Job ID = 2590457 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-12T12:40:33 fasterq-dump.2.9.6 fatal: SIGNAL - Segmentation fault *** Error in `/home/okishinya/chipatlas/bin/sratoolkit.2.9.6-1-ubuntu64/bin/fasterq-dump': corrupted double-linked list: 0x00007fffd4002da0 *** spots read : 7,041,492 reads read : 14,082,984 reads written : 7,041,492 reads 0-length : 7,041,492 spots read : 7,029,892 reads read : 14,059,784 reads written : 7,029,892 reads 0-length : 7,029,892 spots read : 7,050,738 reads read : 14,101,476 reads written : 7,050,738 reads 0-length : 7,050,738 spots read : 7,093,550 reads read : 14,187,100 reads written : 7,093,550 reads 0-length : 7,093,550 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: 00:09:28 28215672 reads; of these: 28215672 (100.00%) were unpaired; of these: 715753 (2.54%) aligned 0 times 21863589 (77.49%) aligned exactly 1 time 5636330 (19.98%) aligned >1 times 97.46% overall alignment rate Time searching: 00:09:28 Overall time: 00:09:28 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] 3647856 / 27499919 = 0.1326 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, 12 Aug 2019 22:09:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981689/SRX3981689.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981689/SRX3981689.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981689/SRX3981689.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981689/SRX3981689.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, 12 Aug 2019 22:09:35: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:09:35: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:09:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981689/SRX3981689.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981689/SRX3981689.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981689/SRX3981689.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981689/SRX3981689.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, 12 Aug 2019 22:09:36: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:09:36: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:09:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981689/SRX3981689.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981689/SRX3981689.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981689/SRX3981689.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981689/SRX3981689.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, 12 Aug 2019 22:09:37: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:09:37: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:09:44: 1000000 INFO @ Mon, 12 Aug 2019 22:09:46: 1000000 INFO @ Mon, 12 Aug 2019 22:09:47: 1000000 INFO @ Mon, 12 Aug 2019 22:09:53: 2000000 INFO @ Mon, 12 Aug 2019 22:09:56: 2000000 INFO @ Mon, 12 Aug 2019 22:09:57: 2000000 INFO @ Mon, 12 Aug 2019 22:10:02: 3000000 INFO @ Mon, 12 Aug 2019 22:10:06: 3000000 INFO @ Mon, 12 Aug 2019 22:10:07: 3000000 INFO @ Mon, 12 Aug 2019 22:10:11: 4000000 INFO @ Mon, 12 Aug 2019 22:10:16: 4000000 INFO @ Mon, 12 Aug 2019 22:10:17: 4000000 INFO @ Mon, 12 Aug 2019 22:10:19: 5000000 INFO @ Mon, 12 Aug 2019 22:10:26: 5000000 INFO @ Mon, 12 Aug 2019 22:10:26: 5000000 INFO @ Mon, 12 Aug 2019 22:10:28: 6000000 INFO @ Mon, 12 Aug 2019 22:10:35: 6000000 INFO @ Mon, 12 Aug 2019 22:10:36: 6000000 INFO @ Mon, 12 Aug 2019 22:10:37: 7000000 INFO @ Mon, 12 Aug 2019 22:10:45: 7000000 INFO @ Mon, 12 Aug 2019 22:10:45: 8000000 INFO @ Mon, 12 Aug 2019 22:10:46: 7000000 INFO @ Mon, 12 Aug 2019 22:10:54: 9000000 INFO @ Mon, 12 Aug 2019 22:10:55: 8000000 INFO @ Mon, 12 Aug 2019 22:10:56: 8000000 INFO @ Mon, 12 Aug 2019 22:11:03: 10000000 INFO @ Mon, 12 Aug 2019 22:11:05: 9000000 INFO @ Mon, 12 Aug 2019 22:11:05: 9000000 INFO @ Mon, 12 Aug 2019 22:11:11: 11000000 INFO @ Mon, 12 Aug 2019 22:11:14: 10000000 INFO @ Mon, 12 Aug 2019 22:11:15: 10000000 INFO @ Mon, 12 Aug 2019 22:11:20: 12000000 INFO @ Mon, 12 Aug 2019 22:11:24: 11000000 INFO @ Mon, 12 