Job ID = 11170878 sra ファイルのダウンロード中... Completed: 473964K bytes transferred in 49 seconds (78440K 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 16902415 spots for /home/okishinya/chipatlas/results/ce10/SRX3942558/SRR7010079.sra Written 16902415 spots for /home/okishinya/chipatlas/results/ce10/SRX3942558/SRR7010079.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: 00:06:38 16902415 reads; of these: 16902415 (100.00%) were unpaired; of these: 1403427 (8.30%) aligned 0 times 12522680 (74.09%) aligned exactly 1 time 2976308 (17.61%) aligned >1 times 91.70% overall alignment rate Time searching: 00:06:38 Overall time: 00:06:38 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] 2966533 / 15498988 = 0.1914 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 @ Sat, 08 Sep 2018 11:37:56: # Command line: callpeak -t SRX3942558.bam -f BAM -g ce -n SRX3942558.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3942558.10 # format = BAM # ChIP-seq file = ['SRX3942558.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 @ Sat, 08 Sep 2018 11:37:56: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:37:56: # Command line: callpeak -t SRX3942558.bam -f BAM -g ce -n SRX3942558.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3942558.05 # format = BAM # ChIP-seq file = ['SRX3942558.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 @ Sat, 08 Sep 2018 11:37:56: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:37:56: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:37:56: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:37:56: # Command line: callpeak -t SRX3942558.bam -f BAM -g ce -n SRX3942558.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3942558.20 # format = BAM # ChIP-seq file = ['SRX3942558.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 @ Sat, 08 Sep 2018 11:37:56: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:37:56: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:38:03: 1000000 INFO @ Sat, 08 Sep 2018 11:38:03: 1000000 INFO @ Sat, 08 Sep 2018 11:38:04: 1000000 INFO @ Sat, 08 Sep 2018 11:38:10: 2000000 INFO @ Sat, 08 Sep 2018 11:38:10: 2000000 INFO @ Sat, 08 Sep 2018 11:38:11: 2000000 INFO @ Sat, 08 Sep 2018 11:38:17: 3000000 INFO @ Sat, 08 Sep 2018 11:38:18: 3000000 INFO @ Sat, 08 Sep 2018 11:38:18: 3000000 INFO @ Sat, 08 Sep 2018 11:38:24: 4000000 INFO @ Sat, 08 Sep 2018 11:38:25: 4000000 INFO @ Sat, 08 Sep 2018 11:38:25: 4000000 INFO @ Sat, 08 Sep 2018 11:38:31: 5000000 INFO @ Sat, 08 Sep 2018 11:38:32: 5000000 INFO @ Sat, 08 Sep 2018 11:38:32: 5000000 INFO @ Sat, 08 Sep 2018 11:38:38: 6000000 INFO @ Sat, 08 Sep 2018 11:38:39: 6000000 INFO @ Sat, 08 Sep 2018 11:38:39: 6000000 INFO @ Sat, 08 Sep 2018 11:38:45: 7000000 INFO @ Sat, 08 Sep 2018 11:38:46: 7000000 INFO @ Sat, 08 Sep 2018 11:38:46: 7000000 INFO @ Sat, 08 Sep 2018 11:38:52: 8000000 INFO @ Sat, 08 Sep 2018 11:38:53: 8000000 INFO @ Sat, 08 Sep 2018 11:38:54: 8000000 INFO @ Sat, 08 Sep 2018 11:38:59: 9000000 INFO @ Sat, 08 Sep 2018 11:39:00: 9000000 INFO @ Sat, 08 Sep 2018 11:39:01: 9000000 INFO @ Sat, 08 Sep 2018 11:39:07: 10000000 INFO @ Sat, 08 Sep 2018 11:39:07: 10000000 INFO @ Sat, 08 Sep 2018 11:39:08: 10000000 INFO @ Sat, 08 Sep 2018 11:39:14: 11000000 INFO @ Sat, 08 Sep 2018 11:39:14: 11000000 INFO @ Sat, 08 Sep 2018 11:39:15: 11000000 INFO @ Sat, 08 Sep 2018 11:39:21: 12000000 INFO @ Sat, 08 Sep 2018 11:39:21: 12000000 INFO @ Sat, 08 Sep 2018 11:39:23: 12000000 INFO @ Sat, 08 Sep 2018 11:39:24: #1 tag size is determined as 75 bps INFO @ Sat, 08 Sep 2018 11:39:24: #1 tag size = 75 INFO @ Sat, 08 Sep 2018 11:39:24: #1 total tags in treatment: 12532455 INFO @ Sat, 08 Sep 2018 11:39:24: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 11:39:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 11:39:25: #1 tag size is determined as 75 bps INFO @ Sat, 08 Sep 2018 11:39:25: #1 tag size = 75 INFO @ Sat, 08 Sep 2018 11:39:25: #1 total tags in treatment: 12532455 INFO @ Sat, 08 Sep 2018 11:39:25: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 11:39:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 11:39:25: #1 tags after filtering in treatment: 12532455 INFO @ Sat, 08 Sep 2018 11:39:25: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 11:39:25: #1 finished! INFO @ Sat, 08 Sep 2018 11:39:25: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 11:39:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 11:39:25: #1 tags after filtering in treatment: 12532455 INFO @ Sat, 08 Sep 2018 11:39:25: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 11:39:25: #1 finished! INFO @ Sat, 08 Sep 2018 11:39:25: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 11:39:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 11:39:26: #2 number of paired peaks: 394 WARNING @ Sat, 08 Sep 2018 11:39:26: Fewer paired peaks (394) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 394 pairs to build model! INFO @ Sat, 08 Sep 2018 