Job ID = 10609065 sra ファイルのダウンロード中... Completed: 347377K bytes transferred in 13 seconds (206489K 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... 2018-05-03T22:03:18 fastq-dump.2.9.0 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2018-05-03T22:04:11 fastq-dump.2.9.0 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) Read 11010878 spots for /home/okishinya/chipatlas/results/ce10/SRX2249333/SRR4427772.sra Written 11010878 spots for /home/okishinya/chipatlas/results/ce10/SRX2249333/SRR4427772.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: 00:04:49 11010878 reads; of these: 11010878 (100.00%) were unpaired; of these: 1559604 (14.16%) aligned 0 times 7934586 (72.06%) aligned exactly 1 time 1516688 (13.77%) aligned >1 times 85.84% overall alignment rate Time searching: 00:04:49 Overall time: 00:04:49 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_rmdupse_core] 1775048 / 9451274 = 0.1878 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, 04 May 2018 07:12:48: # Command line: callpeak -t SRX2249333.bam -f BAM -g ce -n SRX2249333.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2249333.05 # format = BAM # ChIP-seq file = ['SRX2249333.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 @ Fri, 04 May 2018 07:12:48: # Command line: callpeak -t SRX2249333.bam -f BAM -g ce -n SRX2249333.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2249333.20 # format = BAM # ChIP-seq file = ['SRX2249333.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 @ Fri, 04 May 2018 07:12:48: # Command line: callpeak -t SRX2249333.bam -f BAM -g ce -n SRX2249333.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2249333.10 # format = BAM # ChIP-seq file = ['SRX2249333.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 @ Fri, 04 May 2018 07:12:48: #1 read tag files... INFO @ Fri, 04 May 2018 07:12:48: #1 read tag files... INFO @ Fri, 04 May 2018 07:12:48: #1 read tag files... INFO @ Fri, 04 May 2018 07:12:48: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:12:48: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:12:48: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:12:56: 1000000 INFO @ Fri, 04 May 2018 07:12:57: 1000000 INFO @ Fri, 04 May 2018 07:12:57: 1000000 INFO @ Fri, 04 May 2018 07:13:04: 2000000 INFO @ Fri, 04 May 2018 07:13:05: 2000000 INFO @ Fri, 04 May 2018 07:13:05: 2000000 INFO @ Fri, 04 May 2018 07:13:12: 3000000 INFO @ Fri, 04 May 2018 07:13:13: 3000000 INFO @ Fri, 04 May 2018 07:13:13: 3000000 INFO @ Fri, 04 May 2018 07:13:20: 4000000 INFO @ Fri, 04 May 2018 07:13:21: 4000000 INFO @ Fri, 04 May 2018 07:13:21: 4000000 INFO @ Fri, 04 May 2018 07:13:29: 5000000 INFO @ Fri, 04 May 2018 07:13:30: 5000000 INFO @ Fri, 04 May 2018 07:13:30: 5000000 INFO @ Fri, 04 May 2018 07:13:37: 6000000 INFO @ Fri, 04 May 2018 07:13:38: 6000000 INFO @ Fri, 04 May 2018 07:13:38: 6000000 INFO @ Fri, 04 May 2018 07:13:45: 7000000 INFO @ Fri, 04 May 2018 07:13:46: 7000000 INFO @ Fri, 04 May 2018 07:13:47: 7000000 INFO @ Fri, 04 May 2018 07:13:51: #1 tag size is determined as 101 bps INFO @ Fri, 04 May 2018 07:13:51: #1 tag size = 101 INFO @ Fri, 04 May 2018 07:13:51: #1 total tags in treatment: 7676226 INFO @ Fri, 04 May 2018 07:13:51: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:13:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 07:13:51: #1 tag size is determined as 101 bps INFO @ Fri, 04 May 2018 07:13:51: #1 tag size = 101 INFO @ Fri, 04 May 2018 07:13:51: #1 total tags in treatment: 7676226 INFO @ Fri, 04 May 2018 07:13:51: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:13:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 07:13:51: #1 tags after filtering in treatment: 7676226 INFO @ Fri, 04 May 2018 07:13:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:13:51: #1 finished! INFO @ Fri, 04 May 2018 07:13:51: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:13:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:13:51: #1 tags after filtering in treatment: 7676226 INFO @ Fri, 04 May 2018 07:13:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:13:51: #1 finished! INFO @ Fri, 04 May 2018 07:13:51: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:13:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:13:52: #2 number of paired peaks: 365 WARNING @ Fri, 04 May 2018 07:13:52: Fewer paired peaks (365) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 365 pairs to build model! INFO @ Fri, 04 May 2018 07:13:52: start model_add_line... INFO @ Fri, 04 May 2018 07:13:52: start X-correlation... INFO @ Fri, 04 May 2018 07:13:52: #2 number of paired peaks: 365 WARNING @ Fri, 04 May 2018 07:13:52: Fewer paired peaks (365) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 365 