Job ID = 6458550 SRX = SRX5343087 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:40:14 prefetch.2.10.7: 1) Downloading 'SRR8540864'... 2020-06-21T12:40:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:44:10 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:44:10 prefetch.2.10.7: 1) 'SRR8540864' was downloaded successfully 2020-06-21T12:44:10 prefetch.2.10.7: 'SRR8540864' has 0 unresolved dependencies Read 25954242 spots for SRR8540864/SRR8540864.sra Written 25954242 spots for SRR8540864/SRR8540864.sra 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: 00:07:13 25954242 reads; of these: 25954242 (100.00%) were unpaired; of these: 1242755 (4.79%) aligned 0 times 22354764 (86.13%) aligned exactly 1 time 2356723 (9.08%) aligned >1 times 95.21% overall alignment rate Time searching: 00:07:13 Overall time: 00:07:13 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 7850699 / 24711487 = 0.3177 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 21:59:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343087/SRX5343087.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343087/SRX5343087.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343087/SRX5343087.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343087/SRX5343087.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 @ Sun, 21 Jun 2020 21:59:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:59:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:59:12: 1000000 INFO @ Sun, 21 Jun 2020 21:59:17: 2000000 INFO @ Sun, 21 Jun 2020 21:59:23: 3000000 INFO @ Sun, 21 Jun 2020 21:59:29: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 21:59:35: 5000000 INFO @ Sun, 21 Jun 2020 21:59:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343087/SRX5343087.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343087/SRX5343087.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343087/SRX5343087.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343087/SRX5343087.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 @ Sun, 21 Jun 2020 21:59:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:59:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:59:41: 6000000 INFO @ Sun, 21 Jun 2020 21:59:42: 1000000 INFO @ Sun, 21 Jun 2020 21:59:47: 7000000 INFO @ Sun, 21 Jun 2020 21:59:49: 2000000 INFO @ Sun, 21 Jun 2020 21:59:54: 8000000 INFO @ Sun, 21 Jun 2020 21:59:55: 3000000 INFO @ Sun, 21 Jun 2020 22:00:00: 9000000 INFO @ Sun, 21 Jun 2020 22:00:01: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 22:00:06: 10000000 INFO @ Sun, 21 Jun 2020 22:00:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343087/SRX5343087.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343087/SRX5343087.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343087/SRX5343087.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343087/SRX5343087.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 @ Sun, 21 Jun 2020 22:00:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:00:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:00:08: 5000000 INFO @ Sun, 21 Jun 2020 22:00:13: 11000000 INFO @ Sun, 21 Jun 2020 22:00:14: 1000000 INFO @ Sun, 21 Jun 2020 22:00:15: 6000000 INFO @ Sun, 21 Jun 2020 22:00:20: 12000000 INFO @ Sun, 21 Jun 2020 22:00:22: 2000000 INFO @ Sun, 21 Jun 2020 22:00:22: 7000000 INFO @ Sun, 21 Jun 2020 22:00:27: 13000000 INFO @ Sun, 21 Jun 2020 22:00:29: 8000000 INFO @ Sun, 21 Jun 2020 22:00:29: 3000000 INFO @ Sun, 21 Jun 2020 22:00:34: 14000000 INFO @ Sun, 21 Jun 2020 22:00:36: 9000000 INFO @ Sun, 21 Jun 2020 22:00:37: 4000000 INFO @ Sun, 21 Jun 2020 22:00:42: 15000000 INFO @ Sun, 21 Jun 2020 22:00:43: 10000000 INFO @ Sun, 21 Jun 2020 22:00:45: 5000000 INFO @ Sun, 21 Jun 2020 22:00:49: 16000000 INFO @ Sun, 21 Jun 2020 22:00:50: 11000000 INFO @ Sun, 21 Jun 2020 22:00:52: 6000000 INFO @ Sun, 21 Jun 2020 22:00:55: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 22:00:55: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 22:00:55: #1 total tags in treatment: 16860788 INFO @ Sun, 21 Jun 2020 22:00:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:00:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:00:56: #1 tags after filtering in treatment: 16860779 INFO @ Sun, 21 Jun 2020 22:00:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:00:56: #1 finished! INFO @ Sun, 21 Jun 2020 22:00:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:00:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:00:57: #2 number of paired peaks: 257 WARNING @ Sun, 21 Jun 2020 22:00:57: Fewer paired peaks (257) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 257 pairs to build model! INFO @ Sun, 21 Jun 2020 22:00:57: start model_add_line... INFO @ Sun, 21 Jun 2020 22:00:57: start X-correlation... INFO @ Sun, 21 Jun 2020 22:00:57: end of X-cor INFO @ Sun, 21 Jun 2020 22:00:57: #2 finished! INFO @ Sun, 21 Jun 2020 22:00:57: #2 predicted fragment length is 123 bps INFO @ Sun, 21 Jun 2020 22:00:57: #2 alternative fragment length(s) may be 123,596 bps INFO @ Sun, 21 Jun 2020 22:00:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343087/SRX5343087.05_model.r WARNING @ Sun, 21 Jun 2020 22:00:57: #2 Since the d (123) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:00:57: #2 You may need to consider one of the other alternative d(s): 123,596 WARNING @ Sun, 21 Jun 2020 22:00:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 22:00:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:00:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:00:57: 12000000 INFO @ Sun, 21 Jun 2020 22:01:00: 7000000 INFO @ Sun, 21 Jun 2020 22:01:04: 13000000 INFO @ Sun, 21 Jun 2020 22:01:07: 