Job ID = 1301082 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T10:37:41 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 ) 2019-06-03T10:37:41 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 : 14,515,822 reads read : 29,031,644 reads written : 14,515,822 reads 0-length : 14,515,822 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: 00:05:46 14515822 reads; of these: 14515822 (100.00%) were unpaired; of these: 1115933 (7.69%) aligned 0 times 10300048 (70.96%) aligned exactly 1 time 3099841 (21.35%) aligned >1 times 92.31% overall alignment rate Time searching: 00:05:46 Overall time: 00:05:46 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] 3024619 / 13399889 = 0.2257 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 19:47:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4828019/SRX4828019.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4828019/SRX4828019.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4828019/SRX4828019.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4828019/SRX4828019.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 19:47:51: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:47:51: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:47:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4828019/SRX4828019.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4828019/SRX4828019.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4828019/SRX4828019.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4828019/SRX4828019.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 19:47:51: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:47:51: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:47:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4828019/SRX4828019.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4828019/SRX4828019.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4828019/SRX4828019.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4828019/SRX4828019.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 19:47:51: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:47:51: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:48:01: 1000000 INFO @ Mon, 03 Jun 2019 19:48:02: 1000000 INFO @ Mon, 03 Jun 2019 19:48:02: 1000000 INFO @ Mon, 03 Jun 2019 19:48:11: 2000000 INFO @ Mon, 03 Jun 2019 19:48:12: 2000000 INFO @ Mon, 03 Jun 2019 19:48:13: 2000000 INFO @ Mon, 03 Jun 2019 19:48:20: 3000000 INFO @ Mon, 03 Jun 2019 19:48:23: 3000000 INFO @ Mon, 03 Jun 2019 19:48:24: 3000000 INFO @ Mon, 03 Jun 2019 19:48:30: 4000000 INFO @ Mon, 03 Jun 2019 19:48:35: 4000000 INFO @ Mon, 03 Jun 2019 19:48:36: 4000000 INFO @ Mon, 03 Jun 2019 19:48:40: 5000000 INFO @ Mon, 03 Jun 2019 19:48:46: 5000000 INFO @ Mon, 03 Jun 2019 19:48:47: 5000000 INFO @ Mon, 03 Jun 2019 19:48:50: 6000000 INFO @ Mon, 03 Jun 2019 19:48:57: 6000000 INFO @ Mon, 03 Jun 2019 19:48:58: 6000000 INFO @ Mon, 03 Jun 2019 19:49:00: 7000000 INFO @ Mon, 03 Jun 2019 19:49:08: 7000000 INFO @ Mon, 03 Jun 2019 19:49:09: 7000000 INFO @ Mon, 03 Jun 2019 19:49:10: 8000000 INFO @ Mon, 03 Jun 2019 19:49:19: 8000000 INFO @ Mon, 03 Jun 2019 19:49:20: 9000000 INFO @ Mon, 03 Jun 2019 19:49:20: 8000000 INFO @ Mon, 03 Jun 2019 19:49:29: 10000000 INFO @ Mon, 03 Jun 2019 19:49:30: 9000000 INFO @ Mon, 03 Jun 2019 19:49:31: 9000000 INFO @ Mon, 03 Jun 2019 19:49:33: #1 tag size is determined as 49 bps INFO @ Mon, 03 Jun 2019 19:49:33: #1 tag size = 49 INFO @ Mon, 03 Jun 2019 19:49:33: #1 total tags in treatment: 10375270 INFO @ Mon, 03 Jun 2019 19:49:33: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:49:33: #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 19:49:33: #1 tags after filtering in treatment: 10375270 INFO @ Mon, 03 Jun 2019 19:49:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:49:33: #1 finished! INFO @ Mon, 03 Jun 2019 19:49:33: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:49:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:49:34: #2 number of paired peaks: 104 WARNING @ Mon, 03 Jun 2019 19:49:34: Fewer paired peaks (104) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 104 pairs to build model! INFO @ Mon, 03 Jun 2019 19:49:34: start model_add_line... INFO @ Mon, 03 Jun 2019 19:49:34: start X-correlation... INFO @ Mon, 03 Jun 2019 19:49:34: end of X-cor INFO @ Mon, 03 Jun 2019 19:49:34: #2 finished! INFO @ Mon, 03 Jun 2019 19:49:34: #2 predicted fragment length is 61 bps INFO @ Mon, 03 Jun 2019 19:49:34: #2 alternative fragment length(s) may be 61 bps INFO @ Mon, 03 Jun 2019 19:49:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4828019/SRX4828019.10_model.r WARNING @ Mon, 03 Jun 2019 19:49:34: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 19:49:34: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Mon, 03 Jun 2019 19:49:34: #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 19:49:34: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:49:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:49:40: 