Job ID = 1308882 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T14:02:35 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 ) 2019-06-03T14:08:04 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 : 31,647,145 reads read : 63,294,290 reads written : 31,647,145 reads 0-length : 31,647,145 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: 00:13:43 31647145 reads; of these: 31647145 (100.00%) were unpaired; of these: 5350787 (16.91%) aligned 0 times 19406748 (61.32%) aligned exactly 1 time 6889610 (21.77%) aligned >1 times 83.09% overall alignment rate Time searching: 00:13:43 Overall time: 00:13:43 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 12 files... [bam_rmdupse_core] 14955728 / 26296358 = 0.5687 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 23:29:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5661479/SRX5661479.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5661479/SRX5661479.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5661479/SRX5661479.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5661479/SRX5661479.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 23:29:52: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:29:52: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:29:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5661479/SRX5661479.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5661479/SRX5661479.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5661479/SRX5661479.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5661479/SRX5661479.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 23:29:52: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:29:52: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:29:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5661479/SRX5661479.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5661479/SRX5661479.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5661479/SRX5661479.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5661479/SRX5661479.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 23:29:53: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:29:53: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:30:01: 1000000 INFO @ Mon, 03 Jun 2019 23:30:01: 1000000 INFO @ Mon, 03 Jun 2019 23:30:03: 1000000 INFO @ Mon, 03 Jun 2019 23:30:08: 2000000 INFO @ Mon, 03 Jun 2019 23:30:11: 2000000 INFO @ Mon, 03 Jun 2019 23:30:13: 2000000 INFO @ Mon, 03 Jun 2019 23:30:16: 3000000 INFO @ Mon, 03 Jun 2019 23:30:20: 3000000 INFO @ Mon, 03 Jun 2019 23:30:23: 3000000 INFO @ Mon, 03 Jun 2019 23:30:23: 4000000 INFO @ Mon, 03 Jun 2019 23:30:28: 4000000 INFO @ Mon, 03 Jun 2019 23:30:31: 5000000 INFO @ Mon, 03 Jun 2019 23:30:33: 4000000 INFO @ Mon, 03 Jun 2019 23:30:36: 5000000 INFO @ Mon, 03 Jun 2019 23:30:38: 6000000 INFO @ Mon, 03 Jun 2019 23:30:43: 5000000 INFO @ Mon, 03 Jun 2019 23:30:44: 6000000 INFO @ Mon, 03 Jun 2019 23:30:46: 7000000 INFO @ Mon, 03 Jun 2019 23:30:52: 6000000 INFO @ Mon, 03 Jun 2019 23:30:53: 7000000 INFO @ Mon, 03 Jun 2019 23:30:53: 8000000 INFO @ Mon, 03 Jun 2019 23:31:00: 9000000 INFO @ Mon, 03 Jun 2019 23:31:01: 8000000 INFO @ Mon, 03 Jun 2019 23:31:02: 7000000 INFO @ Mon, 03 Jun 2019 23:31:08: 10000000 INFO @ Mon, 03 Jun 2019 23:31:09: 9000000 INFO @ Mon, 03 Jun 2019 23:31:12: 8000000 INFO @ Mon, 03 Jun 2019 23:31:16: 11000000 INFO @ Mon, 03 Jun 2019 23:31:18: 10000000 INFO @ Mon, 03 Jun 2019 23:31:18: #1 tag size is determined as 62 bps INFO @ Mon, 03 Jun 2019 23:31:18: #1 tag size = 62 INFO @ Mon, 03 Jun 2019 23:31:18: #1 total tags in treatment: 11340630 INFO @ Mon, 03 Jun 2019 23:31:18: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:31:18: #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 23:31:19: #1 tags after filtering in treatment: 11340630 INFO @ Mon, 03 Jun 2019 23:31:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:31:19: #1 finished! INFO @ Mon, 03 Jun 2019 23:31:19: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:31:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:31:20: #2 number of paired peaks: 326 WARNING @ Mon, 03 Jun 2019 23:31:20: Fewer paired peaks (326) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 326 pairs to build model! INFO @ Mon, 03 Jun 2019 23:31:20: start model_add_line... INFO @ Mon, 03 Jun 2019 23:31:20: start X-correlation... INFO @ Mon, 03 Jun 2019 23:31:20: end of X-cor INFO @ Mon, 03 Jun 2019 23:31:20: #2 finished! INFO @ Mon, 03 Jun 2019 23:31:20: #2 predicted fragment length is 56 bps INFO @ Mon, 03 Jun 2019 23:31:20: #2 alternative fragment length(s) may be 56 bps INFO @ Mon, 03 Jun 2019 23:31:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5661479/SRX5661479.20_model.r WARNING @ Mon, 03 Jun 2019 23:31:20: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 23:31:20: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Mon, 03 Jun 2019 23:31:20: #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 23:31:20: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:31:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:31:22: 