Job ID = 1294743 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T00:53:22 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 ) 2019-06-03T00:53:22 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 ) 2019-06-03T00:54:56 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 : 17,639,345 reads read : 17,639,345 reads written : 17,639,345 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: 00:09:09 17639345 reads; of these: 17639345 (100.00%) were unpaired; of these: 1069101 (6.06%) aligned 0 times 10497262 (59.51%) aligned exactly 1 time 6072982 (34.43%) aligned >1 times 93.94% overall alignment rate Time searching: 00:09:10 Overall time: 00:09:10 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] 2794667 / 16570244 = 0.1687 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 10:12:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287853/SRX287853.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287853/SRX287853.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287853/SRX287853.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287853/SRX287853.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 10:12:20: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:12:20: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:12:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287853/SRX287853.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287853/SRX287853.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287853/SRX287853.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287853/SRX287853.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 10:12:20: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:12:20: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:12:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287853/SRX287853.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287853/SRX287853.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287853/SRX287853.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287853/SRX287853.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 10:12:20: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:12:20: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:12:28: 1000000 INFO @ Mon, 03 Jun 2019 10:12:28: 1000000 INFO @ Mon, 03 Jun 2019 10:12:31: 1000000 INFO @ Mon, 03 Jun 2019 10:12:37: 2000000 INFO @ Mon, 03 Jun 2019 10:12:37: 2000000 INFO @ Mon, 03 Jun 2019 10:12:41: 2000000 INFO @ Mon, 03 Jun 2019 10:12:45: 3000000 INFO @ Mon, 03 Jun 2019 10:12:45: 3000000 INFO @ Mon, 03 Jun 2019 10:12:51: 3000000 INFO @ Mon, 03 Jun 2019 10:12:52: 4000000 INFO @ Mon, 03 Jun 2019 10:12:53: 4000000 INFO @ Mon, 03 Jun 2019 10:12:59: 5000000 INFO @ Mon, 03 Jun 2019 10:13:00: 5000000 INFO @ Mon, 03 Jun 2019 10:13:01: 4000000 INFO @ Mon, 03 Jun 2019 10:13:06: 6000000 INFO @ Mon, 03 Jun 2019 10:13:08: 6000000 INFO @ Mon, 03 Jun 2019 10:13:10: 5000000 INFO @ Mon, 03 Jun 2019 10:13:13: 7000000 INFO @ Mon, 03 Jun 2019 10:13:15: 7000000 INFO @ Mon, 03 Jun 2019 10:13:20: 6000000 INFO @ Mon, 03 Jun 2019 10:13:20: 8000000 INFO @ Mon, 03 Jun 2019 10:13:23: 8000000 INFO @ Mon, 03 Jun 2019 10:13:27: 9000000 INFO @ Mon, 03 Jun 2019 10:13:30: 7000000 INFO @ Mon, 03 Jun 2019 10:13:30: 9000000 INFO @ Mon, 03 Jun 2019 10:13:34: 10000000 INFO @ Mon, 03 Jun 2019 10:13:38: 10000000 INFO @ Mon, 03 Jun 2019 10:13:39: 8000000 INFO @ Mon, 03 Jun 2019 10:13:41: 11000000 INFO @ Mon, 03 Jun 2019 10:13:46: 11000000 INFO @ Mon, 03 Jun 2019 10:13:48: 12000000 INFO @ Mon, 03 Jun 2019 10:13:49: 9000000 INFO @ Mon, 03 Jun 2019 10:13:54: 12000000 INFO @ Mon, 03 Jun 2019 10:13:56: 13000000 INFO @ Mon, 03 Jun 2019 10:13:58: 10000000 INFO @ Mon, 03 Jun 2019 10:14:01: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:14:01: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:14:01: #1 total tags in treatment: 13775577 INFO @ Mon, 03 Jun 2019 10:14:01: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:14:01: #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 10:14:01: #1 tags after filtering in treatment: 13775577 INFO @ Mon, 03 Jun 2019 10:14:01: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:14:01: #1 finished! INFO @ Mon, 03 Jun 2019 10:14:01: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:14:01: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:14:02: 13000000 INFO @ Mon, 03 Jun 2019 10:14:03: #2 number of paired peaks: 406 WARNING @ Mon, 03 Jun 2019 10:14:03: Fewer paired peaks (406) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 406 pairs to build model! INFO @ Mon, 03 Jun 2019 10:14:03: start model_add_line... INFO @ Mon, 03 Jun 2019 10:14:03: start X-correlation... INFO @ Mon, 03 Jun 2019 10:14:03: end of X-cor INFO @ Mon, 03 Jun 2019 10:14:03: #2 finished! INFO @ Mon, 03 Jun 2019 10:14:03: #2 predicted fragment length is 44 bps INFO @ Mon, 03 Jun 2019 10:14:03: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 03 Jun 2019 10:14:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287853/SRX287853.05_model.r WARNING @ Mon, 03 Jun 2019 10:14:03: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:14:03: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 03 Jun 