Job ID = 1308551 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T13:53:41 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 ) 2019-06-03T13:53:41 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 ) 2019-06-03T13:53:41 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 : 20,780,672 reads read : 41,561,344 reads written : 20,780,672 reads 0-length : 20,780,672 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 20780672 reads; of these: 20780672 (100.00%) were unpaired; of these: 3620918 (17.42%) aligned 0 times 12492965 (60.12%) aligned exactly 1 time 4666789 (22.46%) aligned >1 times 82.58% 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] 6992698 / 17159754 = 0.4075 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 23:14:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343151/SRX5343151.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343151/SRX5343151.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343151/SRX5343151.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343151/SRX5343151.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 23:14:01: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:14:01: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:14:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343151/SRX5343151.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343151/SRX5343151.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343151/SRX5343151.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343151/SRX5343151.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 23:14:01: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:14:01: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:14:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343151/SRX5343151.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343151/SRX5343151.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343151/SRX5343151.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343151/SRX5343151.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 23:14:02: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:14:02: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:14:12: 1000000 INFO @ Mon, 03 Jun 2019 23:14:12: 1000000 INFO @ Mon, 03 Jun 2019 23:14:12: 1000000 INFO @ Mon, 03 Jun 2019 23:14:22: 2000000 INFO @ Mon, 03 Jun 2019 23:14:22: 2000000 INFO @ Mon, 03 Jun 2019 23:14:23: 2000000 INFO @ Mon, 03 Jun 2019 23:14:31: 3000000 INFO @ Mon, 03 Jun 2019 23:14:32: 3000000 INFO @ Mon, 03 Jun 2019 23:14:32: 3000000 INFO @ Mon, 03 Jun 2019 23:14:39: 4000000 INFO @ Mon, 03 Jun 2019 23:14:42: 4000000 INFO @ Mon, 03 Jun 2019 23:14:42: 4000000 INFO @ Mon, 03 Jun 2019 23:14:48: 5000000 INFO @ Mon, 03 Jun 2019 23:14:51: 5000000 INFO @ Mon, 03 Jun 2019 23:14:51: 5000000 INFO @ Mon, 03 Jun 2019 23:14:57: 6000000 INFO @ Mon, 03 Jun 2019 23:15:01: 6000000 INFO @ Mon, 03 Jun 2019 23:15:01: 6000000 INFO @ Mon, 03 Jun 2019 23:15:06: 7000000 INFO @ Mon, 03 Jun 2019 23:15:11: 7000000 INFO @ Mon, 03 Jun 2019 23:15:11: 7000000 INFO @ Mon, 03 Jun 2019 23:15:14: 8000000 INFO @ Mon, 03 Jun 2019 23:15:20: 8000000 INFO @ Mon, 03 Jun 2019 23:15:22: 8000000 INFO @ Mon, 03 Jun 2019 23:15:22: 9000000 INFO @ Mon, 03 Jun 2019 23:15:30: 9000000 INFO @ Mon, 03 Jun 2019 23:15:31: 10000000 INFO @ Mon, 03 Jun 2019 23:15:32: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 23:15:32: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 23:15:32: #1 total tags in treatment: 10167056 INFO @ Mon, 03 Jun 2019 23:15:32: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:15:32: #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 23:15:32: #1 tags after filtering in treatment: 10167056 INFO @ Mon, 03 Jun 2019 23:15:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:15:32: #1 finished! INFO @ Mon, 03 Jun 2019 23:15:32: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:15:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:15:33: #2 number of paired peaks: 825 WARNING @ Mon, 03 Jun 2019 23:15:33: Fewer paired peaks (825) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 825 pairs to build model! INFO @ Mon, 03 Jun 2019 23:15:33: start model_add_line... INFO @ Mon, 03 Jun 2019 23:15:34: start X-correlation... INFO @ Mon, 03 Jun 2019 23:15:34: end of X-cor INFO @ Mon, 03 Jun 2019 23:15:34: #2 finished! INFO @ Mon, 03 Jun 2019 23:15:34: #2 predicted fragment length is 90 bps INFO @ Mon, 03 Jun 2019 23:15:34: #2 alternative fragment length(s) may be 90 bps INFO @ Mon, 03 Jun 2019 23:15:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343151/SRX5343151.20_model.r WARNING @ Mon, 03 Jun 2019 23:15:34: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 23:15:34: #2 You may need to consider one of the other alternative d(s): 90 WARNING @ Mon, 03 Jun 2019 23:15:34: #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 23:15:34: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:15:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:15:34: 9000000 INFO @ Mon, 03 Jun 2019 23:15:39: 10000000 