Job ID = 1300207 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T10:05:09 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 ) 2019-06-03T10:05:09 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 ) 2019-06-03T10:05:09 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 ) 2019-06-03T10:05:09 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 : 12,987,980 reads read : 12,987,980 reads written : 12,987,980 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: 00:06:50 12987980 reads; of these: 12987980 (100.00%) were unpaired; of these: 326863 (2.52%) aligned 0 times 8550201 (65.83%) aligned exactly 1 time 4110916 (31.65%) aligned >1 times 97.48% overall alignment rate Time searching: 00:06:50 Overall time: 00:06:50 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] 1139377 / 12661117 = 0.0900 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 19:19:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4801812/SRX4801812.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4801812/SRX4801812.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4801812/SRX4801812.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4801812/SRX4801812.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 19:19:33: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:19:33: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:19:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4801812/SRX4801812.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4801812/SRX4801812.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4801812/SRX4801812.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4801812/SRX4801812.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 19:19:33: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:19:33: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:19:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4801812/SRX4801812.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4801812/SRX4801812.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4801812/SRX4801812.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4801812/SRX4801812.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 19:19:33: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:19:33: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:19:41: 1000000 INFO @ Mon, 03 Jun 2019 19:19:42: 1000000 INFO @ Mon, 03 Jun 2019 19:19:43: 1000000 INFO @ Mon, 03 Jun 2019 19:19:49: 2000000 INFO @ Mon, 03 Jun 2019 19:19:50: 2000000 INFO @ Mon, 03 Jun 2019 19:19:52: 2000000 INFO @ Mon, 03 Jun 2019 19:19:57: 3000000 INFO @ Mon, 03 Jun 2019 19:19:57: 3000000 INFO @ Mon, 03 Jun 2019 19:20:00: 3000000 INFO @ Mon, 03 Jun 2019 19:20:04: 4000000 INFO @ Mon, 03 Jun 2019 19:20:05: 4000000 INFO @ Mon, 03 Jun 2019 19:20:09: 4000000 INFO @ Mon, 03 Jun 2019 19:20:12: 5000000 INFO @ Mon, 03 Jun 2019 19:20:12: 5000000 INFO @ Mon, 03 Jun 2019 19:20:18: 5000000 INFO @ Mon, 03 Jun 2019 19:20:19: 6000000 INFO @ Mon, 03 Jun 2019 19:20:20: 6000000 INFO @ Mon, 03 Jun 2019 19:20:26: 6000000 INFO @ Mon, 03 Jun 2019 19:20:26: 7000000 INFO @ Mon, 03 Jun 2019 19:20:27: 7000000 INFO @ Mon, 03 Jun 2019 19:20:34: 8000000 INFO @ Mon, 03 Jun 2019 19:20:35: 8000000 INFO @ Mon, 03 Jun 2019 19:20:35: 7000000 INFO @ Mon, 03 Jun 2019 19:20:41: 9000000 INFO @ Mon, 03 Jun 2019 19:20:42: 9000000 INFO @ Mon, 03 Jun 2019 19:20:44: 8000000 INFO @ Mon, 03 Jun 2019 19:20:48: 10000000 INFO @ Mon, 03 Jun 2019 19:20:50: 10000000 INFO @ Mon, 03 Jun 2019 19:20:52: 9000000 INFO @ Mon, 03 Jun 2019 19:20:56: 11000000 INFO @ Mon, 03 Jun 2019 19:20:57: 11000000 INFO @ Mon, 03 Jun 2019 19:21:00: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 19:21:00: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 19:21:00: #1 total tags in treatment: 11521740 INFO @ Mon, 03 Jun 2019 19:21:00: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:21:00: #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 19:21:00: #1 tags after filtering in treatment: 11521740 INFO @ Mon, 03 Jun 2019 19:21:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:21:00: #1 finished! INFO @ Mon, 03 Jun 2019 19:21:00: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:21:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:21:01: 10000000 INFO @ Mon, 03 Jun 2019 19:21:01: #2 number of paired peaks: 1144 INFO @ Mon, 03 Jun 2019 19:21:01: start model_add_line... INFO @ Mon, 03 Jun 2019 19:21:01: start X-correlation... INFO @ Mon, 03 Jun 2019 19:21:01: end of X-cor INFO @ Mon, 03 Jun 2019 19:21:01: #2 finished! INFO @ Mon, 03 Jun 2019 19:21:01: #2 predicted fragment length is 69 bps INFO @ Mon, 03 Jun 2019 19:21:01: #2 alternative fragment length(s) may be 4,69 bps INFO @ Mon, 03 Jun 2019 19:21:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4801812/SRX4801812.20_model.r WARNING @ Mon, 03 Jun 2019 19:21:01: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 19:21:01: #2 You may need to consider one of the other alternative