Job ID = 1294650 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T00:34:36 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 : 21,266,404 reads read : 21,266,404 reads written : 21,266,404 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: 00:09:21 21266404 reads; of these: 21266404 (100.00%) were unpaired; of these: 1402758 (6.60%) aligned 0 times 13365829 (62.85%) aligned exactly 1 time 6497817 (30.55%) aligned >1 times 93.40% overall alignment rate Time searching: 00:09:21 Overall time: 00:09:21 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] 3845051 / 19863646 = 0.1936 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 09:54:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287801/SRX287801.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287801/SRX287801.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287801/SRX287801.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287801/SRX287801.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 09:54:58: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:54:58: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:54:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287801/SRX287801.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287801/SRX287801.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287801/SRX287801.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287801/SRX287801.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 09:54:58: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:54:58: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:54:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287801/SRX287801.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287801/SRX287801.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287801/SRX287801.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287801/SRX287801.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 09:54:58: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:54:58: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:55:06: 1000000 INFO @ Mon, 03 Jun 2019 09:55:07: 1000000 INFO @ Mon, 03 Jun 2019 09:55:07: 1000000 INFO @ Mon, 03 Jun 2019 09:55:13: 2000000 INFO @ Mon, 03 Jun 2019 09:55:15: 2000000 INFO @ Mon, 03 Jun 2019 09:55:16: 2000000 INFO @ Mon, 03 Jun 2019 09:55:20: 3000000 INFO @ Mon, 03 Jun 2019 09:55:24: 3000000 INFO @ Mon, 03 Jun 2019 09:55:24: 3000000 INFO @ Mon, 03 Jun 2019 09:55:28: 4000000 INFO @ Mon, 03 Jun 2019 09:55:32: 4000000 INFO @ Mon, 03 Jun 2019 09:55:32: 4000000 INFO @ Mon, 03 Jun 2019 09:55:35: 5000000 INFO @ Mon, 03 Jun 2019 09:55:40: 5000000 INFO @ Mon, 03 Jun 2019 09:55:41: 5000000 INFO @ Mon, 03 Jun 2019 09:55:43: 6000000 INFO @ Mon, 03 Jun 2019 09:55:49: 6000000 INFO @ Mon, 03 Jun 2019 09:55:50: 6000000 INFO @ Mon, 03 Jun 2019 09:55:50: 7000000 INFO @ Mon, 03 Jun 2019 09:55:57: 7000000 INFO @ Mon, 03 Jun 2019 09:55:57: 8000000 INFO @ Mon, 03 Jun 2019 09:55:58: 7000000 INFO @ Mon, 03 Jun 2019 09:56:05: 8000000 INFO @ Mon, 03 Jun 2019 09:56:05: 9000000 INFO @ Mon, 03 Jun 2019 09:56:07: 8000000 INFO @ Mon, 03 Jun 2019 09:56:12: 10000000 INFO @ Mon, 03 Jun 2019 09:56:12: 9000000 INFO @ Mon, 03 Jun 2019 09:56:15: 9000000 INFO @ Mon, 03 Jun 2019 09:56:20: 10000000 INFO @ Mon, 03 Jun 2019 09:56:20: 11000000 INFO @ Mon, 03 Jun 2019 09:56:22: 10000000 INFO @ Mon, 03 Jun 2019 09:56:27: 11000000 INFO @ Mon, 03 Jun 2019 09:56:27: 12000000 INFO @ Mon, 03 Jun 2019 09:56:29: 11000000 INFO @ Mon, 03 Jun 2019 09:56:35: 13000000 INFO @ Mon, 03 Jun 2019 09:56:36: 12000000 INFO @ Mon, 03 Jun 2019 09:56:38: 12000000 INFO @ Mon, 03 Jun 2019 09:56:43: 14000000 INFO @ Mon, 03 Jun 2019 09:56:43: 13000000 INFO @ Mon, 03 Jun 2019 09:56:45: 13000000 INFO @ Mon, 03 Jun 2019 09:56:50: 15000000 INFO @ Mon, 03 Jun 2019 09:56:50: 14000000 INFO @ Mon, 03 Jun 2019 09:56:52: 14000000 INFO @ Mon, 03 Jun 2019 09:56:57: 16000000 INFO @ Mon, 03 Jun 2019 09:56:58: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:56:58: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:56:58: #1 total tags in treatment: 16018595 INFO @ Mon, 03 Jun 2019 09:56:58: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:56:58: #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 09:56:58: #1 tags after filtering in treatment: 16018595 INFO @ Mon, 03 Jun 2019 09:56:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:56:58: #1 finished! INFO @ Mon, 03 Jun 2019 09:56:58: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:56:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:56:58: 15000000 INFO @ Mon, 03 Jun 2019 09:57:00: #2 number of paired peaks: 232 WARNING @ Mon, 03 Jun 2019 09:57:00: Fewer paired peaks (232) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 232 pairs to build model! INFO @ Mon, 03 Jun 2019 09:57:00: start model_add_line... INFO @ Mon, 03 Jun 2019 09:57:00: start X-correlation... INFO @ Mon, 03 Jun 2019 09:57:00: end of X-cor INFO @ Mon, 03 Jun 2019 09:57:00: #2 finished! INFO @ Mon, 03 Jun 2019 09:57:00: #2 predicted fragment length is 47 bps INFO @ Mon, 03 Jun 2019 09:57:00: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 03 Jun 2019 09:57:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287801/SRX287801.05_model.r WARNING @ Mon, 03 Jun 2019 09:57:00: #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 09:57:00: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 03 Jun 2019 09:57:00: #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 09:57:00: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:57:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:57:00: 15000000 INFO @ Mon, 03 Jun 2019 09:57:06: 16000000 INFO @ Mon, 03 Jun 2019 09:57:06: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:57:06: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:57:06: #1 total tags in treatment: 16018595 INFO @ Mon, 03 Jun 2019 09:57:06: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:57:06: #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 09:57:07: #1 tags after filtering in treatment: 16018595 INFO @ Mon, 03 Jun 2019 09:57:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:57:07: #1 finished! INFO @ Mon, 03 Jun 2019 09:57:07: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:57:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:57:08: #2 number of paired peaks: 232 WARNING @ Mon, 03 Jun 2019 09:57:08: Fewer paired peaks (232) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 232 pairs to build model! INFO @ Mon, 03 Jun 2019 09:57:08: start model_add_line... INFO @ Mon, 03 Jun 2019 09:57:08: start X-correlation... INFO @ Mon, 03 Jun 2019 09:57:08: end of X-cor INFO @ Mon, 03 Jun 2019 09:57:08: #2 finished! INFO @ Mon, 03 Jun 2019 09:57:08: #2 predicted fragment length is 47 bps INFO @ Mon, 03 Jun 2019 09:57:08: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 03 Jun 2019 09:57:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287801/SRX287801.20_model.r WARNING @ Mon, 03 Jun 2019 09:57:08: #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 09:57:08: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 03 Jun 2019 09:57:08: #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 09:57:08: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:57:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:57:08: 16000000 INFO @ Mon, 03 Jun 2019 09:57:09: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:57:09: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:57:09: #1 total tags in treatment: 16018595 INFO @ Mon, 03 Jun 2019 09:57:09: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:57:09: #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 09:57:09: #1 tags after filtering in treatment: 16018595 INFO @ Mon, 03 Jun 2019 09:57:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:57:09: #1 finished! INFO @ Mon, 03 Jun 2019 09:57:09: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:57:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:57:10: #2 number of paired peaks: 232 WARNING @ Mon, 03 Jun 2019 09:57:10: Fewer paired peaks (232) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 232 pairs to build model! INFO @ Mon, 03 Jun 2019 09:57:10: start model_add_line... INFO @ Mon, 03 Jun 2019 09:57:10: start X-correlation... INFO @ Mon, 03 Jun 2019 09:57:11: end of X-cor INFO @ Mon, 03 Jun 2019 09:57:11: #2 finished! INFO @ Mon, 03 Jun 2019 09:57:11: #2 predicted fragment length is 47 bps INFO @ Mon, 03 Jun 2019 09:57:11: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 03 Jun 2019 09:57:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287801/SRX287801.10_model.r WARNING @ Mon, 03 Jun 2019 09:57:11: #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 09:57:11: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 03 Jun 2019 09:57:11: #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 09:57:11: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:57:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:57:43: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:57:50: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:57:52: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:58:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287801/SRX287801.05_peaks.xls INFO @ Mon, 03 Jun 2019 09:58:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287801/SRX287801.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:58:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287801/SRX287801.05_summits.bed INFO @ Mon, 03 Jun 2019 09:58:04: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2062 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:58:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287801/SRX287801.20_peaks.xls INFO @ Mon, 03 Jun 2019 09:58:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287801/SRX287801.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:58:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287801/SRX287801.20_summits.bed INFO @ Mon, 03 Jun 2019 09:58:10: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1271 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:58:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287801/SRX287801.10_peaks.xls INFO @ Mon, 03 Jun 2019 09:58:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287801/SRX287801.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:58:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287801/SRX287801.10_summits.bed INFO @ Mon, 03 Jun 2019 09:58:13: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1731 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。