Job ID = 1294507 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T23:35:26 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 : 17,570,684 reads read : 17,570,684 reads written : 17,570,684 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: 00:09:11 17570684 reads; of these: 17570684 (100.00%) were unpaired; of these: 850044 (4.84%) aligned 0 times 11024803 (62.75%) aligned exactly 1 time 5695837 (32.42%) aligned >1 times 95.16% overall alignment rate Time searching: 00:09:11 Overall time: 00:09:11 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] 2897628 / 16720640 = 0.1733 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 08:52:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287705/SRX287705.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287705/SRX287705.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287705/SRX287705.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287705/SRX287705.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 08:52:34: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:52:34: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:52:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287705/SRX287705.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287705/SRX287705.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287705/SRX287705.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287705/SRX287705.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 08:52:34: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:52:34: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:52:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287705/SRX287705.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287705/SRX287705.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287705/SRX287705.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287705/SRX287705.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 08:52:34: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:52:34: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:52:44: 1000000 INFO @ Mon, 03 Jun 2019 08:52:45: 1000000 INFO @ Mon, 03 Jun 2019 08:52:45: 1000000 INFO @ Mon, 03 Jun 2019 08:52:52: 2000000 INFO @ Mon, 03 Jun 2019 08:52:55: 2000000 INFO @ Mon, 03 Jun 2019 08:52:55: 2000000 INFO @ Mon, 03 Jun 2019 08:53:01: 3000000 INFO @ Mon, 03 Jun 2019 08:53:04: 3000000 INFO @ Mon, 03 Jun 2019 08:53:05: 3000000 INFO @ Mon, 03 Jun 2019 08:53:09: 4000000 INFO @ Mon, 03 Jun 2019 08:53:14: 4000000 INFO @ Mon, 03 Jun 2019 08:53:15: 4000000 INFO @ Mon, 03 Jun 2019 08:53:18: 5000000 INFO @ Mon, 03 Jun 2019 08:53:23: 5000000 INFO @ Mon, 03 Jun 2019 08:53:25: 5000000 INFO @ Mon, 03 Jun 2019 08:53:27: 6000000 INFO @ Mon, 03 Jun 2019 08:53:33: 6000000 INFO @ Mon, 03 Jun 2019 08:53:35: 6000000 INFO @ Mon, 03 Jun 2019 08:53:35: 7000000 INFO @ Mon, 03 Jun 2019 08:53:42: 7000000 INFO @ Mon, 03 Jun 2019 08:53:44: 8000000 INFO @ Mon, 03 Jun 2019 08:53:45: 7000000 INFO @ Mon, 03 Jun 2019 08:53:51: 8000000 INFO @ Mon, 03 Jun 2019 08:53:52: 9000000 INFO @ Mon, 03 Jun 2019 08:53:55: 8000000 INFO @ Mon, 03 Jun 2019 08:54:01: 9000000 INFO @ Mon, 03 Jun 2019 08:54:01: 10000000 INFO @ Mon, 03 Jun 2019 08:54:04: 9000000 INFO @ Mon, 03 Jun 2019 08:54:09: 11000000 INFO @ Mon, 03 Jun 2019 08:54:10: 10000000 INFO @ Mon, 03 Jun 2019 08:54:14: 10000000 INFO @ Mon, 03 Jun 2019 08:54:18: 12000000 INFO @ Mon, 03 Jun 2019 08:54:20: 11000000 INFO @ Mon, 03 Jun 2019 08:54:24: 11000000 INFO @ Mon, 03 Jun 2019 08:54:26: 13000000 INFO @ Mon, 03 Jun 2019 08:54:29: 12000000 INFO @ Mon, 03 Jun 2019 08:54:33: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:54:33: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:54:33: #1 total tags in treatment: 13823012 INFO @ Mon, 03 Jun 2019 08:54:33: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:54:33: #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 08:54:34: #1 tags after filtering in treatment: 13823012 INFO @ Mon, 03 Jun 2019 08:54:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:54:34: #1 finished! INFO @ Mon, 03 Jun 2019 08:54:34: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:54:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:54:34: 12000000 INFO @ Mon, 03 Jun 2019 08:54:35: #2 number of paired peaks: 487 WARNING @ Mon, 03 Jun 2019 08:54:35: Fewer paired peaks (487) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 487 pairs to build model! INFO @ Mon, 03 Jun 2019 08:54:35: start model_add_line... INFO @ Mon, 03 Jun 2019 08:54:35: start X-correlation... INFO @ Mon, 03 Jun 2019 08:54:35: end of X-cor INFO @ Mon, 03 Jun 2019 08:54:35: #2 finished! INFO @ Mon, 03 Jun 2019 08:54:35: #2 predicted fragment length is 41 bps INFO @ Mon, 03 Jun 2019 08:54:35: #2 alternative fragment length(s) may be 41 bps INFO @ Mon, 03 Jun 2019 08:54:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287705/SRX287705.10_model.r WARNING @ Mon, 03 Jun 2019 08:54:35: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 08:54:35: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Mon, 03 Jun 2019 08:54:35: #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 