Job ID = 1294497 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T23:30:09 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 ) 2019-06-02T23:30:09 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 : 19,930,693 reads read : 19,930,693 reads written : 19,930,693 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: 00:08:58 19930693 reads; of these: 19930693 (100.00%) were unpaired; of these: 1257645 (6.31%) aligned 0 times 12952865 (64.99%) aligned exactly 1 time 5720183 (28.70%) aligned >1 times 93.69% overall alignment rate Time searching: 00:08:58 Overall time: 00:08:58 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 8 files... [bam_rmdupse_core] 2338968 / 18673048 = 0.1253 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 08:51:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287697/SRX287697.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287697/SRX287697.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287697/SRX287697.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287697/SRX287697.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 08:51:34: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:51:34: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:51:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287697/SRX287697.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287697/SRX287697.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287697/SRX287697.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287697/SRX287697.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 08:51:34: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:51:34: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:51:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287697/SRX287697.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287697/SRX287697.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287697/SRX287697.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287697/SRX287697.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 08:51:34: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:51:34: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:51:42: 1000000 INFO @ Mon, 03 Jun 2019 08:51:42: 1000000 INFO @ Mon, 03 Jun 2019 08:51:45: 1000000 INFO @ Mon, 03 Jun 2019 08:51:50: 2000000 INFO @ Mon, 03 Jun 2019 08:51:51: 2000000 INFO @ Mon, 03 Jun 2019 08:51:55: 2000000 INFO @ Mon, 03 Jun 2019 08:51:58: 3000000 INFO @ Mon, 03 Jun 2019 08:52:00: 3000000 INFO @ Mon, 03 Jun 2019 08:52:05: 3000000 INFO @ Mon, 03 Jun 2019 08:52:06: 4000000 INFO @ Mon, 03 Jun 2019 08:52:08: 4000000 INFO @ Mon, 03 Jun 2019 08:52:13: 5000000 INFO @ Mon, 03 Jun 2019 08:52:15: 4000000 INFO @ Mon, 03 Jun 2019 08:52:16: 5000000 INFO @ Mon, 03 Jun 2019 08:52:21: 6000000 INFO @ Mon, 03 Jun 2019 08:52:23: 6000000 INFO @ Mon, 03 Jun 2019 08:52:25: 5000000 INFO @ Mon, 03 Jun 2019 08:52:28: 7000000 INFO @ Mon, 03 Jun 2019 08:52:31: 7000000 INFO @ Mon, 03 Jun 2019 08:52:35: 6000000 INFO @ Mon, 03 Jun 2019 08:52:35: 8000000 INFO @ Mon, 03 Jun 2019 08:52:39: 8000000 INFO @ Mon, 03 Jun 2019 08:52:43: 9000000 INFO @ Mon, 03 Jun 2019 08:52:45: 7000000 INFO @ Mon, 03 Jun 2019 08:52:47: 9000000 INFO @ Mon, 03 Jun 2019 08:52:51: 10000000 INFO @ Mon, 03 Jun 2019 08:52:55: 8000000 INFO @ Mon, 03 Jun 2019 08:52:55: 10000000 INFO @ Mon, 03 Jun 2019 08:52:58: 11000000 INFO @ Mon, 03 Jun 2019 08:53:02: 11000000 INFO @ Mon, 03 Jun 2019 08:53:04: 9000000 INFO @ Mon, 03 Jun 2019 08:53:06: 12000000 INFO @ Mon, 03 Jun 2019 08:53:10: 12000000 INFO @ Mon, 03 Jun 2019 08:53:13: 13000000 INFO @ Mon, 03 Jun 2019 08:53:14: 10000000 INFO @ Mon, 03 Jun 2019 08:53:18: 13000000 INFO @ Mon, 03 Jun 2019 08:53:21: 14000000 INFO @ Mon, 03 Jun 2019 08:53:25: 11000000 INFO @ Mon, 03 Jun 2019 08:53:27: 14000000 INFO @ Mon, 03 Jun 2019 08:53:29: 15000000 INFO @ Mon, 03 Jun 2019 08:53:35: 12000000 INFO @ Mon, 03 Jun 2019 08:53:35: 15000000 INFO @ Mon, 03 Jun 2019 08:53:36: 16000000 INFO @ Mon, 03 Jun 2019 08:53:39: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:53:39: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:53:39: #1 total tags in treatment: 16334080 INFO @ Mon, 03 Jun 2019 08:53:39: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:53:39: #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 08:53:39: #1 tags after filtering in treatment: 16334080 INFO @ Mon, 03 Jun 2019 08:53:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:53:39: #1 finished! INFO @ Mon, 03 Jun 2019 08:53:39: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:53:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:53:41: #2 number of paired peaks: 202 WARNING @ Mon, 03 Jun 2019 08:53:41: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Mon, 03 Jun 2019 08:53:41: start model_add_line... INFO @ Mon, 03 Jun 2019 08:53:41: start X-correlation... INFO @ Mon, 03 Jun 2019 08:53:41: end of X-cor INFO @ Mon, 03 Jun 2019 08:53:41: #2 finished! INFO @ Mon, 03 Jun 2019 08:53:41: #2 predicted fragment length is 42 bps INFO @ Mon, 03 Jun 2019 08:53:41: #2 alternative fragment length(s) may be 42 bps INFO @ Mon, 03 Jun 2019 08:53:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287697/SRX287697.05_model.r WARNING @ Mon, 03 Jun 2019 08:53:41: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 