2019 10:14:03: #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 10:14:03: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:14:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:14:08: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:14:08: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:14:08: #1 total tags in treatment: 13775577 INFO @ Mon, 03 Jun 2019 10:14:08: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:14:08: #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 10:14:08: 11000000 INFO @ Mon, 03 Jun 2019 10:14:08: #1 tags after filtering in treatment: 13775577 INFO @ Mon, 03 Jun 2019 10:14:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:14:08: #1 finished! INFO @ Mon, 03 Jun 2019 10:14:08: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:14:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:14:09: #2 number of paired peaks: 406 WARNING @ Mon, 03 Jun 2019 10:14:09: Fewer paired peaks (406) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 406 pairs to build model! INFO @ Mon, 03 Jun 2019 10:14:09: start model_add_line... INFO @ Mon, 03 Jun 2019 10:14:09: start X-correlation... INFO @ Mon, 03 Jun 2019 10:14:09: end of X-cor INFO @ Mon, 03 Jun 2019 10:14:09: #2 finished! INFO @ Mon, 03 Jun 2019 10:14:09: #2 predicted fragment length is 44 bps INFO @ Mon, 03 Jun 2019 10:14:09: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 03 Jun 2019 10:14:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287853/SRX287853.20_model.r WARNING @ Mon, 03 Jun 2019 10:14:09: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:14:09: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 03 Jun 2019 10:14:09: #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 10:14:09: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:14:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:14:17: 12000000 INFO @ Mon, 03 Jun 2019 10:14:26: 13000000 INFO @ Mon, 03 Jun 2019 10:14:33: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:14:33: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:14:33: #1 total tags in treatment: 13775577 INFO @ Mon, 03 Jun 2019 10:14:33: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:14:33: #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 10:14:33: #1 tags after filtering in treatment: 13775577 INFO @ Mon, 03 Jun 2019 10:14:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:14:33: #1 finished! INFO @ Mon, 03 Jun 2019 10:14:33: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:14:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:14:35: #2 number of paired peaks: 406 WARNING @ Mon, 03 Jun 2019 10:14:35: Fewer paired peaks (406) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 406 pairs to build model! INFO @ Mon, 03 Jun 2019 10:14:35: start model_add_line... INFO @ Mon, 03 Jun 2019 10:14:35: start X-correlation... INFO @ Mon, 03 Jun 2019 10:14:35: end of X-cor INFO @ Mon, 03 Jun 2019 10:14:35: #2 finished! INFO @ Mon, 03 Jun 2019 10:14:35: #2 predicted fragment length is 44 bps INFO @ Mon, 03 Jun 2019 10:14:35: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 03 Jun 2019 10:14:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287853/SRX287853.10_model.r WARNING @ Mon, 03 Jun 2019 10:14:35: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:14:35: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 03 Jun 2019 10:14:35: #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 10:14:35: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:14:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:14:40: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:14:46: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:14:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287853/SRX287853.05_peaks.xls INFO @ Mon, 03 Jun 2019 10:14:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287853/SRX287853.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:14:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287853/SRX287853.05_summits.bed INFO @ Mon, 03 Jun 2019 10:14:58: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (2268 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:15:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287853/SRX287853.20_peaks.xls INFO @ Mon, 03 Jun 2019 10:15:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287853/SRX287853.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:15:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287853/SRX287853.20_summits.bed INFO @ Mon, 03 Jun 2019 10:15:04: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1530 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:15:12: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:15:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287853/SRX287853.10_peaks.xls INFO @ Mon, 03 Jun 2019 10:15:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287853/SRX287853.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:15:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287853/SRX287853.10_summits.bed INFO @ Mon, 03 Jun 2019 10:15:31: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1921 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。