08:54:35: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:54:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:54:39: 13000000 INFO @ Mon, 03 Jun 2019 08:54:44: 13000000 INFO @ Mon, 03 Jun 2019 08:54:47: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:54:47: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:54:47: #1 total tags in treatment: 13823012 INFO @ Mon, 03 Jun 2019 08:54:47: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:54:47: #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 08:54:47: #1 tags after filtering in treatment: 13823012 INFO @ Mon, 03 Jun 2019 08:54:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:54:47: #1 finished! INFO @ Mon, 03 Jun 2019 08:54:47: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:54:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:54:48: #2 number of paired peaks: 487 WARNING @ Mon, 03 Jun 2019 08:54:48: Fewer paired peaks (487) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 487 pairs to build model! INFO @ Mon, 03 Jun 2019 08:54:48: start model_add_line... INFO @ Mon, 03 Jun 2019 08:54:48: start X-correlation... INFO @ Mon, 03 Jun 2019 08:54:48: end of X-cor INFO @ Mon, 03 Jun 2019 08:54:48: #2 finished! INFO @ Mon, 03 Jun 2019 08:54:48: #2 predicted fragment length is 41 bps INFO @ Mon, 03 Jun 2019 08:54:48: #2 alternative fragment length(s) may be 41 bps INFO @ Mon, 03 Jun 2019 08:54:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287705/SRX287705.05_model.r WARNING @ Mon, 03 Jun 2019 08:54:48: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 08:54:48: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Mon, 03 Jun 2019 08:54:48: #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 08:54:48: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:54:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:54:51: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:54:51: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:54:51: #1 total tags in treatment: 13823012 INFO @ Mon, 03 Jun 2019 08:54:51: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:54:51: #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 08:54:52: #1 tags after filtering in treatment: 13823012 INFO @ Mon, 03 Jun 2019 08:54:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:54:52: #1 finished! INFO @ Mon, 03 Jun 2019 08:54:52: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:54:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:54:53: #2 number of paired peaks: 487 WARNING @ Mon, 03 Jun 2019 08:54:53: Fewer paired peaks (487) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 487 pairs to build model! INFO @ Mon, 03 Jun 2019 08:54:53: start model_add_line... INFO @ Mon, 03 Jun 2019 08:54:53: start X-correlation... INFO @ Mon, 03 Jun 2019 08:54:53: end of X-cor INFO @ Mon, 03 Jun 2019 08:54:53: #2 finished! INFO @ Mon, 03 Jun 2019 08:54:53: #2 predicted fragment length is 41 bps INFO @ Mon, 03 Jun 2019 08:54:53: #2 alternative fragment length(s) may be 41 bps INFO @ Mon, 03 Jun 2019 08:54:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287705/SRX287705.20_model.r WARNING @ Mon, 03 Jun 2019 08:54:53: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 08:54:53: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Mon, 03 Jun 2019 08:54:53: #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 08:54:53: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:54:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:55:12: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:55:26: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:55:30: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:55:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287705/SRX287705.10_peaks.xls INFO @ Mon, 03 Jun 2019 08:55:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287705/SRX287705.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:55:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287705/SRX287705.10_summits.bed INFO @ Mon, 03 Jun 2019 08:55:31: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1910 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:55:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287705/SRX287705.05_peaks.xls INFO @ Mon, 03 Jun 2019 08:55:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287705/SRX287705.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:55:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287705/SRX287705.05_summits.bed INFO @ Mon, 03 Jun 2019 08:55:44: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2155 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:55:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287705/SRX287705.20_peaks.xls INFO @ Mon, 03 Jun 2019 08:55:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287705/SRX287705.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:55:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287705/SRX287705.20_summits.bed INFO @ Mon, 03 Jun 2019 08:55:49: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1496 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。