Job ID = 1308104 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T13:43:33 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 ) 2019-06-03T13:43:33 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 : 26,357,067 reads read : 52,714,134 reads written : 26,357,067 reads 0-length : 26,357,067 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: 00:10:25 26357067 reads; of these: 26357067 (100.00%) were unpaired; of these: 4193942 (15.91%) aligned 0 times 17444283 (66.18%) aligned exactly 1 time 4718842 (17.90%) aligned >1 times 84.09% overall alignment rate Time searching: 00:10:25 Overall time: 00:10:25 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] 9304343 / 22163125 = 0.4198 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 23:06:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343131/SRX5343131.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343131/SRX5343131.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343131/SRX5343131.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343131/SRX5343131.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 23:06:50: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:06:50: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:06:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343131/SRX5343131.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343131/SRX5343131.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343131/SRX5343131.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343131/SRX5343131.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 23:06:50: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:06:50: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:06:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343131/SRX5343131.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343131/SRX5343131.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343131/SRX5343131.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343131/SRX5343131.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 23:06:50: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:06:50: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:06:58: 1000000 INFO @ Mon, 03 Jun 2019 23:07:00: 1000000 INFO @ Mon, 03 Jun 2019 23:07:00: 1000000 INFO @ Mon, 03 Jun 2019 23:07:06: 2000000 INFO @ Mon, 03 Jun 2019 23:07:09: 2000000 INFO @ Mon, 03 Jun 2019 23:07:09: 2000000 INFO @ Mon, 03 Jun 2019 23:07:15: 3000000 INFO @ Mon, 03 Jun 2019 23:07:19: 3000000 INFO @ Mon, 03 Jun 2019 23:07:19: 3000000 INFO @ Mon, 03 Jun 2019 23:07:23: 4000000 INFO @ Mon, 03 Jun 2019 23:07:28: 4000000 INFO @ Mon, 03 Jun 2019 23:07:28: 4000000 INFO @ Mon, 03 Jun 2019 23:07:31: 5000000 INFO @ Mon, 03 Jun 2019 23:07:38: 5000000 INFO @ Mon, 03 Jun 2019 23:07:38: 5000000 INFO @ Mon, 03 Jun 2019 23:07:40: 6000000 INFO @ Mon, 03 Jun 2019 23:07:47: 6000000 INFO @ Mon, 03 Jun 2019 23:07:48: 6000000 INFO @ Mon, 03 Jun 2019 23:07:48: 7000000 INFO @ Mon, 03 Jun 2019 23:07:56: 8000000 INFO @ Mon, 03 Jun 2019 23:07:57: 7000000 INFO @ Mon, 03 Jun 2019 23:07:57: 7000000 INFO @ Mon, 03 Jun 2019 23:08:04: 9000000 INFO @ Mon, 03 Jun 2019 23:08:06: 8000000 INFO @ Mon, 03 Jun 2019 23:08:07: 8000000 INFO @ Mon, 03 Jun 2019 23:08:13: 10000000 INFO @ Mon, 03 Jun 2019 23:08:16: 9000000 INFO @ Mon, 03 Jun 2019 23:08:16: 9000000 INFO @ Mon, 03 Jun 2019 23:08:21: 11000000 INFO @ Mon, 03 Jun 2019 23:08:25: 10000000 INFO @ Mon, 03 Jun 2019 23:08:26: 10000000 INFO @ Mon, 03 Jun 2019 23:08:29: 12000000 INFO @ Mon, 03 Jun 2019 23:08:35: 11000000 INFO @ Mon, 03 Jun 2019 23:08:35: 11000000 INFO @ Mon, 03 Jun 2019 23:08:36: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 23:08:36: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 23:08:36: #1 total tags in treatment: 12858782 INFO @ Mon, 03 Jun 2019 23:08:36: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:08:36: #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 23:08:37: #1 tags after filtering in treatment: 12858782 INFO @ Mon, 03 Jun 2019 23:08:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:08:37: #1 finished! INFO @ Mon, 03 Jun 2019 23:08:37: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:08:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:08:38: #2 number of paired peaks: 265 WARNING @ Mon, 03 Jun 2019 23:08:38: Fewer paired peaks (265) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 265 pairs to build model! INFO @ Mon, 03 Jun 2019 23:08:38: start model_add_line... INFO @ Mon, 03 Jun 2019 23:08:38: start X-correlation... INFO @ Mon, 03 Jun 2019 23:08:38: end of X-cor INFO @ Mon, 03 Jun 2019 23:08:38: #2 finished! INFO @ Mon, 03 Jun 2019 23:08:38: #2 predicted fragment length is 70 bps INFO @ Mon, 03 Jun 2019 23:08:38: #2 alternative fragment length(s) may be 70 bps INFO @ Mon, 03 Jun 2019 23:08:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343131/SRX5343131.05_model.r WARNING @ Mon, 03 Jun 2019 23:08:38: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 23:08:38: #2 You may need to consider one of the other alternative d(s): 70 WARNING @ Mon, 03 Jun 2019 23:08:38: #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 