9000000 INFO @ Mon, 03 Jun 2019 23:31:27: 11000000 INFO @ Mon, 03 Jun 2019 23:31:29: #1 tag size is determined as 62 bps INFO @ Mon, 03 Jun 2019 23:31:29: #1 tag size = 62 INFO @ Mon, 03 Jun 2019 23:31:29: #1 total tags in treatment: 11340630 INFO @ Mon, 03 Jun 2019 23:31:29: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:31:29: #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 23:31:30: #1 tags after filtering in treatment: 11340630 INFO @ Mon, 03 Jun 2019 23:31:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:31:30: #1 finished! INFO @ Mon, 03 Jun 2019 23:31:30: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:31:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:31:31: #2 number of paired peaks: 326 WARNING @ Mon, 03 Jun 2019 23:31:31: Fewer paired peaks (326) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 326 pairs to build model! INFO @ Mon, 03 Jun 2019 23:31:31: start model_add_line... INFO @ Mon, 03 Jun 2019 23:31:31: start X-correlation... INFO @ Mon, 03 Jun 2019 23:31:31: end of X-cor INFO @ Mon, 03 Jun 2019 23:31:31: #2 finished! INFO @ Mon, 03 Jun 2019 23:31:31: #2 predicted fragment length is 56 bps INFO @ Mon, 03 Jun 2019 23:31:31: #2 alternative fragment length(s) may be 56 bps INFO @ Mon, 03 Jun 2019 23:31:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5661479/SRX5661479.10_model.r WARNING @ Mon, 03 Jun 2019 23:31:31: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 23:31:31: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Mon, 03 Jun 2019 23:31:31: #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 23:31:31: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:31:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:31:31: 10000000 INFO @ Mon, 03 Jun 2019 23:31:41: 11000000 INFO @ Mon, 03 Jun 2019 23:31:44: #1 tag size is determined as 62 bps INFO @ Mon, 03 Jun 2019 23:31:44: #1 tag size = 62 INFO @ Mon, 03 Jun 2019 23:31:44: #1 total tags in treatment: 11340630 INFO @ Mon, 03 Jun 2019 23:31:44: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:31:44: #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 23:31:44: #1 tags after filtering in treatment: 11340630 INFO @ Mon, 03 Jun 2019 23:31:44: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:31:44: #1 finished! INFO @ Mon, 03 Jun 2019 23:31:44: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:31:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:31:45: #2 number of paired peaks: 326 WARNING @ Mon, 03 Jun 2019 23:31:45: Fewer paired peaks (326) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 326 pairs to build model! INFO @ Mon, 03 Jun 2019 23:31:45: start model_add_line... INFO @ Mon, 03 Jun 2019 23:31:45: start X-correlation... INFO @ Mon, 03 Jun 2019 23:31:45: end of X-cor INFO @ Mon, 03 Jun 2019 23:31:45: #2 finished! INFO @ Mon, 03 Jun 2019 23:31:45: #2 predicted fragment length is 56 bps INFO @ Mon, 03 Jun 2019 23:31:45: #2 alternative fragment length(s) may be 56 bps INFO @ Mon, 03 Jun 2019 23:31:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5661479/SRX5661479.05_model.r WARNING @ Mon, 03 Jun 2019 23:31:45: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 23:31:45: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Mon, 03 Jun 2019 23:31:45: #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 23:31:45: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:31:45: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:31:51: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:32:02: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:32:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5661479/SRX5661479.20_peaks.xls INFO @ Mon, 03 Jun 2019 23:32:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5661479/SRX5661479.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:32:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5661479/SRX5661479.20_summits.bed INFO @ Mon, 03 Jun 2019 23:32:06: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (954 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 23:32:17: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:32:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5661479/SRX5661479.10_peaks.xls INFO @ Mon, 03 Jun 2019 23:32:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5661479/SRX5661479.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:32:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5661479/SRX5661479.10_summits.bed INFO @ Mon, 03 Jun 2019 23:32:18: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1571 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 23:32:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5661479/SRX5661479.05_peaks.xls INFO @ Mon, 03 Jun 2019 23:32:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5661479/SRX5661479.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:32:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5661479/SRX5661479.05_summits.bed INFO @ Mon, 03 Jun 2019 23:32:33: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2914 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。