11:39:26: start model_add_line... INFO @ Sat, 08 Sep 2018 11:39:26: start X-correlation... INFO @ Sat, 08 Sep 2018 11:39:26: #2 number of paired peaks: 394 WARNING @ Sat, 08 Sep 2018 11:39:26: Fewer paired peaks (394) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 394 pairs to build model! INFO @ Sat, 08 Sep 2018 11:39:26: start model_add_line... INFO @ Sat, 08 Sep 2018 11:39:26: start X-correlation... INFO @ Sat, 08 Sep 2018 11:39:26: end of X-cor INFO @ Sat, 08 Sep 2018 11:39:26: #2 finished! INFO @ Sat, 08 Sep 2018 11:39:26: #2 predicted fragment length is 64 bps INFO @ Sat, 08 Sep 2018 11:39:26: #2 alternative fragment length(s) may be 2,64,571 bps INFO @ Sat, 08 Sep 2018 11:39:26: #2.2 Generate R script for model : SRX3942558.20_model.r INFO @ Sat, 08 Sep 2018 11:39:26: end of X-cor INFO @ Sat, 08 Sep 2018 11:39:26: #2 finished! INFO @ Sat, 08 Sep 2018 11:39:26: #2 predicted fragment length is 64 bps INFO @ Sat, 08 Sep 2018 11:39:26: #2 alternative fragment length(s) may be 2,64,571 bps INFO @ Sat, 08 Sep 2018 11:39:26: #2.2 Generate R script for model : SRX3942558.05_model.r WARNING @ Sat, 08 Sep 2018 11:39:26: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 11:39:26: #2 You may need to consider one of the other alternative d(s): 2,64,571 WARNING @ Sat, 08 Sep 2018 11:39:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 11:39:26: #3 Call peaks... WARNING @ Sat, 08 Sep 2018 11:39:26: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 11:39:26: #2 You may need to consider one of the other alternative d(s): 2,64,571 WARNING @ Sat, 08 Sep 2018 11:39:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 11:39:26: #3 Call peaks... INFO @ Sat, 08 Sep 2018 11:39:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 11:39:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 11:39:26: #1 tag size is determined as 75 bps INFO @ Sat, 08 Sep 2018 11:39:26: #1 tag size = 75 INFO @ Sat, 08 Sep 2018 11:39:26: #1 total tags in treatment: 12532455 INFO @ Sat, 08 Sep 2018 11:39:26: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 11:39:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 11:39:26: #1 tags after filtering in treatment: 12532455 INFO @ Sat, 08 Sep 2018 11:39:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 11:39:26: #1 finished! INFO @ Sat, 08 Sep 2018 11:39:26: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 11:39:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 11:39:27: #2 number of paired peaks: 394 WARNING @ Sat, 08 Sep 2018 11:39:27: Fewer paired peaks (394) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 394 pairs to build model! INFO @ Sat, 08 Sep 2018 11:39:27: start model_add_line... INFO @ Sat, 08 Sep 2018 11:39:27: start X-correlation... INFO @ Sat, 08 Sep 2018 11:39:27: end of X-cor INFO @ Sat, 08 Sep 2018 11:39:27: #2 finished! INFO @ Sat, 08 Sep 2018 11:39:27: #2 predicted fragment length is 64 bps INFO @ Sat, 08 Sep 2018 11:39:27: #2 alternative fragment length(s) may be 2,64,571 bps INFO @ Sat, 08 Sep 2018 11:39:27: #2.2 Generate R script for model : SRX3942558.10_model.r WARNING @ Sat, 08 Sep 2018 11:39:27: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 11:39:27: #2 You may need to consider one of the other alternative d(s): 2,64,571 WARNING @ Sat, 08 Sep 2018 11:39:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 11:39:27: #3 Call peaks... INFO @ Sat, 08 Sep 2018 11:39:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 11:39:52: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 11:39:52: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 11:39:54: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 11:40:05: #4 Write output xls file... SRX3942558.20_peaks.xls INFO @ Sat, 08 Sep 2018 11:40:05: #4 Write peak in narrowPeak format file... SRX3942558.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 11:40:05: #4 Write summits bed file... SRX3942558.20_summits.bed INFO @ Sat, 08 Sep 2018 11:40:05: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (187 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 11:40:06: #4 Write output xls file... SRX3942558.10_peaks.xls INFO @ Sat, 08 Sep 2018 11:40:06: #4 Write peak in narrowPeak format file... SRX3942558.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 11:40:06: #4 Write summits bed file... SRX3942558.10_summits.bed INFO @ Sat, 08 Sep 2018 11:40:06: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (515 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 11:40:10: #4 Write output xls file... SRX3942558.05_peaks.xls INFO @ Sat, 08 Sep 2018 11:40:10: #4 Write peak in narrowPeak format file... SRX3942558.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 11:40:10: #4 Write summits bed file... SRX3942558.05_summits.bed INFO @ Sat, 08 Sep 2018 11:40:10: Done! pass1 - making usageList (6 chroms): 9 millis pass2 - checking and writing primary data (1734 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。