Job ID = 1294987 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T02:06:32 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 16,539,414 reads read : 16,539,414 reads written : 16,539,414 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: 00:08:11 16539414 reads; of these: 16539414 (100.00%) were unpaired; of these: 698576 (4.22%) aligned 0 times 10319638 (62.39%) aligned exactly 1 time 5521200 (33.38%) aligned >1 times 95.78% overall alignment rate Time searching: 00:08:11 Overall time: 00:08:11 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] 2190848 / 15840838 = 0.1383 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 11:24:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288043/SRX288043.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288043/SRX288043.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288043/SRX288043.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288043/SRX288043.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 11:24:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:24:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:24:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288043/SRX288043.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288043/SRX288043.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288043/SRX288043.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288043/SRX288043.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 11:24:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:24:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:24:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288043/SRX288043.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288043/SRX288043.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288043/SRX288043.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288043/SRX288043.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 11:24:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:24:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:24:49: 1000000 INFO @ Mon, 03 Jun 2019 11:24:51: 1000000 INFO @ Mon, 03 Jun 2019 11:24:51: 1000000 INFO @ Mon, 03 Jun 2019 11:24:58: 2000000 INFO @ Mon, 03 Jun 2019 11:25:03: 2000000 INFO @ Mon, 03 Jun 2019 11:25:03: 2000000 INFO @ Mon, 03 Jun 2019 11:25:08: 3000000 INFO @ Mon, 03 Jun 2019 11:25:15: 3000000 INFO @ Mon, 03 Jun 2019 11:25:15: 3000000 INFO @ Mon, 03 Jun 2019 11:25:17: 4000000 INFO @ Mon, 03 Jun 2019 11:25:26: 5000000 INFO @ Mon, 03 Jun 2019 11:25:27: 4000000 INFO @ Mon, 03 Jun 2019 11:25:27: 4000000 INFO @ Mon, 03 Jun 2019 11:25:35: 6000000 INFO @ Mon, 03 Jun 2019 11:25:38: 5000000 INFO @ Mon, 03 Jun 2019 11:25:38: 5000000 INFO @ Mon, 03 Jun 2019 11:25:43: 7000000 INFO @ Mon, 03 Jun 2019 11:25:48: 6000000 INFO @ Mon, 03 Jun 2019 11:25:48: 6000000 INFO @ Mon, 03 Jun 2019 11:25:52: 8000000 INFO @ Mon, 03 Jun 2019 11:25:58: 7000000 INFO @ Mon, 03 Jun 2019 11:25:59: 7000000 INFO @ Mon, 03 Jun 2019 11:26:01: 9000000 INFO @ Mon, 03 Jun 2019 11:26:09: 8000000 INFO @ Mon, 03 Jun 2019 11:26:09: 8000000 INFO @ Mon, 03 Jun 2019 11:26:10: 10000000 INFO @ Mon, 03 Jun 2019 11:26:19: 11000000 INFO @ Mon, 03 Jun 2019 11:26:19: 9000000 INFO @ Mon, 03 Jun 2019 11:26:20: 9000000 INFO @ Mon, 03 Jun 2019 11:26:28: 12000000 INFO @ Mon, 03 Jun 2019 11:26:30: 10000000 INFO @ Mon, 03 Jun 2019 11:26:31: 10000000 INFO @ Mon, 03 Jun 2019 11:26:36: 13000000 INFO @ Mon, 03 Jun 2019 11:26:40: 11000000 INFO @ Mon, 03 Jun 2019 11:26:42: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:26:42: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:26:42: #1 total tags in treatment: 13649990 INFO @ Mon, 03 Jun 2019 11:26:42: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:26:42: #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 11:26:42: 11000000 INFO @ Mon, 03 Jun 2019 11:26:42: #1 tags after filtering in treatment: 13649990 INFO @ Mon, 03 Jun 2019 11:26:42: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:26:42: #1 finished! INFO @ Mon, 03 Jun 2019 11:26:42: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:26:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:26:44: #2 number of paired peaks: 410 WARNING @ Mon, 03 Jun 2019 11:26:44: Fewer paired peaks (410) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 410 pairs to build model! INFO @ Mon, 03 Jun 2019 11:26:44: start model_add_line... INFO @ Mon, 03 Jun 2019 11:26:44: start X-correlation... INFO @ Mon, 03 Jun 2019 11:26:44: end of X-cor INFO @ Mon, 03 Jun 2019 11:26:44: #2 finished! INFO @ Mon, 03 Jun 2019 11:26:44: #2 predicted fragment length is 44 bps INFO @ Mon, 03 Jun 2019 11:26:44: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 03 Jun 2019 11:26:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288043/SRX288043.05_model.r WARNING @ Mon, 03 Jun 2019 11:26:44: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:26:44: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 03 Jun 2019 11:26:44: #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 11:26:44: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:26:44: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:26:51: 