23:08:38: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:08:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:08:44: 12000000 INFO @ Mon, 03 Jun 2019 23:08:45: 12000000 INFO @ Mon, 03 Jun 2019 23:08:52: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 23:08:52: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 23:08:52: #1 total tags in treatment: 12858782 INFO @ Mon, 03 Jun 2019 23:08:52: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:08:52: #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 23:08:53: #1 tags after filtering in treatment: 12858782 INFO @ Mon, 03 Jun 2019 23:08:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:08:53: #1 finished! INFO @ Mon, 03 Jun 2019 23:08:53: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:08:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:08:53: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 23:08:53: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 23:08:53: #1 total tags in treatment: 12858782 INFO @ Mon, 03 Jun 2019 23:08:53: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:08:53: #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 23:08:53: #1 tags after filtering in treatment: 12858782 INFO @ Mon, 03 Jun 2019 23:08:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:08:53: #1 finished! INFO @ Mon, 03 Jun 2019 23:08:53: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:08:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:08:54: #2 number of paired peaks: 265 WARNING @ Mon, 03 Jun 2019 23:08:54: Fewer paired peaks (265) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 265 pairs to build model! INFO @ Mon, 03 Jun 2019 23:08:54: start model_add_line... INFO @ Mon, 03 Jun 2019 23:08:54: start X-correlation... INFO @ Mon, 03 Jun 2019 23:08:54: end of X-cor INFO @ Mon, 03 Jun 2019 23:08:54: #2 finished! INFO @ Mon, 03 Jun 2019 23:08:54: #2 predicted fragment length is 70 bps INFO @ Mon, 03 Jun 2019 23:08:54: #2 alternative fragment length(s) may be 70 bps INFO @ Mon, 03 Jun 2019 23:08:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343131/SRX5343131.20_model.r WARNING @ Mon, 03 Jun 2019 23:08:54: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 23:08:54: #2 You may need to consider one of the other alternative d(s): 70 WARNING @ Mon, 03 Jun 2019 23:08:54: #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 23:08:54: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:08:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:08:54: #2 number of paired peaks: 265 WARNING @ Mon, 03 Jun 2019 23:08:54: Fewer paired peaks (265) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 265 pairs to build model! INFO @ Mon, 03 Jun 2019 23:08:54: start model_add_line... INFO @ Mon, 03 Jun 2019 23:08:54: start X-correlation... INFO @ Mon, 03 Jun 2019 23:08:54: end of X-cor INFO @ Mon, 03 Jun 2019 23:08:54: #2 finished! INFO @ Mon, 03 Jun 2019 23:08:54: #2 predicted fragment length is 70 bps INFO @ Mon, 03 Jun 2019 23:08:54: #2 alternative fragment length(s) may be 70 bps INFO @ Mon, 03 Jun 2019 23:08:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343131/SRX5343131.10_model.r WARNING @ Mon, 03 Jun 2019 23:08:54: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 23:08:54: #2 You may need to consider one of the other alternative d(s): 70 WARNING @ Mon, 03 Jun 2019 23:08:54: #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 23:08:54: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:08:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:09:13: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:09:29: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:09:30: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:09:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343131/SRX5343131.05_peaks.xls INFO @ Mon, 03 Jun 2019 23:09:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343131/SRX5343131.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:09:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343131/SRX5343131.05_summits.bed INFO @ Mon, 03 Jun 2019 23:09:31: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (4180 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 23:09:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343131/SRX5343131.20_peaks.xls INFO @ Mon, 03 Jun 2019 23:09:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343131/SRX5343131.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:09:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343131/SRX5343131.20_summits.bed INFO @ Mon, 03 Jun 2019 23:09:47: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (912 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 23:09:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343131/SRX5343131.10_peaks.xls INFO @ Mon, 03 Jun 2019 23:09:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343131/SRX5343131.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:09:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343131/SRX5343131.10_summits.bed INFO @ Mon, 03 Jun 2019 23:09:48: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1727 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。