pairs to build model! INFO @ Fri, 04 May 2018 07:13:52: start model_add_line... INFO @ Fri, 04 May 2018 07:13:52: start X-correlation... INFO @ Fri, 04 May 2018 07:13:52: end of X-cor INFO @ Fri, 04 May 2018 07:13:52: end of X-cor INFO @ Fri, 04 May 2018 07:13:52: #2 finished! INFO @ Fri, 04 May 2018 07:13:52: #2 finished! INFO @ Fri, 04 May 2018 07:13:52: #2 predicted fragment length is 96 bps INFO @ Fri, 04 May 2018 07:13:52: #2 predicted fragment length is 96 bps INFO @ Fri, 04 May 2018 07:13:52: #2 alternative fragment length(s) may be 96 bps INFO @ Fri, 04 May 2018 07:13:52: #2 alternative fragment length(s) may be 96 bps INFO @ Fri, 04 May 2018 07:13:52: #2.2 Generate R script for model : SRX2249333.10_model.r INFO @ Fri, 04 May 2018 07:13:52: #2.2 Generate R script for model : SRX2249333.05_model.r INFO @ Fri, 04 May 2018 07:13:52: #1 tag size is determined as 101 bps INFO @ Fri, 04 May 2018 07:13:52: #1 tag size = 101 INFO @ Fri, 04 May 2018 07:13:52: #1 total tags in treatment: 7676226 INFO @ Fri, 04 May 2018 07:13:52: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:13:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) WARNING @ Fri, 04 May 2018 07:13:52: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 May 2018 07:13:52: #2 You may need to consider one of the other alternative d(s): 96 WARNING @ Fri, 04 May 2018 07:13:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 04 May 2018 07:13:52: #3 Call peaks... INFO @ Fri, 04 May 2018 07:13:52: #3 Pre-compute pvalue-qvalue table... WARNING @ Fri, 04 May 2018 07:13:52: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 May 2018 07:13:52: #2 You may need to consider one of the other alternative d(s): 96 WARNING @ Fri, 04 May 2018 07:13:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 04 May 2018 07:13:52: #3 Call peaks... INFO @ Fri, 04 May 2018 07:13:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:13:52: #1 tags after filtering in treatment: 7676226 INFO @ Fri, 04 May 2018 07:13:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:13:52: #1 finished! INFO @ Fri, 04 May 2018 07:13:52: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:13:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:13:53: #2 number of paired peaks: 365 WARNING @ Fri, 04 May 2018 07:13:53: Fewer paired peaks (365) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 365 pairs to build model! INFO @ Fri, 04 May 2018 07:13:53: start model_add_line... INFO @ Fri, 04 May 2018 07:13:53: start X-correlation... INFO @ Fri, 04 May 2018 07:13:53: end of X-cor INFO @ Fri, 04 May 2018 07:13:53: #2 finished! INFO @ Fri, 04 May 2018 07:13:53: #2 predicted fragment length is 96 bps INFO @ Fri, 04 May 2018 07:13:53: #2 alternative fragment length(s) may be 96 bps INFO @ Fri, 04 May 2018 07:13:53: #2.2 Generate R script for model : SRX2249333.20_model.r WARNING @ Fri, 04 May 2018 07:13:53: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 May 2018 07:13:53: #2 You may need to consider one of the other alternative d(s): 96 WARNING @ Fri, 04 May 2018 07:13:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 04 May 2018 07:13:53: #3 Call peaks... INFO @ Fri, 04 May 2018 07:13:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:14:09: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:14:10: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:14:11: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:14:18: #4 Write output xls file... SRX2249333.10_peaks.xls INFO @ Fri, 04 May 2018 07:14:18: #4 Write peak in narrowPeak format file... SRX2249333.10_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:14:18: #4 Write summits bed file... SRX2249333.10_summits.bed INFO @ Fri, 04 May 2018 07:14:18: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (334 records, 4 fields): 45 millis CompletedMACS2peakCalling INFO @ Fri, 04 May 2018 07:14:19: #4 Write output xls file... SRX2249333.20_peaks.xls INFO @ Fri, 04 May 2018 07:14:19: #4 Write peak in narrowPeak format file... SRX2249333.20_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:14:19: #4 Write summits bed file... SRX2249333.20_summits.bed INFO @ Fri, 04 May 2018 07:14:19: Done! INFO @ Fri, 04 May 2018 07:14:20: #4 Write output xls file... SRX2249333.05_peaks.xls INFO @ Fri, 04 May 2018 07:14:20: #4 Write peak in narrowPeak format file... SRX2249333.05_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:14:20: #4 Write summits bed file... SRX2249333.05_summits.bed pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (223 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 04 May 2018 07:14:20: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (451 records, 4 fields): 23 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。