Job ID = 1308905 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T14:08:04 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 36,582,891 reads read : 73,165,782 reads written : 36,582,891 reads 0-length : 36,582,891 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: No such file or directory 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: 00:15:58 36582891 reads; of these: 36582891 (100.00%) were unpaired; of these: 4234885 (11.58%) aligned 0 times 23514375 (64.28%) aligned exactly 1 time 8833631 (24.15%) aligned >1 times 88.42% overall alignment rate Time searching: 00:15:58 Overall time: 00:15:58 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 16 files... [bam_rmdupse_core] 14318476 / 32348006 = 0.4426 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 @ Mon, 03 Jun 2019 23:35:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5661481/SRX5661481.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5661481/SRX5661481.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5661481/SRX5661481.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5661481/SRX5661481.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 @ Mon, 03 Jun 2019 23:35:04: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:35:04: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:35:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5661481/SRX5661481.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5661481/SRX5661481.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5661481/SRX5661481.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5661481/SRX5661481.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 @ Mon, 03 Jun 2019 23:35:04: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:35:04: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:35:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5661481/SRX5661481.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5661481/SRX5661481.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5661481/SRX5661481.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5661481/SRX5661481.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 @ Mon, 03 Jun 2019 23:35:04: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:35:04: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:35:15: 1000000 INFO @ Mon, 03 Jun 2019 23:35:15: 1000000 INFO @ Mon, 03 Jun 2019 23:35:16: 1000000 INFO @ Mon, 03 Jun 2019 23:35:25: 2000000 INFO @ Mon, 03 Jun 2019 23:35:25: 2000000 INFO @ Mon, 03 Jun 2019 23:35:28: 2000000 INFO @ Mon, 03 Jun 2019 23:35:37: 3000000 INFO @ Mon, 03 Jun 2019 23:35:37: 3000000 INFO @ Mon, 03 Jun 2019 23:35:40: 3000000 INFO @ Mon, 03 Jun 2019 23:35:49: 4000000 INFO @ Mon, 03 Jun 2019 23:35:49: 4000000 INFO @ Mon, 03 Jun 2019 23:35:53: 4000000 INFO @ Mon, 03 Jun 2019 23:36:01: 5000000 INFO @ Mon, 03 Jun 2019 23:36:01: 5000000 INFO @ Mon, 03 Jun 2019 23:36:05: 5000000 INFO @ Mon, 03 Jun 2019 23:36:12: 6000000 INFO @ Mon, 03 Jun 2019 23:36:12: 6000000 INFO @ Mon, 03 Jun 2019 23:36:17: 6000000 INFO @ Mon, 03 Jun 2019 23:36:22: 7000000 INFO @ Mon, 03 Jun 2019 23:36:22: 7000000 INFO @ Mon, 03 Jun 2019 23:36:28: 7000000 INFO @ Mon, 03 Jun 2019 23:36:32: 8000000 INFO @ Mon, 03 Jun 2019 23:36:32: 8000000 INFO @ Mon, 03 Jun 2019 23:36:39: 8000000 INFO @ Mon, 03 Jun 2019 23:36:44: 9000000 INFO @ Mon, 03 Jun 2019 23:36:44: 9000000 INFO @ Mon, 03 Jun 2019 23:36:51: 9000000 INFO @ Mon, 03 Jun 2019 23:36:57: 10000000 INFO @ Mon, 03 Jun 2019 23:36:57: 10000000 INFO @ Mon, 03 Jun 2019 23:37:04: 10000000 INFO @ Mon, 03 Jun 2019 23:37:08: 11000000 INFO @ Mon, 03 Jun 2019 23:37:08: 11000000 INFO @ Mon, 03 Jun 2019 23:37:15: 11000000 INFO @ Mon, 03 Jun 2019 23:37:19: 12000000 INFO @ Mon, 03 Jun 2019 23:37:19: 12000000 INFO @ Mon, 03 Jun 2019 23:37:27: 12000000 INFO @ Mon, 03 Jun 2019 23:37:30: 13000000 INFO @ Mon, 03 Jun 2019 23:37:30: 13000000 INFO @ Mon, 03 Jun 2019 23:37:39: 13000000 INFO @ Mon, 03 Jun 2019 23:37:40: 14000000 INFO @ Mon, 03 Jun 2019 23:37:40: 14000000 INFO @ Mon, 03 Jun 2019 23:37:52: 14000000 INFO @ Mon, 03 Jun 2019 23:37:52: 15000000 INFO @ Mon, 03 Jun 2019 23:37:52: 15000000 INFO @ Mon, 03 Jun 2019 23:38:05: 15000000 INFO @ Mon, 03 Jun 2019 23:38:05: 16000000 INFO @ Mon, 03 Jun 2019 23:38:05: 16000000 INFO @ Mon, 03 Jun 2019 23:38:16: 17000000 INFO @ Mon, 03 Jun 2019 23:38:16: 17000000 INFO @ Mon, 03 Jun 2019 23:38:17: 16000000 INFO @ Mon, 03 Jun 2019 23:38:26: 18000000 INFO @ Mon, 03 Jun 2019 23:38:26: 18000000 INFO @ Mon, 03 Jun 2019 23:38:26: #1 tag size is determined as 62 bps INFO @ Mon, 03 Jun 2019 23:38:26: #1 tag size = 62 INFO @ Mon, 03 Jun 2019 23:38:26: #1 total tags in treatment: 18029530 INFO @ Mon, 03 Jun 2019 23:38:26: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:38:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 23:38:26: #1 tag size is determined as 62 bps INFO @ Mon, 03 Jun 2019 23:38:26: #1 tag size = 62 INFO @ Mon, 03 Jun 2019 23:38:26: #1 total tags in treatment: 18029530 INFO @ Mon, 03 Jun 2019 23:38:26: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:38:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 23:38:27: #1 tags after filtering in treatment: 18029530 INFO @ Mon, 03 Jun 2019 23:38:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:38:27: #1 finished! INFO @ Mon, 03 Jun 2019 23:38:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:38:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:38:27: #1 tags after filtering in treatment: 18029530 INFO @ Mon, 03 Jun 2019 