Job ID = 6456430 SRX = SRX3404025 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:48:31 prefetch.2.10.7: 1) Downloading 'SRR6303502'... 2020-06-21T10:48:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:52:10 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:52:11 prefetch.2.10.7: 'SRR6303502' is valid 2020-06-21T10:52:11 prefetch.2.10.7: 1) 'SRR6303502' was downloaded successfully 2020-06-21T10:52:11 prefetch.2.10.7: 'SRR6303502' has 0 unresolved dependencies Read 23397826 spots for SRR6303502/SRR6303502.sra Written 23397826 spots for SRR6303502/SRR6303502.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: 00:05:55 23397826 reads; of these: 23397826 (100.00%) were unpaired; of these: 555509 (2.37%) aligned 0 times 17495854 (74.78%) aligned exactly 1 time 5346463 (22.85%) aligned >1 times 97.63% overall alignment rate Time searching: 00:05:55 Overall time: 00:05:55 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] 2463794 / 22842317 = 0.1079 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 20:04:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3404025/SRX3404025.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3404025/SRX3404025.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3404025/SRX3404025.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3404025/SRX3404025.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 20:04:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:04:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:04:37: 1000000 INFO @ Sun, 21 Jun 2020 20:04:44: 2000000 INFO @ Sun, 21 Jun 2020 20:04:51: 3000000 INFO @ Sun, 21 Jun 2020 20:04:57: 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 20:05:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3404025/SRX3404025.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3404025/SRX3404025.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3404025/SRX3404025.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3404025/SRX3404025.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 20:05:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:05:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:05:05: 5000000 INFO @ Sun, 21 Jun 2020 20:05:06: 1000000 INFO @ Sun, 21 Jun 2020 20:05:12: 6000000 INFO @ Sun, 21 Jun 2020 20:05:13: 2000000 INFO @ Sun, 21 Jun 2020 20:05:20: 7000000 INFO @ Sun, 21 Jun 2020 20:05:20: 3000000 INFO @ Sun, 21 Jun 2020 20:05:27: 4000000 INFO @ Sun, 21 Jun 2020 20:05:27: 8000000 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 20:05:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3404025/SRX3404025.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3404025/SRX3404025.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3404025/SRX3404025.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3404025/SRX3404025.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 20:05:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:05:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:05:34: 5000000 INFO @ Sun, 21 Jun 2020 20:05:35: 9000000 INFO @ Sun, 21 Jun 2020 20:05:37: 1000000 INFO @ Sun, 21 Jun 2020 20:05:40: 6000000 INFO @ Sun, 21 Jun 2020 20:05:42: 10000000 INFO @ Sun, 21 Jun 2020 20:05:43: 2000000 INFO @ Sun, 21 Jun 2020 20:05:47: 7000000 INFO @ Sun, 21 Jun 2020 20:05:50: 11000000 INFO @ Sun, 21 Jun 2020 20:05:50: 3000000 INFO @ Sun, 21 Jun 2020 20:05:54: 8000000 INFO @ Sun, 21 Jun 2020 20:05:57: 4000000 INFO @ Sun, 21 Jun 2020 20:05:57: 12000000 INFO @ Sun, 21 Jun 2020 20:06:01: 9000000 INFO @ Sun, 21 Jun 2020 20:06:04: 5000000 INFO @ Sun, 21 Jun 2020 20:06:04: 13000000 INFO @ Sun, 21 Jun 2020 20:06:08: 10000000 INFO @ Sun, 21 Jun 2020 20:06:11: 6000000 INFO @ Sun, 21 Jun 2020 20:06:12: 14000000 INFO @ Sun, 21 Jun 2020 20:06:15: 11000000 INFO @ Sun, 21 Jun 2020 20:06:18: 7000000 INFO @ Sun, 21 Jun 2020 20:06:19: 15000000 INFO @ Sun, 21 Jun 2020 20:06:22: 12000000 INFO @ Sun, 21 Jun 2020 20:06:24: 8000000 INFO @ Sun, 21 Jun 2020 20:06:26: 16000000 INFO @ Sun, 21 Jun 2020 20:06:28: 13000000 INFO @ Sun, 21 Jun 2020 20:06:31: 9000000 INFO @ Sun, 21 Jun 2020 20:06:33: 17000000 INFO @ Sun, 21 Jun 2020 20:06:35: 14000000 INFO @ Sun, 21 Jun 2020 20:06:38: 10000000 INFO @ Sun, 21 Jun 2020 20:06:41: 18000000 INFO @ Sun, 21 Jun 2020 20:06:42: 15000000 INFO @ Sun, 21 Jun 2020 20:06:45: 11000000 INFO @ Sun, 21 Jun 2020 20:06:48: 19000000 INFO @ Sun, 21 Jun 2020 20:06:48: 16000000 INFO @ Sun, 21 Jun 2020 20:06:51: 12000000 INFO @ Sun, 21 Jun 2020 20:06:55: 20000000 INFO @ Sun, 21 Jun 2020 20:06:55: 17000000 INFO @ Sun, 21 Jun 2020 20:06:58: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:06:58: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:06:58: #1 total tags in treatment: 20378523 INFO @ Sun, 21 Jun 2020 20:06:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:06:58: #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 20:06:58: 13000000 INFO @ Sun, 21 Jun 2020 20:06:58: #1 tags after filtering in treatment: 20378450 INFO @ Sun, 21 Jun 2020 20:06:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:06:58: #1 finished! INFO @ Sun, 21 Jun 2020 20:06:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:06:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:07:00: #2 number of paired peaks: 552 WARNING @ Sun, 21 Jun 2020 20:07:00: Fewer paired peaks (552) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 552 pairs to build model! INFO @ Sun, 21 Jun 2020 20:07:00: start model_add_line... INFO @ Sun, 21 Jun 2020 20:07:00: start X-correlation... INFO @ Sun, 21 Jun 2020 20:07:00: end of X-cor INFO @ Sun, 21 Jun 2020 20:07:00: #2 finished! INFO @ Sun, 21 Jun 2020 20:07:00: #2 predicted fragment length is 64 bps INFO @ Sun, 21 Jun 2020 20:07:00: #2 alternative fragment length(s) may be 3,64 bps INFO @ Sun, 21 Jun 2020 20:07:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3404025/SRX3404025.05_model.r WARNING @ Sun, 