Job ID = 1294962 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T02:00:09 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 ) 2019-06-03T02:00:09 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 ) 2019-06-03T02:00:09 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 : 14,811,631 reads read : 14,811,631 reads written : 14,811,631 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: 00:05:41 14811631 reads; of these: 14811631 (100.00%) were unpaired; of these: 1094611 (7.39%) aligned 0 times 10685176 (72.14%) aligned exactly 1 time 3031844 (20.47%) aligned >1 times 92.61% overall alignment rate Time searching: 00:05:41 Overall time: 00:05:41 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] 1391538 / 13717020 = 0.1014 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 11:13:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288023/SRX288023.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288023/SRX288023.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288023/SRX288023.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288023/SRX288023.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 11:13:23: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:13:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288023/SRX288023.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288023/SRX288023.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288023/SRX288023.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288023/SRX288023.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 11:13:23: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:13:23: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:13:23: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:13:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288023/SRX288023.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288023/SRX288023.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288023/SRX288023.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288023/SRX288023.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 11:13:23: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:13:23: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:13:31: 1000000 INFO @ Mon, 03 Jun 2019 11:13:32: 1000000 INFO @ Mon, 03 Jun 2019 11:13:32: 1000000 INFO @ Mon, 03 Jun 2019 11:13:37: 2000000 INFO @ Mon, 03 Jun 2019 11:13:39: 2000000 INFO @ Mon, 03 Jun 2019 11:13:39: 2000000 INFO @ Mon, 03 Jun 2019 11:13:44: 3000000 INFO @ Mon, 03 Jun 2019 11:13:47: 3000000 INFO @ Mon, 03 Jun 2019 11:13:47: 3000000 INFO @ Mon, 03 Jun 2019 11:13:51: 4000000 INFO @ Mon, 03 Jun 2019 11:13:56: 4000000 INFO @ Mon, 03 Jun 2019 11:13:56: 4000000 INFO @ Mon, 03 Jun 2019 11:13:58: 5000000 INFO @ Mon, 03 Jun 2019 11:14:04: 5000000 INFO @ Mon, 03 Jun 2019 11:14:04: 5000000 INFO @ Mon, 03 Jun 2019 11:14:05: 6000000 INFO @ Mon, 03 Jun 2019 11:14:11: 6000000 INFO @ Mon, 03 Jun 2019 11:14:11: 6000000 INFO @ Mon, 03 Jun 2019 11:14:12: 7000000 INFO @ Mon, 03 Jun 2019 11:14:19: 8000000 INFO @ Mon, 03 Jun 2019 11:14:19: 7000000 INFO @ Mon, 03 Jun 2019 11:14:19: 7000000 INFO @ Mon, 03 Jun 2019 11:14:26: 9000000 INFO @ Mon, 03 Jun 2019 11:14:28: 8000000 INFO @ Mon, 03 Jun 2019 11:14:28: 8000000 INFO @ Mon, 03 Jun 2019 11:14:33: 10000000 INFO @ Mon, 03 Jun 2019 11:14:35: 9000000 INFO @ Mon, 03 Jun 2019 11:14:37: 9000000 INFO @ Mon, 03 Jun 2019 11:14:40: 11000000 INFO @ Mon, 03 Jun 2019 11:14:44: 10000000 INFO @ Mon, 03 Jun 2019 11:14:45: 10000000 INFO @ Mon, 03 Jun 2019 11:14:48: 12000000 INFO @ Mon, 03 Jun 2019 11:14:50: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:14:50: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:14:50: #1 total tags in treatment: 12325482 INFO @ Mon, 03 Jun 2019 11:14:50: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:14:50: #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 11:14:50: #1 tags after filtering in treatment: 12325482 INFO @ Mon, 03 Jun 2019 11:14:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:14:50: #1 finished! INFO @ Mon, 03 Jun 2019 11:14:50: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:14:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:14:52: #2 number of paired peaks: 154 WARNING @ Mon, 03 Jun 2019 11:14:52: Fewer paired peaks (154) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 154 pairs to build model! INFO @ Mon, 03 Jun 2019 11:14:52: start model_add_line... INFO @ Mon, 03 Jun 2019 11:14:52: start X-correlation... INFO @ Mon, 03 Jun 2019 11:14:52: end of X-cor INFO @ Mon, 03 Jun 2019 11:14:52: #2 finished! INFO @ Mon, 03 Jun 2019 11:14:52: #2 predicted fragment length is 47 bps INFO @ Mon, 03 Jun 2019 11:14:52: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 03 Jun 2019 11:14:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288023/SRX288023.10_model.r WARNING @ Mon, 03 Jun 2019 11:14:52: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:14:52: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 03 Jun 2019 11:14:52: #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 11:14:52: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:14:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:14:52: 