Job ID = 6458197 SRX = SRX495307 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:14:34 prefetch.2.10.7: 1) Downloading 'SRR1198812'... 2020-06-21T12:14:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:17:49 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:17:49 prefetch.2.10.7: 1) 'SRR1198812' was downloaded successfully Read 22570048 spots for SRR1198812/SRR1198812.sra Written 22570048 spots for SRR1198812/SRR1198812.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: 00:04:13 22570048 reads; of these: 22570048 (100.00%) were unpaired; of these: 4624169 (20.49%) aligned 0 times 15704016 (69.58%) aligned exactly 1 time 2241863 (9.93%) aligned >1 times 79.51% overall alignment rate Time searching: 00:04:13 Overall time: 00:04:13 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 8 files... [bam_rmdupse_core] 3811779 / 17945879 = 0.2124 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 21:27:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495307/SRX495307.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495307/SRX495307.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495307/SRX495307.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495307/SRX495307.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 21:27:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:27:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:27:48: 1000000 INFO @ Sun, 21 Jun 2020 21:27:53: 2000000 INFO @ Sun, 21 Jun 2020 21:27:58: 3000000 INFO @ Sun, 21 Jun 2020 21:28:03: 4000000 INFO @ Sun, 21 Jun 2020 21:28:09: 5000000 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 21:28:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495307/SRX495307.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495307/SRX495307.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495307/SRX495307.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495307/SRX495307.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 21:28:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:28:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:28:14: 6000000 INFO @ Sun, 21 Jun 2020 21:28:18: 1000000 INFO @ Sun, 21 Jun 2020 21:28:20: 7000000 INFO @ Sun, 21 Jun 2020 21:28:24: 2000000 INFO @ Sun, 21 Jun 2020 21:28:26: 8000000 INFO @ Sun, 21 Jun 2020 21:28:30: 3000000 INFO @ Sun, 21 Jun 2020 21:28:32: 9000000 INFO @ Sun, 21 Jun 2020 21:28:36: 4000000 INFO @ Sun, 21 Jun 2020 21:28:38: 10000000 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 21:28:41: 5000000 INFO @ Sun, 21 Jun 2020 21:28:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495307/SRX495307.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495307/SRX495307.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495307/SRX495307.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495307/SRX495307.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 21:28:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:28:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:28:43: 11000000 INFO @ Sun, 21 Jun 2020 21:28:48: 6000000 INFO @ Sun, 21 Jun 2020 21:28:49: 1000000 INFO @ Sun, 21 Jun 2020 21:28:50: 12000000 INFO @ Sun, 21 Jun 2020 21:28:54: 7000000 INFO @ Sun, 21 Jun 2020 21:28:56: 2000000 INFO @ Sun, 21 Jun 2020 21:28:57: 13000000 INFO @ Sun, 21 Jun 2020 21:29:00: 8000000 INFO @ Sun, 21 Jun 2020 21:29:03: 14000000 INFO @ Sun, 21 Jun 2020 21:29:04: 3000000 INFO @ Sun, 21 Jun 2020 21:29:04: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:29:04: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:29:04: #1 total tags in treatment: 14134100 INFO @ Sun, 21 Jun 2020 21:29:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:29:04: #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 21:29:04: #1 tags after filtering in treatment: 14134074 INFO @ Sun, 21 Jun 2020 21:29:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:29:04: #1 finished! INFO @ Sun, 21 Jun 2020 21:29:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:29:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:29:05: #2 number of paired peaks: 139 WARNING @ Sun, 21 Jun 2020 21:29:05: Fewer paired peaks (139) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 139 pairs to build model! INFO @ Sun, 21 Jun 2020 21:29:05: start model_add_line... INFO @ Sun, 21 Jun 2020 21:29:05: start X-correlation... INFO @ Sun, 21 Jun 2020 21:29:05: end of X-cor INFO @ Sun, 21 Jun 2020 21:29:05: #2 finished! INFO @ Sun, 21 Jun 2020 21:29:05: #2 predicted fragment length is 4 bps INFO @ Sun, 21 Jun 2020 21:29:05: #2 alternative fragment length(s) may be 4,33,554 bps INFO @ Sun, 21 Jun 2020 21:29:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495307/SRX495307.05_model.r WARNING @ Sun, 21 Jun 2020 21:29:06: #2 Since the d (4) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:29:06: #2 You may need to consider one of the other alternative d(s): 4,33,554 WARNING @ Sun, 21 Jun 2020 21:29:06: #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 21:29:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:29:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:29:07: 9000000 INFO @ Sun, 21 Jun 2020 21:29:11: 4000000 INFO @ Sun, 21 Jun 2020 21:29:13: 10000000 INFO @ Sun, 21 Jun 2020 21:29:18: 5000000 INFO @ Sun, 21 Jun 2020 21:29:19: 11000000 INFO @ Sun, 21 Jun 2020 21:29:25: 6000000 INFO @ Sun, 