:39:20: 6000000 INFO @ Fri, 16 Mar 2018 07:39:21: 6000000 INFO @ Fri, 16 Mar 2018 07:39:22: 6000000 INFO @ Fri, 16 Mar 2018 07:39:27: 7000000 INFO @ Fri, 16 Mar 2018 07:39:29: 7000000 INFO @ Fri, 16 Mar 2018 07:39:31: 7000000 INFO @ Fri, 16 Mar 2018 07:39:33: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:39:33: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:39:33: #1 total tags in treatment: 7789668 INFO @ Fri, 16 Mar 2018 07:39:33: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:39:33: #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 07:39:33: #1 tags after filtering in treatment: 7789668 INFO @ Fri, 16 Mar 2018 07:39:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:39:33: #1 finished! INFO @ Fri, 16 Mar 2018 07:39:33: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:39:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:39:34: #2 number of paired peaks: 756 WARNING @ Fri, 16 Mar 2018 07:39:34: Fewer paired peaks (756) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 756 pairs to build model! INFO @ Fri, 16 Mar 2018 07:39:34: start model_add_line... INFO @ Fri, 16 Mar 2018 07:39:34: start X-correlation... INFO @ Fri, 16 Mar 2018 07:39:34: end of X-cor INFO @ Fri, 16 Mar 2018 07:39:34: #2 finished! INFO @ Fri, 16 Mar 2018 07:39:34: #2 predicted fragment length is 56 bps INFO @ Fri, 16 Mar 2018 07:39:34: #2 alternative fragment length(s) may be 56 bps INFO @ Fri, 16 Mar 2018 07:39:34: #2.2 Generate R script for model : SRX3009516.20_model.r WARNING @ Fri, 16 Mar 2018 07:39:34: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Mar 2018 07:39:34: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Fri, 16 Mar 2018 07:39:34: #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 07:39:34: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:39:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:39:34: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:39:34: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:39:34: #1 total tags in treatment: 7789668 INFO @ Fri, 16 Mar 2018 07:39:34: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:39:34: #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 07:39:35: #1 tags after filtering in treatment: 7789668 INFO @ Fri, 16 Mar 2018 07:39:35: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:39:35: #1 finished! INFO @ Fri, 16 Mar 2018 07:39:35: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:39:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:39:35: #2 number of paired peaks: 756 WARNING @ Fri, 16 Mar 2018 07:39:35: Fewer paired peaks (756) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 756 pairs to build model! INFO @ Fri, 16 Mar 2018 07:39:35: start model_add_line... INFO @ Fri, 16 Mar 2018 07:39:35: start X-correlation... INFO @ Fri, 16 Mar 2018 07:39:35: end of X-cor INFO @ Fri, 16 Mar 2018 07:39:35: #2 finished! INFO @ Fri, 16 Mar 2018 07:39:35: #2 predicted fragment length is 56 bps INFO @ Fri, 16 Mar 2018 07:39:35: #2 alternative fragment length(s) may be 56 bps INFO @ Fri, 16 Mar 2018 07:39:35: #2.2 Generate R script for model : SRX3009516.10_model.r WARNING @ Fri, 16 Mar 2018 07:39:35: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Mar 2018 07:39:35: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Fri, 16 Mar 2018 07:39:35: #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 07:39:35: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:39:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:39:36: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:39:36: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:39:36: #1 total tags in treatment: 7789668 INFO @ Fri, 16 Mar 2018 07:39:36: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:39:36: #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 07:39:36: #1 tags after filtering in treatment: 7789668 INFO @ Fri, 16 Mar 2018 07:39:36: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:39:36: #1 finished! INFO @ Fri, 16 Mar 2018 07:39:36: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:39:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:39:37: #2 number of paired peaks: 756 WARNING @ Fri, 16 Mar 2018 07:39:37: Fewer paired peaks (756) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 756 pairs to build model! INFO @ Fri, 16 Mar 2018 07:39:37: start model_add_line... INFO @ Fri, 16 Mar 2018 07:39:37: start X-correlation... INFO @ Fri, 16 Mar 2018 07:39:37: end of X-cor INFO @ Fri, 16 Mar 2018 07:39:37: #2 finished! INFO @ Fri, 16 Mar 2018 07:39:37: #2 predicted fragment length is 56 bps INFO @ Fri, 16 Mar 2018 07:39:37: #2 alternative fragment length(s) may be 56 bps INFO @ Fri, 16 Mar 2018 07:39:37: #2.2 Generate R script for model : SRX3009516.05_model.r WARNING @ Fri, 16 Mar 2018 07:39:37: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Mar 2018 07:39:37: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Fri, 16 Mar 2018 07:39:37: #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 07:39:37: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:39:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:39:51: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:39:52: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:39:53: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:40:01: #4 Write output xls file... SRX3009516.20_peaks.xls INFO @ Fri, 16 Mar 2018 07:40:01: #4 Write peak in narrowPeak format file... SRX3009516.20_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:40:01: #4 Write summits bed file... SRX3009516.20_summits.bed INFO @ Fri, 16 Mar 2018 07:40:01: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1000 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:40:03: #4 Write output xls file... SRX3009516.10_peaks.xls INFO @ Fri, 16 Mar 2018 07:40:03: #4 Write peak in narrowPeak format file... SRX3009516.10_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:40:03: #4 Write summits bed file... SRX3009516.10_summits.bed INFO @ Fri, 16 Mar 2018 07:40:03: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1455 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:40:03: #4 Write output xls file... SRX3009516.05_peaks.xls INFO @ Fri, 16 Mar 2018 07:40:03: #4 Write peak in narrowPeak format file... SRX3009516.05_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:40:03: #4 Write summits bed file... SRX3009516.05_summits.bed INFO @ Fri, 16 Mar 2018 07:40:03: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2762 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。