11000000 INFO @ Mon, 03 Jun 2019 11:14:54: 11000000 INFO @ Mon, 03 Jun 2019 11:15:00: 12000000 INFO @ Mon, 03 Jun 2019 11:15:03: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:15:03: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:15:03: #1 total tags in treatment: 12325482 INFO @ Mon, 03 Jun 2019 11:15:03: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:15:03: #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 11:15:03: #1 tags after filtering in treatment: 12325482 INFO @ Mon, 03 Jun 2019 11:15:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:15:03: #1 finished! INFO @ Mon, 03 Jun 2019 11:15:03: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:15:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:15:03: 12000000 INFO @ Mon, 03 Jun 2019 11:15:04: #2 number of paired peaks: 154 WARNING @ Mon, 03 Jun 2019 11:15:04: Fewer paired peaks (154) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 154 pairs to build model! INFO @ Mon, 03 Jun 2019 11:15:04: start model_add_line... INFO @ Mon, 03 Jun 2019 11:15:04: start X-correlation... INFO @ Mon, 03 Jun 2019 11:15:04: end of X-cor INFO @ Mon, 03 Jun 2019 11:15:04: #2 finished! INFO @ Mon, 03 Jun 2019 11:15:04: #2 predicted fragment length is 47 bps INFO @ Mon, 03 Jun 2019 11:15:04: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 03 Jun 2019 11:15:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288023/SRX288023.05_model.r WARNING @ Mon, 03 Jun 2019 11:15:04: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:15:04: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 03 Jun 2019 11:15:04: #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 11:15:04: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:15:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:15:06: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:15:06: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:15:06: #1 total tags in treatment: 12325482 INFO @ Mon, 03 Jun 2019 11:15:06: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:15:06: #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 11:15:06: #1 tags after filtering in treatment: 12325482 INFO @ Mon, 03 Jun 2019 11:15:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:15:06: #1 finished! INFO @ Mon, 03 Jun 2019 11:15:06: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:15:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:15:08: #2 number of paired peaks: 154 WARNING @ Mon, 03 Jun 2019 11:15:08: Fewer paired peaks (154) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 154 pairs to build model! INFO @ Mon, 03 Jun 2019 11:15:08: start model_add_line... INFO @ Mon, 03 Jun 2019 11:15:08: start X-correlation... INFO @ Mon, 03 Jun 2019 11:15:08: end of X-cor INFO @ Mon, 03 Jun 2019 11:15:08: #2 finished! INFO @ Mon, 03 Jun 2019 11:15:08: #2 predicted fragment length is 47 bps INFO @ Mon, 03 Jun 2019 11:15:08: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 03 Jun 2019 11:15:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288023/SRX288023.20_model.r WARNING @ Mon, 03 Jun 2019 11:15:08: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:15:08: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 03 Jun 2019 11:15:08: #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 11:15:08: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:15:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:15:24: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:15:38: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:15:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288023/SRX288023.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:15:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288023/SRX288023.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:15:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288023/SRX288023.10_summits.bed INFO @ Mon, 03 Jun 2019 11:15:41: Done! INFO @ Mon, 03 Jun 2019 11:15:41: #3 Call peaks for each chromosome... pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (1289 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:15:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288023/SRX288023.05_peaks.xls INFO @ Mon, 03 Jun 2019 11:15:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288023/SRX288023.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:15:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288023/SRX288023.05_summits.bed INFO @ Mon, 03 Jun 2019 11:15:54: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1559 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:15:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288023/SRX288023.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:15:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288023/SRX288023.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:15:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288023/SRX288023.20_summits.bed INFO @ Mon, 03 Jun 2019 11:15:58: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (890 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。