Job ID = 6527855 SRX = SRX287881 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T13:46:56 prefetch.2.10.7: 1) Downloading 'SRR870070'... 2020-06-29T13:46:56 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:50:23 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:50:23 prefetch.2.10.7: 1) 'SRR870070' was downloaded successfully Read 22133183 spots for SRR870070/SRR870070.sra Written 22133183 spots for SRR870070/SRR870070.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: 00:08:02 22133183 reads; of these: 22133183 (100.00%) were unpaired; of these: 1088477 (4.92%) aligned 0 times 13883153 (62.73%) aligned exactly 1 time 7161553 (32.36%) aligned >1 times 95.08% overall alignment rate Time searching: 00:08:02 Overall time: 00:08:02 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] 3984329 / 21044706 = 0.1893 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 @ Mon, 29 Jun 2020 23:09:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287881/SRX287881.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287881/SRX287881.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287881/SRX287881.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287881/SRX287881.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, 29 Jun 2020 23:09:54: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:09:54: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:09:59: 1000000 INFO @ Mon, 29 Jun 2020 23:10:04: 2000000 INFO @ Mon, 29 Jun 2020 23:10:09: 3000000 INFO @ Mon, 29 Jun 2020 23:10:14: 4000000 INFO @ Mon, 29 Jun 2020 23:10:20: 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 @ Mon, 29 Jun 2020 23:10:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287881/SRX287881.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287881/SRX287881.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287881/SRX287881.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287881/SRX287881.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, 29 Jun 2020 23:10:24: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:10:24: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:10:25: 6000000 INFO @ Mon, 29 Jun 2020 23:10:30: 1000000 INFO @ Mon, 29 Jun 2020 23:10:31: 7000000 INFO @ Mon, 29 Jun 2020 23:10:37: 2000000 INFO @ Mon, 29 Jun 2020 23:10:37: 8000000 INFO @ Mon, 29 Jun 2020 23:10:43: 9000000 INFO @ Mon, 29 Jun 2020 23:10:43: 3000000 INFO @ Mon, 29 Jun 2020 23:10:49: 10000000 INFO @ Mon, 29 Jun 2020 23:10:50: 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 @ Mon, 29 Jun 2020 23:10:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287881/SRX287881.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287881/SRX287881.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287881/SRX287881.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287881/SRX287881.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, 29 Jun 2020 23:10:54: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:10:54: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:10:55: 11000000 INFO @ Mon, 29 Jun 2020 23:10:56: 5000000 INFO @ Mon, 29 Jun 2020 23:11:00: 1000000 INFO @ Mon, 29 Jun 2020 23:11:00: 12000000 INFO @ Mon, 29 Jun 2020 23:11:02: 6000000 INFO @ Mon, 29 Jun 2020 23:11:06: 13000000 INFO @ Mon, 29 Jun 2020 23:11:07: 2000000 INFO @ Mon, 29 Jun 2020 23:11:09: 7000000 INFO @ Mon, 29 Jun 2020 23:11:12: 14000000 INFO @ Mon, 29 Jun 2020 23:11:13: 3000000 INFO @ Mon, 29 Jun 2020 23:11:15: 8000000 INFO @ Mon, 29 Jun 2020 23:11:18: 15000000 INFO @ Mon, 29 Jun 2020 23:11:20: 4000000 INFO @ Mon, 29 Jun 2020 23:11:22: 9000000 INFO @ Mon, 29 Jun 2020 23:11:24: 16000000 INFO @ Mon, 29 Jun 2020 23:11:26: 5000000 INFO @ Mon, 29 Jun 2020 23:11:28: 10000000 INFO @ Mon, 29 Jun 2020 23:11:30: 17000000 INFO @ Mon, 29 Jun 2020 23:11:31: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:11:31: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:11:31: #1 total tags in treatment: 17060377 INFO @ Mon, 29 Jun 2020 23:11:31: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:11:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:11:31: #1 tags after filtering in treatment: 17060377 INFO @ Mon, 29 Jun 2020 23:11:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:11:31: #1 finished! INFO @ Mon, 29 Jun 2020 23:11:31: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:11:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:11:32: #2 number of paired peaks: 245 WARNING @ Mon, 29 Jun 2020 23:11:32: Fewer paired peaks (245) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 245 pairs to build model! INFO @ Mon, 29 Jun 2020 23:11:32: start model_add_line... INFO @ Mon, 29 Jun 2020 23:11:32: start X-correlation... INFO @ Mon, 29 Jun 2020 23:11:32: 6000000 INFO @ Mon, 29 Jun 2020 23:11:32: end of X-cor INFO @ Mon, 29 Jun 2020 23:11:32: #2 finished! INFO @ Mon, 29 Jun 2020 23:11:32: #2 predicted fragment length is 41 bps INFO @ Mon, 29 Jun 2020 23:11:32: #2 alternative fragment length(s) may be 41 bps INFO @ Mon, 29 Jun 2020 23:11:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287881/SRX287881.05_model.r