8000000 INFO @ Sun, 21 Jun 2020 22:01:11: 14000000 INFO @ Sun, 21 Jun 2020 22:01:15: 9000000 INFO @ Sun, 21 Jun 2020 22:01:18: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:01:23: 10000000 INFO @ Sun, 21 Jun 2020 22:01:25: 16000000 INFO @ Sun, 21 Jun 2020 22:01:30: 11000000 INFO @ Sun, 21 Jun 2020 22:01:31: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 22:01:31: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 22:01:31: #1 total tags in treatment: 16860788 INFO @ Sun, 21 Jun 2020 22:01:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:01:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:01:32: #1 tags after filtering in treatment: 16860779 INFO @ Sun, 21 Jun 2020 22:01:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:01:32: #1 finished! INFO @ Sun, 21 Jun 2020 22:01:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:01:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:01:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:01:33: #2 number of paired peaks: 257 WARNING @ Sun, 21 Jun 2020 22:01:33: Fewer paired peaks (257) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 257 pairs to build model! INFO @ Sun, 21 Jun 2020 22:01:33: start model_add_line... INFO @ Sun, 21 Jun 2020 22:01:33: start X-correlation... INFO @ Sun, 21 Jun 2020 22:01:33: end of X-cor INFO @ Sun, 21 Jun 2020 22:01:33: #2 finished! INFO @ Sun, 21 Jun 2020 22:01:33: #2 predicted fragment length is 123 bps INFO @ Sun, 21 Jun 2020 22:01:33: #2 alternative fragment length(s) may be 123,596 bps INFO @ Sun, 21 Jun 2020 22:01:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343087/SRX5343087.10_model.r WARNING @ Sun, 21 Jun 2020 22:01:33: #2 Since the d (123) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:01:33: #2 You may need to consider one of the other alternative d(s): 123,596 WARNING @ Sun, 21 Jun 2020 22:01:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 22:01:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:01:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:01:37: 12000000 INFO @ Sun, 21 Jun 2020 22:01:44: 13000000 INFO @ Sun, 21 Jun 2020 22:01:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343087/SRX5343087.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:01:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343087/SRX5343087.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:01:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343087/SRX5343087.05_summits.bed INFO @ Sun, 21 Jun 2020 22:01:49: Done! pass1 - making usageList (121 chroms): 2 millis pass2 - checking and writing primary data (6676 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:01:51: 14000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:01:59: 15000000 INFO @ Sun, 21 Jun 2020 22:02:06: 16000000 INFO @ Sun, 21 Jun 2020 22:02:09: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:02:13: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 22:02:13: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 22:02:13: #1 total tags in treatment: 16860788 INFO @ Sun, 21 Jun 2020 22:02:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:02:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:02:13: #1 tags after filtering in treatment: 16860779 INFO @ Sun, 21 Jun 2020 22:02:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:02:13: #1 finished! INFO @ Sun, 21 Jun 2020 22:02:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:02:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:02:14: #2 number of paired peaks: 257 WARNING @ Sun, 21 Jun 2020 22:02:14: Fewer paired peaks (257) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 257 pairs to build model! INFO @ Sun, 21 Jun 2020 22:02:14: start model_add_line... INFO @ Sun, 21 Jun 2020 22:02:14: start X-correlation... INFO @ Sun, 21 Jun 2020 22:02:14: end of X-cor INFO @ Sun, 21 Jun 2020 22:02:14: #2 finished! INFO @ Sun, 21 Jun 2020 22:02:14: #2 predicted fragment length is 123 bps INFO @ Sun, 21 Jun 2020 22:02:14: #2 alternative fragment length(s) may be 123,596 bps INFO @ Sun, 21 Jun 2020 22:02:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343087/SRX5343087.20_model.r WARNING @ Sun, 21 Jun 2020 22:02:14: #2 Since the d (123) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:02:14: #2 You may need to consider one of the other alternative d(s): 123,596 WARNING @ Sun, 21 Jun 2020 22:02:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 22:02:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:02:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:02:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343087/SRX5343087.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:02:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343087/SRX5343087.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:02:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343087/SRX5343087.10_summits.bed INFO @ Sun, 21 Jun 2020 22:02:27: Done! pass1 - making usageList (109 chroms): 2 millis pass2 - checking and writing primary data (4414 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:02:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:03:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343087/SRX5343087.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:03:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343087/SRX5343087.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:03:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343087/SRX5343087.20_summits.bed INFO @ Sun, 21 Jun 2020 22:03:05: Done! pass1 - making usageList (90 chroms): 1 millis pass2 - checking and writing primary data (2132 records, 4 fields): 6 millis CompletedMACS2peakCalling