21 Jun 2020 21:29:25: 12000000 INFO @ Sun, 21 Jun 2020 21:29:32: 13000000 INFO @ Sun, 21 Jun 2020 21:29:32: 7000000 INFO @ Sun, 21 Jun 2020 21:29:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:29:38: 14000000 INFO @ Sun, 21 Jun 2020 21:29:39: 8000000 INFO @ Sun, 21 Jun 2020 21:29:39: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:29:39: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:29:39: #1 total tags in treatment: 14134100 INFO @ Sun, 21 Jun 2020 21:29:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:29:39: #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 21:29:39: #1 tags after filtering in treatment: 14134074 INFO @ Sun, 21 Jun 2020 21:29:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:29:39: #1 finished! INFO @ Sun, 21 Jun 2020 21:29:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:29:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:29:40: #2 number of paired peaks: 139 WARNING @ Sun, 21 Jun 2020 21:29:40: Fewer paired peaks (139) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 139 pairs to build model! INFO @ Sun, 21 Jun 2020 21:29:40: start model_add_line... INFO @ Sun, 21 Jun 2020 21:29:40: start X-correlation... INFO @ Sun, 21 Jun 2020 21:29:40: end of X-cor INFO @ Sun, 21 Jun 2020 21:29:40: #2 finished! INFO @ Sun, 21 Jun 2020 21:29:40: #2 predicted fragment length is 4 bps INFO @ Sun, 21 Jun 2020 21:29:40: #2 alternative fragment length(s) may be 4,33,554 bps INFO @ Sun, 21 Jun 2020 21:29:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495307/SRX495307.10_model.r WARNING @ Sun, 21 Jun 2020 21:29:40: #2 Since the d (4) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:29:40: #2 You may need to consider one of the other alternative d(s): 4,33,554 WARNING @ Sun, 21 Jun 2020 21:29:40: #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 21:29:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:29:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:29:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495307/SRX495307.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:29:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495307/SRX495307.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:29:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495307/SRX495307.05_summits.bed INFO @ Sun, 21 Jun 2020 21:29:45: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:29:45: 9000000 INFO @ Sun, 21 Jun 2020 21:29:52: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:29:58: 11000000 INFO @ Sun, 21 Jun 2020 21:30:05: 12000000 INFO @ Sun, 21 Jun 2020 21:30:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:30:12: 13000000 INFO @ Sun, 21 Jun 2020 21:30:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495307/SRX495307.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:30:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495307/SRX495307.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:30:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495307/SRX495307.10_summits.bed INFO @ Sun, 21 Jun 2020 21:30:19: Done! INFO @ Sun, 21 Jun 2020 21:30:19: 14000000 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:30:20: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:30:20: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:30:20: #1 total tags in treatment: 14134100 INFO @ Sun, 21 Jun 2020 21:30:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:30:20: #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 21:30:20: #1 tags after filtering in treatment: 14134074 INFO @ Sun, 21 Jun 2020 21:30:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:30:20: #1 finished! INFO @ Sun, 21 Jun 2020 21:30:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:30:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:30:21: #2 number of paired peaks: 139 WARNING @ Sun, 21 Jun 2020 21:30:21: Fewer paired peaks (139) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 139 pairs to build model! INFO @ Sun, 21 Jun 2020 21:30:21: start model_add_line... INFO @ Sun, 21 Jun 2020 21:30:21: start X-correlation... INFO @ Sun, 21 Jun 2020 21:30:21: end of X-cor INFO @ Sun, 21 Jun 2020 21:30:21: #2 finished! INFO @ Sun, 21 Jun 2020 21:30:21: #2 predicted fragment length is 4 bps INFO @ Sun, 21 Jun 2020 21:30:21: #2 alternative fragment length(s) may be 4,33,554 bps INFO @ Sun, 21 Jun 2020 21:30:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495307/SRX495307.20_model.r WARNING @ Sun, 21 Jun 2020 21:30:21: #2 Since the d (4) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:30:21: #2 You may need to consider one of the other alternative d(s): 4,33,554 WARNING @ Sun, 21 Jun 2020 21:30:21: #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 21:30:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:30:21: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:30:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:31:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495307/SRX495307.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:31:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495307/SRX495307.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:31:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495307/SRX495307.20_summits.bed INFO @ Sun, 21 Jun 2020 21:31:01: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling