Job ID = 1299976 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T09:41:48 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 ) 2019-06-03T09:45:38 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 ) 2019-06-03T09:45:38 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 ) 2019-06-03T09:47:20 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 : 13,268,284 reads read : 13,268,284 reads written : 13,268,284 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: 00:07:28 13268284 reads; of these: 13268284 (100.00%) were unpaired; of these: 282738 (2.13%) aligned 0 times 8679785 (65.42%) aligned exactly 1 time 4305761 (32.45%) aligned >1 times 97.87% overall alignment rate Time searching: 00:07:29 Overall time: 00:07:29 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] 1186933 / 12985546 = 0.0914 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 19:04:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4801801/SRX4801801.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4801801/SRX4801801.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4801801/SRX4801801.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4801801/SRX4801801.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 19:04:04: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:04:04: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:04:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4801801/SRX4801801.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4801801/SRX4801801.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4801801/SRX4801801.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4801801/SRX4801801.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 19:04:04: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:04:04: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:04:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4801801/SRX4801801.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4801801/SRX4801801.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4801801/SRX4801801.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4801801/SRX4801801.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 19:04:04: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:04:04: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:04:13: 1000000 INFO @ Mon, 03 Jun 2019 19:04:14: 1000000 INFO @ Mon, 03 Jun 2019 19:04:14: 1000000 INFO @ Mon, 03 Jun 2019 19:04:22: 2000000 INFO @ Mon, 03 Jun 2019 19:04:23: 2000000 INFO @ Mon, 03 Jun 2019 19:04:24: 2000000 INFO @ Mon, 03 Jun 2019 19:04:30: 3000000 INFO @ Mon, 03 Jun 2019 19:04:32: 3000000 INFO @ Mon, 03 Jun 2019 19:04:33: 3000000 INFO @ Mon, 03 Jun 2019 19:04:40: 4000000 INFO @ Mon, 03 Jun 2019 19:04:42: 4000000 INFO @ Mon, 03 Jun 2019 19:04:42: 4000000 INFO @ Mon, 03 Jun 2019 19:04:50: 5000000 INFO @ Mon, 03 Jun 2019 19:04:50: 5000000 INFO @ Mon, 03 Jun 2019 19:04:53: 5000000 INFO @ Mon, 03 Jun 2019 19:04:59: 6000000 INFO @ Mon, 03 Jun 2019 19:05:00: 6000000 INFO @ Mon, 03 Jun 2019 19:05:03: 6000000 INFO @ Mon, 03 Jun 2019 19:05:07: 7000000 INFO @ Mon, 03 Jun 2019 19:05:10: 7000000 INFO @ Mon, 03 Jun 2019 19:05:13: 7000000 INFO @ Mon, 03 Jun 2019 19:05:15: 8000000 INFO @ Mon, 03 Jun 2019 19:05:20: 8000000 INFO @ Mon, 03 Jun 2019 19:05:23: 9000000 INFO @ Mon, 03 Jun 2019 19:05:23: 8000000 INFO @ Mon, 03 Jun 2019 19:05:29: 9000000 INFO @ Mon, 03 Jun 2019 19:05:31: 10000000 INFO @ Mon, 03 Jun 2019 19:05:33: 9000000 INFO @ Mon, 03 Jun 2019 19:05:39: 11000000 INFO @ Mon, 03 Jun 2019 19:05:39: 10000000 INFO @ Mon, 03 Jun 2019 19:05:43: 10000000 INFO @ Mon, 03 Jun 2019 19:05:45: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 19:05:45: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 19:05:45: #1 total tags in treatment: 11798613 INFO @ Mon, 03 Jun 2019 19:05:45: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:05:45: #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 19:05:45: #1 tags after filtering in treatment: 11798613 INFO @ Mon, 03 Jun 2019 19:05:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:05:45: #1 finished! INFO @ Mon, 03 Jun 2019 19:05:45: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:05:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:05:47: #2 number of paired peaks: 1101 INFO @ Mon, 03 Jun 2019 19:05:47: start model_add_line... INFO @ Mon, 03 Jun 2019 19:05:47: start X-correlation... INFO @ Mon, 03 Jun 2019 19:05:47: end of X-cor INFO @ Mon, 03 Jun 2019 19:05:47: #2 finished! INFO @ Mon, 03 Jun 2019 19:05:47: #2 predicted fragment length is 66 bps INFO @ Mon, 03 Jun 2019 19:05:47: #2 alternative fragment length(s) may be 4,66 bps INFO @ Mon, 03 Jun 2019 19:05:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4801801/SRX4801801.05_model.r WARNING @ Mon, 03 Jun 2019 19:05:47: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 19:05:47: #2 You may need to consider one of the other alternative d(s): 4,66 WARNING @ Mon, 03 Jun 2019 19:05:47: #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 19:05:47: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:05:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:05:49: 11000000 INFO @ Mon, 03 Jun 2019 19:05:54: 11000000 INFO @ Mon, 03 Jun 2019 19:05:57: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 19:05:57: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 19:05:57: #1 total tags in treatment: 11798613 INFO @ Mon, 03 Jun 2019 19:05:57: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:05:57: #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 19:05:57: #1 tags after filtering in treatment: 11798613 INFO @ Mon, 03 Jun 2019 19:05:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:05:57: #1 finished! INFO @ Mon, 03 Jun 2019 19:05:57: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:05:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:05:59: #2 number of paired peaks: 1101 INFO @ Mon, 03 Jun 2019 19:05:59: start model_add_line... INFO @ Mon, 03 Jun 2019 19:05:59: start X-correlation... INFO @ Mon, 03 Jun 2019 19:05:59: end of X-cor INFO @ Mon, 03 Jun 2019 19:05:59: #2 finished! INFO @ Mon, 03 Jun 2019 19:05:59: #2 predicted fragment length is 66 bps INFO @ Mon, 03 Jun 2019 19:05:59: #2 alternative fragment length(s) may be 4,66 bps INFO @ Mon, 03 Jun 2019 19:05:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4801801/SRX4801801.10_model.r WARNING @ Mon, 03 Jun 2019 19:05:59: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 19:05:59: #2 You may need to consider one of the other alternative d(s): 4,66 WARNING @ Mon, 03 Jun 2019 19:05:59: #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 19:05:59: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:05:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:06:02: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 19:06:02: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 19:06:02: #1 total tags in treatment: 11798613 INFO @ Mon, 03 Jun 2019 19:06:02: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:06:02: #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 19:06:02: #1 tags after filtering in treatment: 11798613 INFO @ Mon, 03 Jun 2019 19:06:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:06:02: #1 finished! INFO @ Mon, 03 Jun 2019 19:06:02: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:06:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:06:03: #2 number of paired peaks: 1101 INFO @ Mon, 03 Jun 2019 19:06:03: start model_add_line... INFO @ Mon, 03 Jun 2019 19:06:04: start X-correlation... INFO @ Mon, 03 Jun 2019 19:06:04: end of X-cor INFO @ Mon, 03 Jun 2019 19:06:04: #2 finished! INFO @ Mon, 03 Jun 2019 19:06:04: #2 predicted fragment length is 66 bps INFO @ Mon, 03 Jun 2019 19:06:04: #2 alternative fragment length(s) may be 4,66 bps INFO @ Mon, 03 Jun 2019 19:06:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4801801/SRX4801801.20_model.r WARNING @ Mon, 03 Jun 2019 19:06:04: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 19:06:04: #2 You may need to consider one of the other alternative d(s): 4,66 WARNING @ Mon, 03 Jun 2019 19:06:04: #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 19:06:04: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:06:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:06:21: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:06:33: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:06:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4801801/SRX4801801.05_peaks.xls INFO @ Mon, 03 Jun 2019 19:06:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4801801/SRX4801801.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:06:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4801801/SRX4801801.05_summits.bed INFO @ Mon, 03 Jun 2019 19:06:37: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3116 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:06:37: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:06:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4801801/SRX4801801.10_peaks.xls INFO @ Mon, 03 Jun 2019 19:06:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4801801/SRX4801801.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:06:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4801801/SRX4801801.10_summits.bed INFO @ Mon, 03 Jun 2019 19:06:49: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (1703 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:06:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4801801/SRX4801801.20_peaks.xls INFO @ Mon, 03 Jun 2019 19:06:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4801801/SRX4801801.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:06:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4801801/SRX4801801.20_summits.bed INFO @ Mon, 03 Jun 2019 19:06:53: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (739 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。