Job ID = 6455663 SRX = SRX287968 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:18:21 prefetch.2.10.7: 1) Downloading 'SRR870157'... 2020-06-21T10:18:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:21:46 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:21:46 prefetch.2.10.7: 1) 'SRR870157' was downloaded successfully Read 17667108 spots for SRR870157/SRR870157.sra Written 17667108 spots for SRR870157/SRR870157.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: 00:05:12 17667108 reads; of these: 17667108 (100.00%) were unpaired; of these: 989033 (5.60%) aligned 0 times 11539934 (65.32%) aligned exactly 1 time 5138141 (29.08%) aligned >1 times 94.40% overall alignment rate Time searching: 00:05:12 Overall time: 00:05:12 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] 2391323 / 16678075 = 0.1434 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 19:32:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287968/SRX287968.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287968/SRX287968.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287968/SRX287968.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287968/SRX287968.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 19:32:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:32:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:32:13: 1000000 INFO @ Sun, 21 Jun 2020 19:32:19: 2000000 INFO @ Sun, 21 Jun 2020 19:32:24: 3000000 INFO @ Sun, 21 Jun 2020 19:32:30: 4000000 INFO @ Sun, 21 Jun 2020 19:32:35: 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 19:32:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287968/SRX287968.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287968/SRX287968.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287968/SRX287968.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287968/SRX287968.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 19:32:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:32:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:32:42: 6000000 INFO @ Sun, 21 Jun 2020 19:32:45: 1000000 INFO @ Sun, 21 Jun 2020 19:32:49: 7000000 INFO @ Sun, 21 Jun 2020 19:32:53: 2000000 INFO @ Sun, 21 Jun 2020 19:32:56: 8000000 INFO @ Sun, 21 Jun 2020 19:33:01: 3000000 INFO @ Sun, 21 Jun 2020 19:33:03: 9000000 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 19:33:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287968/SRX287968.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287968/SRX287968.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287968/SRX287968.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287968/SRX287968.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 19:33:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:33:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:33:09: 4000000 INFO @ Sun, 21 Jun 2020 19:33:10: 10000000 INFO @ Sun, 21 Jun 2020 19:33:14: 1000000 INFO @ Sun, 21 Jun 2020 19:33:16: 5000000 INFO @ Sun, 21 Jun 2020 19:33:17: 11000000 INFO @ Sun, 21 Jun 2020 19:33:22: 2000000 INFO @ Sun, 21 Jun 2020 19:33:24: 6000000 INFO @ Sun, 21 Jun 2020 19:33:25: 12000000 INFO @ Sun, 21 Jun 2020 19:33:29: 3000000 INFO @ Sun, 21 Jun 2020 19:33:32: 13000000 INFO @ Sun, 21 Jun 2020 19:33:32: 7000000 INFO @ Sun, 21 Jun 2020 19:33:36: 4000000 INFO @ Sun, 21 Jun 2020 19:33:40: 14000000 INFO @ Sun, 21 Jun 2020 19:33:40: 8000000 INFO @ Sun, 21 Jun 2020 19:33:42: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:33:42: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:33:42: #1 total tags in treatment: 14286752 INFO @ Sun, 21 Jun 2020 19:33:42: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:33:42: #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 19:33:42: #1 tags after filtering in treatment: 14286752 INFO @ Sun, 21 Jun 2020 19:33:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:33:42: #1 finished! INFO @ Sun, 21 Jun 2020 19:33:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:33:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:33:43: #2 number of paired peaks: 470 WARNING @ Sun, 21 Jun 2020 19:33:43: Fewer paired peaks (470) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 470 pairs to build model! INFO @ Sun, 21 Jun 2020 19:33:43: start model_add_line... INFO @ Sun, 21 Jun 2020 19:33:43: start X-correlation... INFO @ Sun, 21 Jun 2020 19:33:43: end of X-cor INFO @ Sun, 21 Jun 2020 19:33:43: #2 finished! INFO @ Sun, 21 Jun 2020 19:33:43: #2 predicted fragment length is 38 bps INFO @ Sun, 21 Jun 2020 19:33:43: #2 alternative fragment length(s) may be 4,38 bps INFO @ Sun, 21 Jun 2020 19:33:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287968/SRX287968.05_model.r WARNING @ Sun, 21 Jun 2020 19:33:43: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:33:43: #2 You may need to consider one of the other alternative d(s): 4,38 WARNING @ Sun, 21 Jun 2020 19:33:43: #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 19:33:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:33:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:33:43: 5000000 INFO @ Sun, 21 Jun 2020 19:33:48: 9000000 INFO @ Sun, 21 Jun 2020 19:33:51: 6000000 INFO @ Sun, 21 Jun 2020 19:33:55: 10000000 INFO @ Sun, 21 Jun 2020 19:33:58: 7000000 INFO @ Sun, 21 Jun 2020 19:34:03: 11000000 INFO @ Sun, 21 Jun 2020 19:34:05: 8000000 INFO @ Sun, 21 Jun 2020 19:34:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:34:12: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:34:12: 9000000 INFO @ Sun, 21 Jun 2020 19:34:19: 10000000 INFO @ Sun, 21 Jun 2020 19:34:19: 13000000 INFO @ Sun, 21 Jun 2020 19:34:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287968/SRX287968.