Job ID = 1300037 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T09:51:12 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 : 13,520,069 reads read : 13,520,069 reads written : 13,520,069 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:07 13520069 reads; of these: 13520069 (100.00%) were unpaired; of these: 463826 (3.43%) aligned 0 times 8996630 (66.54%) aligned exactly 1 time 4059613 (30.03%) aligned >1 times 96.57% overall alignment rate Time searching: 00:07:08 Overall time: 00:07:08 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] 1357333 / 13056243 = 0.1040 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 19:04:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4801804/SRX4801804.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4801804/SRX4801804.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4801804/SRX4801804.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4801804/SRX4801804.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 19:04:58: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:04:58: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:04:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4801804/SRX4801804.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4801804/SRX4801804.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4801804/SRX4801804.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4801804/SRX4801804.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 19:04:58: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:04:58: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:04:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4801804/SRX4801804.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4801804/SRX4801804.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4801804/SRX4801804.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4801804/SRX4801804.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 19:04:58: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:04:58: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:05:07: 1000000 INFO @ Mon, 03 Jun 2019 19:05:07: 1000000 INFO @ Mon, 03 Jun 2019 19:05:09: 1000000 INFO @ Mon, 03 Jun 2019 19:05:15: 2000000 INFO @ Mon, 03 Jun 2019 19:05:17: 2000000 INFO @ Mon, 03 Jun 2019 19:05:20: 2000000 INFO @ Mon, 03 Jun 2019 19:05:24: 3000000 INFO @ Mon, 03 Jun 2019 19:05:26: 3000000 INFO @ Mon, 03 Jun 2019 19:05:29: 3000000 INFO @ Mon, 03 Jun 2019 19:05:32: 4000000 INFO @ Mon, 03 Jun 2019 19:05:34: 4000000 INFO @ Mon, 03 Jun 2019 19:05:39: 4000000 INFO @ Mon, 03 Jun 2019 19:05:40: 5000000 INFO @ Mon, 03 Jun 2019 19:05:43: 5000000 INFO @ Mon, 03 Jun 2019 19:05:48: 6000000 INFO @ Mon, 03 Jun 2019 19:05:49: 5000000 INFO @ Mon, 03 Jun 2019 19:05:52: 6000000 INFO @ Mon, 03 Jun 2019 19:05:56: 7000000 INFO @ Mon, 03 Jun 2019 19:05:58: 6000000 INFO @ Mon, 03 Jun 2019 19:06:02: 7000000 INFO @ Mon, 03 Jun 2019 19:06:05: 8000000 INFO @ Mon, 03 Jun 2019 19:06:08: 7000000 INFO @ Mon, 03 Jun 2019 19:06:10: 8000000 INFO @ Mon, 03 Jun 2019 19:06:13: 9000000 INFO @ Mon, 03 Jun 2019 19:06:18: 8000000 INFO @ Mon, 03 Jun 2019 19:06:19: 9000000 INFO @ Mon, 03 Jun 2019 19:06:21: 10000000 INFO @ Mon, 03 Jun 2019 19:06:28: 9000000 INFO @ Mon, 03 Jun 2019 19:06:28: 10000000 INFO @ Mon, 03 Jun 2019 19:06:29: 11000000 INFO @ Mon, 03 Jun 2019 19:06:35: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 19:06:35: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 19:06:35: #1 total tags in treatment: 11698910 INFO @ Mon, 03 Jun 2019 19:06:35: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:06:35: #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 19:06:35: #1 tags after filtering in treatment: 11698910 INFO @ Mon, 03 Jun 2019 19:06:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:06:35: #1 finished! INFO @ Mon, 03 Jun 2019 19:06:35: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:06:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:06:36: #2 number of paired peaks: 946 WARNING @ Mon, 03 Jun 2019 19:06:36: Fewer paired peaks (946) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 946 pairs to build model! INFO @ Mon, 03 Jun 2019 19:06:36: start model_add_line... INFO @ Mon, 03 Jun 2019 19:06:36: start X-correlation... INFO @ Mon, 03 Jun 2019 19:06:36: end of X-cor INFO @ Mon, 03 Jun 2019 19:06:36: #2 finished! INFO @ Mon, 03 Jun 2019 19:06:36: #2 predicted fragment length is 75 bps INFO @ Mon, 03 Jun 2019 19:06:36: #2 alternative fragment length(s) may be 4,75 bps INFO @ Mon, 03 Jun 2019 19:06:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4801804/SRX4801804.10_model.r WARNING @ Mon, 03 Jun 2019 19:06:36: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 19:06:36: #2 You may need to consider one of the other alternative d(s): 4,75 WARNING @ Mon, 03 Jun 2019 19:06:36: #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 19:06:36: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:06:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:06:37: 11000000 INFO @ Mon, 03 Jun 2019 19:06:37: 