Aug 2019 22:11:25: 11000000 INFO @ Mon, 12 Aug 2019 22:11:29: 13000000 INFO @ Mon, 12 Aug 2019 22:11:34: 12000000 INFO @ Mon, 12 Aug 2019 22:11:35: 12000000 INFO @ Mon, 12 Aug 2019 22:11:37: 14000000 INFO @ Mon, 12 Aug 2019 22:11:44: 13000000 INFO @ Mon, 12 Aug 2019 22:11:45: 13000000 INFO @ Mon, 12 Aug 2019 22:11:46: 15000000 INFO @ Mon, 12 Aug 2019 22:11:54: 14000000 INFO @ Mon, 12 Aug 2019 22:11:54: 14000000 INFO @ Mon, 12 Aug 2019 22:11:55: 16000000 INFO @ Mon, 12 Aug 2019 22:12:03: 17000000 INFO @ Mon, 12 Aug 2019 22:12:04: 15000000 INFO @ Mon, 12 Aug 2019 22:12:04: 15000000 INFO @ Mon, 12 Aug 2019 22:12:12: 18000000 INFO @ Mon, 12 Aug 2019 22:12:13: 16000000 INFO @ Mon, 12 Aug 2019 22:12:14: 16000000 INFO @ Mon, 12 Aug 2019 22:12:21: 19000000 INFO @ Mon, 12 Aug 2019 22:12:23: 17000000 INFO @ Mon, 12 Aug 2019 22:12:24: 17000000 INFO @ Mon, 12 Aug 2019 22:12:29: 20000000 INFO @ Mon, 12 Aug 2019 22:12:33: 18000000 INFO @ Mon, 12 Aug 2019 22:12:34: 18000000 INFO @ Mon, 12 Aug 2019 22:12:38: 21000000 INFO @ Mon, 12 Aug 2019 22:12:43: 19000000 INFO @ Mon, 12 Aug 2019 22:12:44: 19000000 INFO @ Mon, 12 Aug 2019 22:12:47: 22000000 INFO @ Mon, 12 Aug 2019 22:12:53: 20000000 INFO @ Mon, 12 Aug 2019 22:12:53: 20000000 INFO @ Mon, 12 Aug 2019 22:12:56: 23000000 INFO @ Mon, 12 Aug 2019 22:13:03: 21000000 INFO @ Mon, 12 Aug 2019 22:13:03: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:13:03: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:13:03: #1 total tags in treatment: 23852063 INFO @ Mon, 12 Aug 2019 22:13:03: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:13:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 22:13:03: 21000000 INFO @ Mon, 12 Aug 2019 22:13:04: #1 tags after filtering in treatment: 23852063 INFO @ Mon, 12 Aug 2019 22:13:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:13:04: #1 finished! INFO @ Mon, 12 Aug 2019 22:13:04: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:13:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:13:06: #2 number of paired peaks: 159 WARNING @ Mon, 12 Aug 2019 22:13:06: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Mon, 12 Aug 2019 22:13:06: start model_add_line... INFO @ Mon, 12 Aug 2019 22:13:06: start X-correlation... INFO @ Mon, 12 Aug 2019 22:13:06: end of X-cor INFO @ Mon, 12 Aug 2019 22:13:06: #2 finished! INFO @ Mon, 12 Aug 2019 22:13:06: #2 predicted fragment length is 56 bps INFO @ Mon, 12 Aug 2019 22:13:06: #2 alternative fragment length(s) may be 3,56 bps INFO @ Mon, 12 Aug 2019 22:13:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981689/SRX3981689.05_model.r WARNING @ Mon, 12 Aug 2019 22:13:06: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 22:13:06: #2 You may need to consider one of the other alternative d(s): 3,56 WARNING @ Mon, 12 Aug 2019 22:13:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 22:13:06: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:13:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:13:12: 22000000 INFO @ Mon, 12 Aug 2019 22:13:13: 22000000 INFO @ Mon, 12 Aug 2019 22:13:22: 23000000 INFO @ Mon, 12 Aug 2019 22:13:22: 23000000 INFO @ Mon, 12 Aug 2019 22:13:30: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:13:30: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:13:30: #1 total tags in treatment: 23852063 INFO @ Mon, 12 Aug 2019 22:13:30: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:13:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 22:13:30: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:13:30: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:13:30: #1 total tags in treatment: 23852063 INFO @ Mon, 12 Aug 2019 22:13:30: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:13:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 22:13:30: #1 tags after filtering in treatment: 23852063 INFO @ Mon, 12 Aug 2019 22:13:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:13:30: #1 finished! INFO @ Mon, 12 Aug 2019 