d(s): 4,69 WARNING @ Mon, 03 Jun 2019 19:21:01: #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 19:21:01: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:21:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:21:01: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 19:21:01: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 19:21:01: #1 total tags in treatment: 11521740 INFO @ Mon, 03 Jun 2019 19:21:01: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:21:01: #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 19:21:01: #1 tags after filtering in treatment: 11521740 INFO @ Mon, 03 Jun 2019 19:21:01: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:21:01: #1 finished! INFO @ Mon, 03 Jun 2019 19:21:01: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:21:01: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:21:03: #2 number of paired peaks: 1144 INFO @ Mon, 03 Jun 2019 19:21:03: start model_add_line... INFO @ Mon, 03 Jun 2019 19:21:03: start X-correlation... INFO @ Mon, 03 Jun 2019 19:21:03: end of X-cor INFO @ Mon, 03 Jun 2019 19:21:03: #2 finished! INFO @ Mon, 03 Jun 2019 19:21:03: #2 predicted fragment length is 69 bps INFO @ Mon, 03 Jun 2019 19:21:03: #2 alternative fragment length(s) may be 4,69 bps INFO @ Mon, 03 Jun 2019 19:21:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4801812/SRX4801812.05_model.r WARNING @ Mon, 03 Jun 2019 19:21:03: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 19:21:03: #2 You may need to consider one of the other alternative d(s): 4,69 WARNING @ Mon, 03 Jun 2019 19:21:03: #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 19:21:03: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:21:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:21:09: 11000000 INFO @ Mon, 03 Jun 2019 19:21:14: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 19:21:14: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 19:21:14: #1 total tags in treatment: 11521740 INFO @ Mon, 03 Jun 2019 19:21:14: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:21:14: #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 19:21:14: #1 tags after filtering in treatment: 11521740 INFO @ Mon, 03 Jun 2019 19:21:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:21:14: #1 finished! INFO @ Mon, 03 Jun 2019 19:21:14: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:21:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:21:15: #2 number of paired peaks: 1144 INFO @ Mon, 03 Jun 2019 19:21:15: start model_add_line... INFO @ Mon, 03 Jun 2019 19:21:15: start X-correlation... INFO @ Mon, 03 Jun 2019 19:21:16: end of X-cor INFO @ Mon, 03 Jun 2019 19:21:16: #2 finished! INFO @ Mon, 03 Jun 2019 19:21:16: #2 predicted fragment length is 69 bps INFO @ Mon, 03 Jun 2019 19:21:16: #2 alternative fragment length(s) may be 4,69 bps INFO @ Mon, 03 Jun 2019 19:21:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4801812/SRX4801812.10_model.r WARNING @ Mon, 03 Jun 2019 19:21:16: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 19:21:16: #2 You may need to consider one of the other alternative d(s): 4,69 WARNING @ Mon, 03 Jun 2019 19:21:16: #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 19:21:16: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:21:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:21:33: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:21:35: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:21:48: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:21:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4801812/SRX4801812.20_peaks.xls INFO @ Mon, 03 Jun 2019 19:21:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4801812/SRX4801812.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:21:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4801812/SRX4801812.20_summits.bed INFO @ Mon, 03 Jun 2019 19:21:49: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (967 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:21:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4801812/SRX4801812.05_peaks.xls INFO @ Mon, 03 Jun 2019 19:21:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4801812/SRX4801812.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:21:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4801812/SRX4801812.05_summits.bed INFO @ Mon, 03 Jun 2019 19:21:51: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3107 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:22:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4801812/SRX4801812.10_peaks.xls INFO @ Mon, 03 Jun 2019 19:22:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4801812/SRX4801812.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:22:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4801812/SRX4801812.10_summits.bed INFO @ Mon, 03 Jun 2019 19:22:04: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (1951 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。