Job ID = 1306756 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T12:56:39 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 : 10,228,087 reads read : 10,228,087 reads written : 10,228,087 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: 00:03:59 10228087 reads; of these: 10228087 (100.00%) were unpaired; of these: 1111220 (10.86%) aligned 0 times 5994798 (58.61%) aligned exactly 1 time 3122069 (30.52%) aligned >1 times 89.14% overall alignment rate Time searching: 00:03:59 Overall time: 00:03:59 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_rmdupse_core] 2859776 / 9116867 = 0.3137 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 22:06:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX507387/SRX507387.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX507387/SRX507387.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX507387/SRX507387.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX507387/SRX507387.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 22:06:26: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:06:26: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:06:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX507387/SRX507387.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX507387/SRX507387.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX507387/SRX507387.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX507387/SRX507387.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 22:06:26: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:06:26: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:06:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX507387/SRX507387.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX507387/SRX507387.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX507387/SRX507387.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX507387/SRX507387.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 22:06:26: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:06:26: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:06:34: 1000000 INFO @ Mon, 03 Jun 2019 22:06:36: 1000000 INFO @ Mon, 03 Jun 2019 22:06:37: 1000000 INFO @ Mon, 03 Jun 2019 22:06:42: 2000000 INFO @ Mon, 03 Jun 2019 22:06:46: 2000000 INFO @ Mon, 03 Jun 2019 22:06:47: 2000000 INFO @ Mon, 03 Jun 2019 22:06:49: 3000000 INFO @ Mon, 03 Jun 2019 22:06:55: 3000000 INFO @ Mon, 03 Jun 2019 22:06:57: 3000000 INFO @ Mon, 03 Jun 2019 22:06:57: 4000000 INFO @ Mon, 03 Jun 2019 22:07:05: 5000000 INFO @ Mon, 03 Jun 2019 22:07:05: 4000000 INFO @ Mon, 03 Jun 2019 22:07:07: 4000000 INFO @ Mon, 03 Jun 2019 22:07:13: 6000000 INFO @ Mon, 03 Jun 2019 22:07:15: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 22:07:15: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 22:07:15: #1 total tags in treatment: 6257091 INFO @ Mon, 03 Jun 2019 22:07:15: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:07:15: #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 22:07:15: #1 tags after filtering in treatment: 6257091 INFO @ Mon, 03 Jun 2019 22:07:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:07:15: #1 finished! INFO @ Mon, 03 Jun 2019 22:07:15: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:07:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:07:15: 5000000 INFO @ Mon, 03 Jun 2019 22:07:16: #2 number of paired peaks: 342 WARNING @ Mon, 03 Jun 2019 22:07:16: Fewer paired peaks (342) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 342 pairs to build model! INFO @ Mon, 03 Jun 2019 22:07:16: start model_add_line... INFO @ Mon, 03 Jun 2019 22:07:16: start X-correlation... INFO @ Mon, 03 Jun 2019 22:07:16: end of X-cor INFO @ Mon, 03 Jun 2019 22:07:16: #2 finished! INFO @ Mon, 03 Jun 2019 22:07:16: #2 predicted fragment length is 54 bps INFO @ Mon, 03 Jun 2019 22:07:16: #2 alternative fragment length(s) may be 54 bps INFO @ Mon, 03 Jun 2019 22:07:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX507387/SRX507387.05_model.r WARNING @ Mon, 03 Jun 2019 22:07:16: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:07:16: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Mon, 03 Jun 2019 22:07:16: #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 22:07:16: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:07:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:07:17: 5000000 INFO @ Mon, 03 Jun 2019 22:07:25: 6000000 INFO @ Mon, 03 Jun 2019 22:07:26: 6000000 INFO @ Mon, 03 Jun 2019 22:07:27: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 22:07:27: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 22:07:27: #1 total tags in treatment: 6257091 INFO @ Mon, 03 Jun 2019 22:07:27: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:07:27: #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 22:07:27: #1 tags after filtering in treatment: 6257091 INFO @ Mon, 03 Jun 2019 22:07:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:07:27: #1 finished! INFO @ Mon, 03 Jun 2019 22:07:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:07:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:07:28: #2 number of paired peaks: 342 WARNING @ Mon, 03 Jun 2019 22:07:28: Fewer paired peaks (342) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 342 pairs to build model! INFO @ Mon, 03 Jun 2019 22:07:28: start model_add_line... INFO @ Mon, 03 Jun 2019 22:07:28: start X-correlation... INFO @ Mon, 03 Jun 2019 22:07:28: end of X-cor INFO @ Mon, 03 Jun 2019 22:07:28: #2 finished! INFO @ Mon, 03 Jun 2019 22:07:28: #2 predicted fragment length is 54 bps INFO @ Mon, 03 Jun 2019 22:07:28: #2 alternative fragment length(s) may be 54 bps INFO @ Mon, 03 Jun 2019 22:07:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX507387/SRX507387.20_model.r WARNING @ Mon, 03 Jun 2019 22:07:28: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:07:28: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Mon, 03 Jun 2019 22:07:28: #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 22:07:28: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:07:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:07:28: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 22:07:28: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 22:07:28: #1 total tags in treatment: 6257091 INFO @ Mon, 03 Jun 2019 22:07:28: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:07:28: #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 22:07:29: #1 tags after filtering in treatment: 6257091 INFO @ Mon, 03 Jun 2019 22:07:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:07:29: #1 finished! INFO @ Mon, 03 Jun 2019 22:07:29: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:07:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:07:29: #2 number of paired peaks: 342 WARNING @ Mon, 03 Jun 2019 22:07:29: Fewer paired peaks (342) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 342 pairs to build model! INFO @ Mon, 03 Jun 2019 22:07:29: start model_add_line... INFO @ Mon, 03 Jun 2019 22:07:29: start X-correlation... INFO @ Mon, 03 Jun 2019 22:07:29: end of X-cor INFO @ Mon, 03 Jun 2019 22:07:29: #2 finished! INFO @ Mon, 03 Jun 2019 22:07:29: #2 predicted fragment length is 54 bps INFO @ Mon, 03 Jun 2019 22:07:29: #2 alternative fragment length(s) may be 54 bps INFO @ Mon, 03 Jun 2019 22:07:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX507387/SRX507387.10_model.r WARNING @ Mon, 03 Jun 2019 22:07:29: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:07:29: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Mon, 03 Jun 2019 22:07:29: #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 22:07:29: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:07:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:07:34: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:07:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX507387/SRX507387.05_peaks.xls INFO @ Mon, 03 Jun 2019 22:07:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX507387/SRX507387.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:07:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX507387/SRX507387.05_summits.bed INFO @ Mon, 03 Jun 2019 22:07:44: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1379 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:07:47: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:07:47: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:07:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX507387/SRX507387.20_peaks.xls INFO @ Mon, 03 Jun 2019 22:07:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX507387/SRX507387.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:07:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX507387/SRX507387.20_summits.bed INFO @ Mon, 03 Jun 2019 22:07:57: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (585 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:07:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX507387/SRX507387.10_peaks.xls INFO @ Mon, 03 Jun 2019 22:07:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX507387/SRX507387.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:07:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX507387/SRX507387.10_summits.bed INFO @ Mon, 03 Jun 2019 22:07:58: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (930 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。