Job ID = 1294484 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T23:17:08 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 : 11,258,758 reads read : 11,258,758 reads written : 11,258,758 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: 00:05:26 11258758 reads; of these: 11258758 (100.00%) were unpaired; of these: 550878 (4.89%) aligned 0 times 7134549 (63.37%) aligned exactly 1 time 3573331 (31.74%) aligned >1 times 95.11% overall alignment rate Time searching: 00:05:26 Overall time: 00:05:26 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] 1087205 / 10707880 = 0.1015 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 08:32:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287686/SRX287686.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287686/SRX287686.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287686/SRX287686.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287686/SRX287686.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 08:32:02: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:32:02: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:32:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287686/SRX287686.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287686/SRX287686.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287686/SRX287686.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287686/SRX287686.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 08:32:02: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:32:02: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:32:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287686/SRX287686.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287686/SRX287686.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287686/SRX287686.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287686/SRX287686.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 08:32:02: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:32:02: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:32:10: 1000000 INFO @ Mon, 03 Jun 2019 08:32:11: 1000000 INFO @ Mon, 03 Jun 2019 08:32:13: 1000000 INFO @ Mon, 03 Jun 2019 08:32:19: 2000000 INFO @ Mon, 03 Jun 2019 08:32:19: 2000000 INFO @ Mon, 03 Jun 2019 08:32:24: 2000000 INFO @ Mon, 03 Jun 2019 08:32:26: 3000000 INFO @ Mon, 03 Jun 2019 08:32:27: 3000000 INFO @ Mon, 03 Jun 2019 08:32:34: 4000000 INFO @ Mon, 03 Jun 2019 08:32:34: 3000000 INFO @ Mon, 03 Jun 2019 08:32:35: 4000000 INFO @ Mon, 03 Jun 2019 08:32:42: 5000000 INFO @ Mon, 03 Jun 2019 08:32:44: 5000000 INFO @ Mon, 03 Jun 2019 08:32:45: 4000000 INFO @ Mon, 03 Jun 2019 08:32:50: 6000000 INFO @ Mon, 03 Jun 2019 08:32:52: 6000000 INFO @ Mon, 03 Jun 2019 08:32:56: 5000000 INFO @ Mon, 03 Jun 2019 08:32:58: 7000000 INFO @ Mon, 03 Jun 2019 08:33:00: 7000000 INFO @ Mon, 03 Jun 2019 08:33:06: 8000000 INFO @ Mon, 03 Jun 2019 08:33:07: 6000000 INFO @ Mon, 03 Jun 2019 08:33:08: 8000000 INFO @ Mon, 03 Jun 2019 08:33:13: 9000000 INFO @ Mon, 03 Jun 2019 08:33:16: 9000000 INFO @ Mon, 03 Jun 2019 08:33:18: 7000000 INFO @ Mon, 03 Jun 2019 08:33:18: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:33:18: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:33:18: #1 total tags in treatment: 9620675 INFO @ Mon, 03 Jun 2019 08:33:18: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:33:18: #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 08:33:18: #1 tags after filtering in treatment: 9620675 INFO @ Mon, 03 Jun 2019 08:33:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:33:18: #1 finished! INFO @ Mon, 03 Jun 2019 08:33:18: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:33:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:33:19: #2 number of paired peaks: 399 WARNING @ Mon, 03 Jun 2019 08:33:19: Fewer paired peaks (399) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 399 pairs to build model! INFO @ Mon, 03 Jun 2019 08:33:19: start model_add_line... INFO @ Mon, 03 Jun 2019 08:33:19: start X-correlation... INFO @ Mon, 03 Jun 2019 08:33:19: end of X-cor INFO @ Mon, 03 Jun 2019 08:33:19: #2 finished! INFO @ Mon, 03 Jun 2019 08:33:19: #2 predicted fragment length is 48 bps INFO @ Mon, 03 Jun 2019 08:33:19: #2 alternative fragment length(s) may be 48 bps INFO @ Mon, 03 Jun 2019 08:33:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287686/SRX287686.05_model.r WARNING @ Mon, 03 Jun 2019 08:33:19: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 08:33:19: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Mon, 03 Jun 2019 08:33:19: #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 08:33:19: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:33:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:33:21: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:33:21: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:33:21: #1 total tags in treatment: 9620675 INFO @ Mon, 03 Jun 2019 08:33:21: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:33:21: #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 08:33:21: #1 tags after filtering in treatment: 9620675 INFO @ Mon, 03 Jun 2019 08:33:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:33:21: #1 finished! INFO @ Mon, 03 Jun 2019 08:33:21: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:33:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:33:22: #2 number of paired peaks: 399 WARNING @ Mon, 03 Jun 2019 08:33:22: Fewer paired peaks (399) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 399 pairs to build model! INFO @ Mon, 03 Jun 2019 08:33:22: start model_add_line... INFO @ Mon, 03 Jun 2019 08:33:22: start X-correlation... INFO @ Mon, 03 Jun 2019 08:33:22: end of X-cor INFO @ Mon, 03 Jun 2019 08:33:22: #2 finished! INFO @ Mon, 03 Jun 2019 08:33:22: #2 predicted fragment length is 48 bps INFO @ Mon, 03 Jun 2019 08:33:22: #2 alternative fragment length(s) may be 48 bps INFO @ Mon, 03 Jun 2019 08:33:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287686/SRX287686.20_model.r WARNING @ Mon, 03 Jun 2019 08:33:22: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 08:33:22: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Mon, 03 Jun 2019 08:33:22: #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 08:33:22: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:33:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:33:28: 8000000 INFO @ Mon, 03 Jun 2019 08:33:38: 9000000 INFO @ Mon, 03 Jun 2019 08:33:44: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:33:44: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:33:44: #1 total tags in treatment: 9620675 INFO @ Mon, 03 Jun 2019 08:33:44: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:33:44: #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 08:33:44: #1 tags after filtering in treatment: 9620675 INFO @ Mon, 03 Jun 2019 08:33:44: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:33:44: #1 finished! INFO @ Mon, 03 Jun 2019 08:33:44: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:33:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:33:45: #2 number of paired peaks: 399 WARNING @ Mon, 03 Jun 2019 08:33:45: Fewer paired peaks (399) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 399 pairs to build model! INFO @ Mon, 03 Jun 2019 08:33:45: start model_add_line... INFO @ Mon, 03 Jun 2019 08:33:45: start X-correlation... INFO @ Mon, 03 Jun 2019 08:33:45: end of X-cor INFO @ Mon, 03 Jun 2019 08:33:45: #2 finished! INFO @ Mon, 03 Jun 2019 08:33:45: #2 predicted fragment length is 48 bps INFO @ Mon, 03 Jun 2019 08:33:45: #2 alternative fragment length(s) may be 48 bps INFO @ Mon, 03 Jun 2019 08:33:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287686/SRX287686.10_model.r WARNING @ Mon, 03 Jun 2019 08:33:45: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 08:33:45: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Mon, 03 Jun 2019 08:33:45: #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 08:33:45: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:33:45: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:33:46: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:33:49: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:34:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287686/SRX287686.05_peaks.xls INFO @ Mon, 03 Jun 2019 08:34:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287686/SRX287686.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:34:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287686/SRX287686.05_summits.bed INFO @ Mon, 03 Jun 2019 08:34:00: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1953 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:34:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287686/SRX287686.20_peaks.xls INFO @ Mon, 03 Jun 2019 08:34:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287686/SRX287686.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:34:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287686/SRX287686.20_summits.bed INFO @ Mon, 03 Jun 2019 08:34:02: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (1179 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:34:12: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:34:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287686/SRX287686.10_peaks.xls INFO @ Mon, 03 Jun 2019 08:34:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287686/SRX287686.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:34:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287686/SRX287686.10_summits.bed INFO @ Mon, 03 Jun 2019 08:34:26: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1655 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。