22:13:30: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:13:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:13:31: #1 tags after filtering in treatment: 23852063 INFO @ Mon, 12 Aug 2019 22:13:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:13:31: #1 finished! INFO @ Mon, 12 Aug 2019 22:13:31: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:13:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:13:32: #2 number of paired peaks: 159 WARNING @ Mon, 12 Aug 2019 22:13:32: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Mon, 12 Aug 2019 22:13:32: start model_add_line... INFO @ Mon, 12 Aug 2019 22:13:32: start X-correlation... INFO @ Mon, 12 Aug 2019 22:13:32: end of X-cor INFO @ Mon, 12 Aug 2019 22:13:32: #2 finished! INFO @ Mon, 12 Aug 2019 22:13:32: #2 predicted fragment length is 56 bps INFO @ Mon, 12 Aug 2019 22:13:32: #2 alternative fragment length(s) may be 3,56 bps INFO @ Mon, 12 Aug 2019 22:13:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981689/SRX3981689.10_model.r WARNING @ Mon, 12 Aug 2019 22:13:32: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 22:13:32: #2 You may need to consider one of the other alternative d(s): 3,56 WARNING @ Mon, 12 Aug 2019 22:13:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 22:13:32: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:13:32: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:13:33: #2 number of paired peaks: 159 WARNING @ Mon, 12 Aug 2019 22:13:33: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Mon, 12 Aug 2019 22:13:33: start model_add_line... INFO @ Mon, 12 Aug 2019 22:13:33: start X-correlation... INFO @ Mon, 12 Aug 2019 22:13:33: end of X-cor INFO @ Mon, 12 Aug 2019 22:13:33: #2 finished! INFO @ Mon, 12 Aug 2019 22:13:33: #2 predicted fragment length is 56 bps INFO @ Mon, 12 Aug 2019 22:13:33: #2 alternative fragment length(s) may be 3,56 bps INFO @ Mon, 12 Aug 2019 22:13:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981689/SRX3981689.20_model.r WARNING @ Mon, 12 Aug 2019 22:13:33: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 22:13:33: #2 You may need to consider one of the other alternative d(s): 3,56 WARNING @ Mon, 12 Aug 2019 22:13:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 22:13:33: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:13:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:14:03: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:14:30: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:14:30: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:14:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981689/SRX3981689.05_peaks.xls INFO @ Mon, 12 Aug 2019 22:14:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981689/SRX3981689.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:14:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981689/SRX3981689.05_summits.bed INFO @ Mon, 12 Aug 2019 22:14:31: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2828 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:14:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981689/SRX3981689.10_peaks.xls INFO @ Mon, 12 Aug 2019 22:14:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981689/SRX3981689.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:14:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981689/SRX3981689.10_summits.bed INFO @ Mon, 12 Aug 2019 22:14:58: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1197 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:14:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981689/SRX3981689.20_peaks.xls INFO @ Mon, 12 Aug 2019 22:14:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981689/SRX3981689.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:14:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981689/SRX3981689.20_summits.bed INFO @ Mon, 12 Aug 2019 22:14:59: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (565 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。