12000000 INFO @ Mon, 03 Jun 2019 11:26:53: 12000000 INFO @ Mon, 03 Jun 2019 11:27:01: 13000000 INFO @ Mon, 03 Jun 2019 11:27:03: 13000000 INFO @ Mon, 03 Jun 2019 11:27:08: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:27:08: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:27:08: #1 total tags in treatment: 13649990 INFO @ Mon, 03 Jun 2019 11:27:08: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:27:08: #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 11:27:08: #1 tags after filtering in treatment: 13649990 INFO @ Mon, 03 Jun 2019 11:27:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:27:08: #1 finished! INFO @ Mon, 03 Jun 2019 11:27:08: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:27:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:27:09: #2 number of paired peaks: 410 WARNING @ Mon, 03 Jun 2019 11:27:09: Fewer paired peaks (410) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 410 pairs to build model! INFO @ Mon, 03 Jun 2019 11:27:09: start model_add_line... INFO @ Mon, 03 Jun 2019 11:27:09: start X-correlation... INFO @ Mon, 03 Jun 2019 11:27:09: end of X-cor INFO @ Mon, 03 Jun 2019 11:27:09: #2 finished! INFO @ Mon, 03 Jun 2019 11:27:09: #2 predicted fragment length is 44 bps INFO @ Mon, 03 Jun 2019 11:27:09: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 03 Jun 2019 11:27:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288043/SRX288043.10_model.r WARNING @ Mon, 03 Jun 2019 11:27:09: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:27:09: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 03 Jun 2019 11:27:09: #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 11:27:09: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:27:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:27:09: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:27:09: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:27:09: #1 total tags in treatment: 13649990 INFO @ Mon, 03 Jun 2019 11:27:09: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:27:09: #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 11:27:10: #1 tags after filtering in treatment: 13649990 INFO @ Mon, 03 Jun 2019 11:27:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:27:10: #1 finished! INFO @ Mon, 03 Jun 2019 11:27:10: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:27:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:27:11: #2 number of paired peaks: 410 WARNING @ Mon, 03 Jun 2019 11:27:11: Fewer paired peaks (410) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 410 pairs to build model! INFO @ Mon, 03 Jun 2019 11:27:11: start model_add_line... INFO @ Mon, 03 Jun 2019 11:27:11: start X-correlation... INFO @ Mon, 03 Jun 2019 11:27:11: end of X-cor INFO @ Mon, 03 Jun 2019 11:27:11: #2 finished! INFO @ Mon, 03 Jun 2019 11:27:11: #2 predicted fragment length is 44 bps INFO @ Mon, 03 Jun 2019 11:27:11: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 03 Jun 2019 11:27:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288043/SRX288043.20_model.r WARNING @ Mon, 03 Jun 2019 11:27:11: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:27:11: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 03 Jun 2019 11:27:11: #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 11:27:11: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:27:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:27:21: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:27:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288043/SRX288043.05_peaks.xls INFO @ Mon, 03 Jun 2019 11:27:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288043/SRX288043.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:27:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288043/SRX288043.05_summits.bed INFO @ Mon, 03 Jun 2019 11:27:40: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (2221 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:27:47: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:27:48: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:28:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288043/SRX288043.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:28:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288043/SRX288043.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:28:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288043/SRX288043.10_summits.bed INFO @ Mon, 03 Jun 2019 11:28:05: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1940 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:28:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288043/SRX288043.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:28:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288043/SRX288043.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:28:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288043/SRX288043.20_summits.bed INFO @ Mon, 03 Jun 2019 11:28:06: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1523 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。