INFO @ Mon, 03 Jun 2019 23:15:41: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 23:15:41: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 23:15:41: #1 total tags in treatment: 10167056 INFO @ Mon, 03 Jun 2019 23:15:41: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:15:41: #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 23:15:41: #1 tags after filtering in treatment: 10167056 INFO @ Mon, 03 Jun 2019 23:15:41: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:15:41: #1 finished! INFO @ Mon, 03 Jun 2019 23:15:41: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:15:41: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:15:42: #2 number of paired peaks: 825 WARNING @ Mon, 03 Jun 2019 23:15:42: Fewer paired peaks (825) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 825 pairs to build model! INFO @ Mon, 03 Jun 2019 23:15:42: start model_add_line... INFO @ Mon, 03 Jun 2019 23:15:42: start X-correlation... INFO @ Mon, 03 Jun 2019 23:15:42: end of X-cor INFO @ Mon, 03 Jun 2019 23:15:42: #2 finished! INFO @ Mon, 03 Jun 2019 23:15:42: #2 predicted fragment length is 90 bps INFO @ Mon, 03 Jun 2019 23:15:42: #2 alternative fragment length(s) may be 90 bps INFO @ Mon, 03 Jun 2019 23:15:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343151/SRX5343151.05_model.r WARNING @ Mon, 03 Jun 2019 23:15:42: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 23:15:42: #2 You may need to consider one of the other alternative d(s): 90 WARNING @ Mon, 03 Jun 2019 23:15:42: #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 23:15:42: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:15:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:15:44: 10000000 INFO @ Mon, 03 Jun 2019 23:15:46: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 23:15:46: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 23:15:46: #1 total tags in treatment: 10167056 INFO @ Mon, 03 Jun 2019 23:15:46: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:15:46: #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 23:15:46: #1 tags after filtering in treatment: 10167056 INFO @ Mon, 03 Jun 2019 23:15:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:15:46: #1 finished! INFO @ Mon, 03 Jun 2019 23:15:46: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:15:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:15:47: #2 number of paired peaks: 825 WARNING @ Mon, 03 Jun 2019 23:15:47: Fewer paired peaks (825) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 825 pairs to build model! INFO @ Mon, 03 Jun 2019 23:15:47: start model_add_line... INFO @ Mon, 03 Jun 2019 23:15:47: start X-correlation... INFO @ Mon, 03 Jun 2019 23:15:47: end of X-cor INFO @ Mon, 03 Jun 2019 23:15:47: #2 finished! INFO @ Mon, 03 Jun 2019 23:15:47: #2 predicted fragment length is 90 bps INFO @ Mon, 03 Jun 2019 23:15:47: #2 alternative fragment length(s) may be 90 bps INFO @ Mon, 03 Jun 2019 23:15:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343151/SRX5343151.10_model.r WARNING @ Mon, 03 Jun 2019 23:15:47: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 23:15:47: #2 You may need to consider one of the other alternative d(s): 90 WARNING @ Mon, 03 Jun 2019 23:15:47: #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 23:15:47: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:15:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:16:02: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:16:10: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:16:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343151/SRX5343151.20_peaks.xls INFO @ Mon, 03 Jun 2019 23:16:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343151/SRX5343151.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:16:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343151/SRX5343151.20_summits.bed INFO @ Mon, 03 Jun 2019 23:16:16: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (657 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 23:16:17: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:16:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343151/SRX5343151.05_peaks.xls INFO @ Mon, 03 Jun 2019 23:16:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343151/SRX5343151.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:16:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343151/SRX5343151.05_summits.bed INFO @ Mon, 03 Jun 2019 23:16:24: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2287 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 23:16:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343151/SRX5343151.10_peaks.xls INFO @ Mon, 03 Jun 2019 23:16:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343151/SRX5343151.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:16:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343151/SRX5343151.10_summits.bed INFO @ Mon, 03 Jun 2019 23:16:32: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1142 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。