10000000 INFO @ Mon, 03 Jun 2019 19:06:44: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 19:06:44: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 19:06:44: #1 total tags in treatment: 11698910 INFO @ Mon, 03 Jun 2019 19:06:44: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:06:44: #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 19:06:44: #1 tags after filtering in treatment: 11698910 INFO @ Mon, 03 Jun 2019 19:06:44: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:06:44: #1 finished! INFO @ Mon, 03 Jun 2019 19:06:44: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:06:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:06:45: #2 number of paired peaks: 946 WARNING @ Mon, 03 Jun 2019 19:06:45: Fewer paired peaks (946) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 946 pairs to build model! INFO @ Mon, 03 Jun 2019 19:06:45: start model_add_line... INFO @ Mon, 03 Jun 2019 19:06:45: start X-correlation... INFO @ Mon, 03 Jun 2019 19:06:45: end of X-cor INFO @ Mon, 03 Jun 2019 19:06:45: #2 finished! INFO @ Mon, 03 Jun 2019 19:06:45: #2 predicted fragment length is 75 bps INFO @ Mon, 03 Jun 2019 19:06:45: #2 alternative fragment length(s) may be 4,75 bps INFO @ Mon, 03 Jun 2019 19:06:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4801804/SRX4801804.20_model.r WARNING @ Mon, 03 Jun 2019 19:06:45: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 19:06:45: #2 You may need to consider one of the other alternative d(s): 4,75 WARNING @ Mon, 03 Jun 2019 19:06:45: #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 19:06:45: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:06:45: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:06:48: 11000000 INFO @ Mon, 03 Jun 2019 19:06:55: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 19:06:55: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 19:06:55: #1 total tags in treatment: 11698910 INFO @ Mon, 03 Jun 2019 19:06:55: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:06:55: #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 19:06:55: #1 tags after filtering in treatment: 11698910 INFO @ Mon, 03 Jun 2019 19:06:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:06:55: #1 finished! INFO @ Mon, 03 Jun 2019 19:06:55: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:06:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:06:56: #2 number of paired peaks: 946 WARNING @ Mon, 03 Jun 2019 19:06:56: Fewer paired peaks (946) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 946 pairs to build model! INFO @ Mon, 03 Jun 2019 19:06:56: start model_add_line... INFO @ Mon, 03 Jun 2019 19:06:57: start X-correlation... INFO @ Mon, 03 Jun 2019 19:06:57: end of X-cor INFO @ Mon, 03 Jun 2019 19:06:57: #2 finished! INFO @ Mon, 03 Jun 2019 19:06:57: #2 predicted fragment length is 75 bps INFO @ Mon, 03 Jun 2019 19:06:57: #2 alternative fragment length(s) may be 4,75 bps INFO @ Mon, 03 Jun 2019 19:06:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4801804/SRX4801804.05_model.r WARNING @ Mon, 03 Jun 2019 19:06:57: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 19:06:57: #2 You may need to consider one of the other alternative d(s): 4,75 WARNING @ Mon, 03 Jun 2019 19:06:57: #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 19:06:57: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:06:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:07:10: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:07:19: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:07:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4801804/SRX4801804.10_peaks.xls INFO @ Mon, 03 Jun 2019 19:07:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4801804/SRX4801804.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:07:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4801804/SRX4801804.10_summits.bed INFO @ Mon, 03 Jun 2019 19:07:26: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (1622 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:07:31: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:07:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4801804/SRX4801804.20_peaks.xls INFO @ Mon, 03 Jun 2019 19:07:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4801804/SRX4801804.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:07:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4801804/SRX4801804.20_summits.bed INFO @ Mon, 03 Jun 2019 19:07:35: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (794 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:07:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4801804/SRX4801804.05_peaks.xls INFO @ Mon, 03 Jun 2019 19:07:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4801804/SRX4801804.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:07:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4801804/SRX4801804.05_summits.bed INFO @ Mon, 03 Jun 2019 19:07:47: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3022 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。