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:34:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287968/SRX287968.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:34:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287968/SRX287968.05_summits.bed INFO @ Sun, 21 Jun 2020 19:34:24: Done! pass1 - making usageList (613 chroms): 1 millis pass2 - checking and writing primary data (2487 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:34:26: 11000000 INFO @ Sun, 21 Jun 2020 19:34:27: 14000000 INFO @ Sun, 21 Jun 2020 19:34:30: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:34:30: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:34:30: #1 total tags in treatment: 14286752 INFO @ Sun, 21 Jun 2020 19:34:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:34:30: #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 19:34:30: #1 tags after filtering in treatment: 14286752 INFO @ Sun, 21 Jun 2020 19:34:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:34:30: #1 finished! INFO @ Sun, 21 Jun 2020 19:34:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:34:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:34:31: #2 number of paired peaks: 470 WARNING @ Sun, 21 Jun 2020 19:34:31: Fewer paired peaks (470) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 470 pairs to build model! INFO @ Sun, 21 Jun 2020 19:34:31: start model_add_line... INFO @ Sun, 21 Jun 2020 19:34:31: start X-correlation... INFO @ Sun, 21 Jun 2020 19:34:31: end of X-cor INFO @ Sun, 21 Jun 2020 19:34:31: #2 finished! INFO @ Sun, 21 Jun 2020 19:34:31: #2 predicted fragment length is 38 bps INFO @ Sun, 21 Jun 2020 19:34:31: #2 alternative fragment length(s) may be 4,38 bps INFO @ Sun, 21 Jun 2020 19:34:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287968/SRX287968.10_model.r WARNING @ Sun, 21 Jun 2020 19:34:31: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:34:31: #2 You may need to consider one of the other alternative d(s): 4,38 WARNING @ Sun, 21 Jun 2020 19:34:31: #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 19:34:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:34:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:34:33: 12000000 INFO @ Sun, 21 Jun 2020 19:34:39: 13000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:34:45: 14000000 INFO @ Sun, 21 Jun 2020 19:34:47: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:34:47: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:34:47: #1 total tags in treatment: 14286752 INFO @ Sun, 21 Jun 2020 19:34:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:34:47: #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 19:34:48: #1 tags after filtering in treatment: 14286752 INFO @ Sun, 21 Jun 2020 19:34:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:34:48: #1 finished! INFO @ Sun, 21 Jun 2020 19:34:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:34:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:34:49: #2 number of paired peaks: 470 WARNING @ Sun, 21 Jun 2020 19:34:49: Fewer paired peaks (470) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 470 pairs to build model! INFO @ Sun, 21 Jun 2020 19:34:49: start model_add_line... INFO @ Sun, 21 Jun 2020 19:34:49: start X-correlation... INFO @ Sun, 21 Jun 2020 19:34:49: end of X-cor INFO @ Sun, 21 Jun 2020 19:34:49: #2 finished! INFO @ Sun, 21 Jun 2020 19:34:49: #2 predicted fragment length is 38 bps INFO @ Sun, 21 Jun 2020 19:34:49: #2 alternative fragment length(s) may be 4,38 bps INFO @ Sun, 21 Jun 2020 19:34:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287968/SRX287968.20_model.r WARNING @ Sun, 21 Jun 2020 19:34:49: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:34:49: #2 You may need to consider one of the other alternative d(s): 4,38 WARNING @ Sun, 21 Jun 2020 19:34:49: #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 19:34:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:34:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:34:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:35:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287968/SRX287968.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:35:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287968/SRX287968.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:35:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287968/SRX287968.10_summits.bed INFO @ Sun, 21 Jun 2020 19:35:11: Done! pass1 - making usageList (502 chroms): 1 millis pass2 - checking and writing primary data (1814 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:35:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:35:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287968/SRX287968.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:35:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287968/SRX287968.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:35:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287968/SRX287968.20_summits.bed INFO @ Sun, 21 Jun 2020 19:35:29: Done! pass1 - making usageList (259 chroms): 1 millis pass2 - checking and writing primary data (545 records, 4 fields): 9 millis CompletedMACS2peakCalling