08:53:41: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Mon, 03 Jun 2019 08:53:41: #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 08:53:41: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:53:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:53:43: 16000000 INFO @ Mon, 03 Jun 2019 08:53:44: 13000000 INFO @ Mon, 03 Jun 2019 08:53:46: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:53:46: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:53:46: #1 total tags in treatment: 16334080 INFO @ Mon, 03 Jun 2019 08:53:46: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:53:46: #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 08:53:46: #1 tags after filtering in treatment: 16334080 INFO @ Mon, 03 Jun 2019 08:53:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:53:46: #1 finished! INFO @ Mon, 03 Jun 2019 08:53:46: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:53:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:53:47: #2 number of paired peaks: 202 WARNING @ Mon, 03 Jun 2019 08:53:47: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Mon, 03 Jun 2019 08:53:47: start model_add_line... INFO @ Mon, 03 Jun 2019 08:53:47: start X-correlation... INFO @ Mon, 03 Jun 2019 08:53:47: end of X-cor INFO @ Mon, 03 Jun 2019 08:53:47: #2 finished! INFO @ Mon, 03 Jun 2019 08:53:47: #2 predicted fragment length is 42 bps INFO @ Mon, 03 Jun 2019 08:53:47: #2 alternative fragment length(s) may be 42 bps INFO @ Mon, 03 Jun 2019 08:53:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287697/SRX287697.20_model.r WARNING @ Mon, 03 Jun 2019 08:53:47: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 08:53:47: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Mon, 03 Jun 2019 08:53:47: #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 08:53:47: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:53:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:53:54: 14000000 INFO @ Mon, 03 Jun 2019 08:54:03: 15000000 INFO @ Mon, 03 Jun 2019 08:54:13: 16000000 INFO @ Mon, 03 Jun 2019 08:54:16: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:54:16: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:54:16: #1 total tags in treatment: 16334080 INFO @ Mon, 03 Jun 2019 08:54:16: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:54:16: #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 08:54:16: #1 tags after filtering in treatment: 16334080 INFO @ Mon, 03 Jun 2019 08:54:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:54:16: #1 finished! INFO @ Mon, 03 Jun 2019 08:54:16: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:54:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:54:18: #2 number of paired peaks: 202 WARNING @ Mon, 03 Jun 2019 08:54:18: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Mon, 03 Jun 2019 08:54:18: start model_add_line... INFO @ Mon, 03 Jun 2019 08:54:18: start X-correlation... INFO @ Mon, 03 Jun 2019 08:54:18: end of X-cor INFO @ Mon, 03 Jun 2019 08:54:18: #2 finished! INFO @ Mon, 03 Jun 2019 08:54:18: #2 predicted fragment length is 42 bps INFO @ Mon, 03 Jun 2019 08:54:18: #2 alternative fragment length(s) may be 42 bps INFO @ Mon, 03 Jun 2019 08:54:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287697/SRX287697.10_model.r WARNING @ Mon, 03 Jun 2019 08:54:18: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 08:54:18: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Mon, 03 Jun 2019 08:54:18: #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 08:54:18: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:54:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:54:23: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:54:30: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:54:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287697/SRX287697.05_peaks.xls INFO @ Mon, 03 Jun 2019 08:54:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287697/SRX287697.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:54:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287697/SRX287697.05_summits.bed INFO @ Mon, 03 Jun 2019 08:54:44: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2125 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:54:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287697/SRX287697.20_peaks.xls INFO @ Mon, 03 Jun 2019 08:54:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287697/SRX287697.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:54:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287697/SRX287697.20_summits.bed INFO @ Mon, 03 Jun 2019 08:54:51: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1364 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:55:00: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:55:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287697/SRX287697.10_peaks.xls INFO @ Mon, 03 Jun 2019 08:55:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287697/SRX287697.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:55:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287697/SRX287697.10_summits.bed INFO @ Mon, 03 Jun 2019 08:55:21: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1857 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。