23:38:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:38:27: #1 finished! INFO @ Mon, 03 Jun 2019 23:38:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:38:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:38:28: 17000000 INFO @ Mon, 03 Jun 2019 23:38:28: #2 number of paired peaks: 113 WARNING @ Mon, 03 Jun 2019 23:38:28: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Mon, 03 Jun 2019 23:38:28: start model_add_line... INFO @ Mon, 03 Jun 2019 23:38:28: #2 number of paired peaks: 113 WARNING @ Mon, 03 Jun 2019 23:38:28: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Mon, 03 Jun 2019 23:38:28: start model_add_line... INFO @ Mon, 03 Jun 2019 23:38:28: start X-correlation... INFO @ Mon, 03 Jun 2019 23:38:28: start X-correlation... INFO @ Mon, 03 Jun 2019 23:38:28: end of X-cor INFO @ Mon, 03 Jun 2019 23:38:28: #2 finished! INFO @ Mon, 03 Jun 2019 23:38:28: #2 predicted fragment length is 50 bps INFO @ Mon, 03 Jun 2019 23:38:28: #2 alternative fragment length(s) may be 50 bps INFO @ Mon, 03 Jun 2019 23:38:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5661481/SRX5661481.10_model.r INFO @ Mon, 03 Jun 2019 23:38:28: end of X-cor INFO @ Mon, 03 Jun 2019 23:38:28: #2 finished! INFO @ Mon, 03 Jun 2019 23:38:28: #2 predicted fragment length is 50 bps INFO @ Mon, 03 Jun 2019 23:38:28: #2 alternative fragment length(s) may be 50 bps INFO @ Mon, 03 Jun 2019 23:38:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5661481/SRX5661481.05_model.r WARNING @ Mon, 03 Jun 2019 23:38:28: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 23:38:28: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Mon, 03 Jun 2019 23:38:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. WARNING @ Mon, 03 Jun 2019 23:38:28: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! INFO @ Mon, 03 Jun 2019 23:38:28: #3 Call peaks... WARNING @ Mon, 03 Jun 2019 23:38:28: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Mon, 03 Jun 2019 23:38:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 23:38:28: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:38:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:38:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:38:38: 18000000 INFO @ Mon, 03 Jun 2019 23:38:39: #1 tag size is determined as 62 bps INFO @ Mon, 03 Jun 2019 23:38:39: #1 tag size = 62 INFO @ Mon, 03 Jun 2019 23:38:39: #1 total tags in treatment: 18029530 INFO @ Mon, 03 Jun 2019 23:38:39: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:38:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 23:38:39: #1 tags after filtering in treatment: 18029530 INFO @ Mon, 03 Jun 2019 23:38:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:38:39: #1 finished! INFO @ Mon, 03 Jun 2019 23:38:39: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:38:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:38:41: #2 number of paired peaks: 113 WARNING @ Mon, 03 Jun 2019 23:38:41: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Mon, 03 Jun 2019 23:38:41: start model_add_line... INFO @ Mon, 03 Jun 2019 23:38:41: start X-correlation... INFO @ Mon, 03 Jun 2019 23:38:41: end of X-cor INFO @ Mon, 03 Jun 2019 23:38:41: #2 finished! INFO @ Mon, 03 Jun 2019 23:38:41: #2 predicted fragment length is 50 bps INFO @ Mon, 03 Jun 2019 23:38:41: #2 alternative fragment length(s) may be 50 bps INFO @ Mon, 03 Jun 2019 23:38:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5661481/SRX5661481.20_model.r WARNING @ Mon, 03 Jun 2019 23:38:41: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 23:38:41: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Mon, 03 Jun 2019 23:38:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 23:38:41: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:38:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:39:15: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:39:15: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:39:27: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:39:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5661481/SRX5661481.05_peaks.xls INFO @ Mon, 03 Jun 2019 23:39:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5661481/SRX5661481.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:39:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5661481/SRX5661481.05_summits.bed INFO @ Mon, 03 Jun 2019 23:39:38: Done! INFO @ Mon, 03 Jun 2019 23:39:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5661481/SRX5661481.10_peaks.xls INFO @ Mon, 03 Jun 2019 23:39:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5661481/SRX5661481.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:39:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5661481/SRX5661481.10_summits.bed INFO @ Mon, 03 Jun 2019 23:39:38: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2581 records, 4 fields): 6 millis CompletedMACS2peakCalling pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1559 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 23:39:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5661481/SRX5661481.20_peaks.xls INFO @ Mon, 03 Jun 2019 23:39:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5661481/SRX5661481.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:39:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5661481/SRX5661481.20_summits.bed INFO @ Mon, 03 Jun 2019 23:39:49: Done! pass1 - making usageList (8 chroms): 2 millis pass2 - checking and writing primary data (1061 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。