10000000 INFO @ Mon, 03 Jun 2019 19:49:41: 10000000 INFO @ Mon, 03 Jun 2019 19:49:44: #1 tag size is determined as 49 bps INFO @ Mon, 03 Jun 2019 19:49:44: #1 tag size = 49 INFO @ Mon, 03 Jun 2019 19:49:44: #1 total tags in treatment: 10375270 INFO @ Mon, 03 Jun 2019 19:49:44: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:49:44: #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 19:49:44: #1 tags after filtering in treatment: 10375270 INFO @ Mon, 03 Jun 2019 19:49:44: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:49:44: #1 finished! INFO @ Mon, 03 Jun 2019 19:49:44: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:49:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:49:45: #1 tag size is determined as 49 bps INFO @ Mon, 03 Jun 2019 19:49:45: #1 tag size = 49 INFO @ Mon, 03 Jun 2019 19:49:45: #1 total tags in treatment: 10375270 INFO @ Mon, 03 Jun 2019 19:49:45: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:49:45: #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 19:49:45: #1 tags after filtering in treatment: 10375270 INFO @ Mon, 03 Jun 2019 19:49:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:49:45: #1 finished! INFO @ Mon, 03 Jun 2019 19:49:45: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:49:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:49:45: #2 number of paired peaks: 104 WARNING @ Mon, 03 Jun 2019 19:49:45: Fewer paired peaks (104) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 104 pairs to build model! INFO @ Mon, 03 Jun 2019 19:49:45: start model_add_line... INFO @ Mon, 03 Jun 2019 19:49:45: start X-correlation... INFO @ Mon, 03 Jun 2019 19:49:45: end of X-cor INFO @ Mon, 03 Jun 2019 19:49:45: #2 finished! INFO @ Mon, 03 Jun 2019 19:49:45: #2 predicted fragment length is 61 bps INFO @ Mon, 03 Jun 2019 19:49:45: #2 alternative fragment length(s) may be 61 bps INFO @ Mon, 03 Jun 2019 19:49:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4828019/SRX4828019.20_model.r WARNING @ Mon, 03 Jun 2019 19:49:45: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 19:49:45: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Mon, 03 Jun 2019 19:49:45: #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 19:49:45: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:49:45: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:49:46: #2 number of paired peaks: 104 WARNING @ Mon, 03 Jun 2019 19:49:46: Fewer paired peaks (104) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 104 pairs to build model! INFO @ Mon, 03 Jun 2019 19:49:46: start model_add_line... INFO @ Mon, 03 Jun 2019 19:49:46: start X-correlation... INFO @ Mon, 03 Jun 2019 19:49:46: end of X-cor INFO @ Mon, 03 Jun 2019 19:49:46: #2 finished! INFO @ Mon, 03 Jun 2019 19:49:46: #2 predicted fragment length is 61 bps INFO @ Mon, 03 Jun 2019 19:49:46: #2 alternative fragment length(s) may be 61 bps INFO @ Mon, 03 Jun 2019 19:49:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4828019/SRX4828019.05_model.r WARNING @ Mon, 03 Jun 2019 19:49:46: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 19:49:46: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Mon, 03 Jun 2019 19:49:46: #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 19:49:46: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:49:46: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:50:03: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:50:14: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:50:15: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:50:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4828019/SRX4828019.10_peaks.xls INFO @ Mon, 03 Jun 2019 19:50:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4828019/SRX4828019.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:50:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4828019/SRX4828019.10_summits.bed INFO @ Mon, 03 Jun 2019 19:50:17: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (376 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:50:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4828019/SRX4828019.20_peaks.xls INFO @ Mon, 03 Jun 2019 19:50:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4828019/SRX4828019.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:50:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4828019/SRX4828019.20_summits.bed INFO @ Mon, 03 Jun 2019 19:50:28: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (191 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:50:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4828019/SRX4828019.05_peaks.xls INFO @ Mon, 03 Jun 2019 19:50:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4828019/SRX4828019.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:50:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4828019/SRX4828019.05_summits.bed INFO @ Mon, 03 Jun 2019 19:50:29: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (725 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。