21 Jun 2020 20:07:00: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:07:00: #2 You may need to consider one of the other alternative d(s): 3,64 WARNING @ Sun, 21 Jun 2020 20:07:00: #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 20:07:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:07:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:07:02: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:07:04: 14000000 INFO @ Sun, 21 Jun 2020 20:07:08: 19000000 INFO @ Sun, 21 Jun 2020 20:07:10: 15000000 INFO @ Sun, 21 Jun 2020 20:07:14: 20000000 INFO @ Sun, 21 Jun 2020 20:07:17: 16000000 INFO @ Sun, 21 Jun 2020 20:07:17: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:07:17: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:07:17: #1 total tags in treatment: 20378523 INFO @ Sun, 21 Jun 2020 20:07:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:07:17: #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 20:07:18: #1 tags after filtering in treatment: 20378450 INFO @ Sun, 21 Jun 2020 20:07:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:07:18: #1 finished! INFO @ Sun, 21 Jun 2020 20:07:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:07:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:07:19: #2 number of paired peaks: 552 WARNING @ Sun, 21 Jun 2020 20:07:19: Fewer paired peaks (552) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 552 pairs to build model! INFO @ Sun, 21 Jun 2020 20:07:19: start model_add_line... INFO @ Sun, 21 Jun 2020 20:07:19: start X-correlation... INFO @ Sun, 21 Jun 2020 20:07:19: end of X-cor INFO @ Sun, 21 Jun 2020 20:07:19: #2 finished! INFO @ Sun, 21 Jun 2020 20:07:19: #2 predicted fragment length is 64 bps INFO @ Sun, 21 Jun 2020 20:07:19: #2 alternative fragment length(s) may be 3,64 bps INFO @ Sun, 21 Jun 2020 20:07:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3404025/SRX3404025.10_model.r WARNING @ Sun, 21 Jun 2020 20:07:19: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:07:19: #2 You may need to consider one of the other alternative d(s): 3,64 WARNING @ Sun, 21 Jun 2020 20:07:19: #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 20:07:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:07:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:07:22: 17000000 INFO @ Sun, 21 Jun 2020 20:07:28: 18000000 INFO @ Sun, 21 Jun 2020 20:07:33: 19000000 INFO @ Sun, 21 Jun 2020 20:07:39: 20000000 INFO @ Sun, 21 Jun 2020 20:07:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:07:41: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:07:41: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:07:41: #1 total tags in treatment: 20378523 INFO @ Sun, 21 Jun 2020 20:07:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:07:41: #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 20:07:42: #1 tags after filtering in treatment: 20378450 INFO @ Sun, 21 Jun 2020 20:07:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:07:42: #1 finished! INFO @ Sun, 21 Jun 2020 20:07:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:07:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:07:43: #2 number of paired peaks: 552 WARNING @ Sun, 21 Jun 2020 20:07:43: Fewer paired peaks (552) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 552 pairs to build model! INFO @ Sun, 21 Jun 2020 20:07:43: start model_add_line... INFO @ Sun, 21 Jun 2020 20:07:43: start X-correlation... INFO @ Sun, 21 Jun 2020 20:07:43: end of X-cor INFO @ Sun, 21 Jun 2020 20:07:43: #2 finished! INFO @ Sun, 21 Jun 2020 20:07:43: #2 predicted fragment length is 64 bps INFO @ Sun, 21 Jun 2020 20:07:43: #2 alternative fragment length(s) may be 3,64 bps INFO @ Sun, 21 Jun 2020 20:07:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3404025/SRX3404025.20_model.r WARNING @ Sun, 21 Jun 2020 20:07:43: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:07:43: #2 You may need to consider one of the other alternative d(s): 3,64 WARNING @ Sun, 21 Jun 2020 20:07:43: #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 20:07:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:07:43: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:07:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:07:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3404025/SRX3404025.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:07:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3404025/SRX3404025.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:07:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3404025/SRX3404025.05_summits.bed INFO @ Sun, 21 Jun 2020 20:07:58: Done! pass1 - making usageList (641 chroms): 1 millis pass2 - checking and writing primary data (3535 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:08:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3404025/SRX3404025.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:08:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3404025/SRX3404025.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:08:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3404025/SRX3404025.10_summits.bed INFO @ Sun, 21 Jun 2020 20:08:16: Done! pass1 - making usageList (390 chroms): 1 millis pass2 - checking and writing primary data (1672 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:08:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:08:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3404025/SRX3404025.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:08:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3404025/SRX3404025.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:08:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3404025/SRX3404025.20_summits.bed INFO @ Sun, 21 Jun 2020 20:08:42: Done! pass1 - making usageList (174 chroms): 1 millis pass2 - checking and writing primary data (526 records, 4 fields): 8 millis CompletedMACS2peakCalling