WARNING @ Mon, 29 Jun 2020 23:11:32: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:11:32: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Mon, 29 Jun 2020 23:11:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:11:32: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:11:32: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:11:35: 11000000 INFO @ Mon, 29 Jun 2020 23:11:39: 7000000 INFO @ Mon, 29 Jun 2020 23:11:41: 12000000 INFO @ Mon, 29 Jun 2020 23:11:45: 8000000 INFO @ Mon, 29 Jun 2020 23:11:47: 13000000 INFO @ Mon, 29 Jun 2020 23:11:51: 9000000 INFO @ Mon, 29 Jun 2020 23:11:54: 14000000 INFO @ Mon, 29 Jun 2020 23:11:58: 10000000 INFO @ Mon, 29 Jun 2020 23:12:00: 15000000 INFO @ Mon, 29 Jun 2020 23:12:03: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:12:04: 11000000 INFO @ Mon, 29 Jun 2020 23:12:07: 16000000 INFO @ Mon, 29 Jun 2020 23:12:10: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 23:12:13: 17000000 INFO @ Mon, 29 Jun 2020 23:12:14: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:12:14: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:12:14: #1 total tags in treatment: 17060377 INFO @ Mon, 29 Jun 2020 23:12:14: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:12:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:12:14: #1 tags after filtering in treatment: 17060377 INFO @ Mon, 29 Jun 2020 23:12:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:12:14: #1 finished! INFO @ Mon, 29 Jun 2020 23:12:14: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:12:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:12:15: #2 number of paired peaks: 245 WARNING @ Mon, 29 Jun 2020 23:12:15: Fewer paired peaks (245) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 245 pairs to build model! INFO @ Mon, 29 Jun 2020 23:12:15: start model_add_line... INFO @ Mon, 29 Jun 2020 23:12:15: start X-correlation... INFO @ Mon, 29 Jun 2020 23:12:15: end of X-cor INFO @ Mon, 29 Jun 2020 23:12:15: #2 finished! INFO @ Mon, 29 Jun 2020 23:12:15: #2 predicted fragment length is 41 bps INFO @ Mon, 29 Jun 2020 23:12:15: #2 alternative fragment length(s) may be 41 bps INFO @ Mon, 29 Jun 2020 23:12:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287881/SRX287881.10_model.r WARNING @ Mon, 29 Jun 2020 23:12:15: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:12:15: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Mon, 29 Jun 2020 23:12:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:12:15: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:12:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:12:16: 13000000 INFO @ Mon, 29 Jun 2020 23:12:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287881/SRX287881.05_peaks.xls INFO @ Mon, 29 Jun 2020 23:12:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287881/SRX287881.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:12:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287881/SRX287881.05_summits.bed INFO @ Mon, 29 Jun 2020 23:12:19: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2279 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:12:23: 14000000 INFO @ Mon, 29 Jun 2020 23:12:29: 15000000 INFO @ Mon, 29 Jun 2020 23:12:35: 16000000 INFO @ Mon, 29 Jun 2020 23:12:41: 17000000 INFO @ Mon, 29 Jun 2020 23:12:42: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:12:42: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:12:42: #1 total tags in treatment: 17060377 INFO @ Mon, 29 Jun 2020 23:12:42: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:12:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:12:42: #1 tags after filtering in treatment: 17060377 INFO @ Mon, 29 Jun 2020 23:12:42: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:12:42: #1 finished! INFO @ Mon, 29 Jun 2020 23:12:42: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:12:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:12:43: #2 number of paired peaks: 245 WARNING @ Mon, 29 Jun 2020 23:12:43: Fewer paired peaks (245) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 245 pairs to build model! INFO @ Mon, 29 Jun 2020 23:12:43: start model_add_line... INFO @ Mon, 29 Jun 2020 23:12:43: start X-correlation... INFO @ Mon, 29 Jun 2020 23:12:43: end of X-cor INFO @ Mon, 29 Jun 2020 23:12:43: #2 finished! INFO @ Mon, 29 Jun 2020 23:12:43: #2 predicted fragment length is 41 bps INFO @ Mon, 29 Jun 2020 23:12:43: #2 alternative fragment length(s) may be 41 bps INFO @ Mon, 29 Jun 2020 23:12:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287881/SRX287881.20_model.r WARNING @ Mon, 29 Jun 2020 23:12:43: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:12:43: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Mon, 29 Jun 2020 23:12:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:12:43: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:12:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:12:46: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 23:13:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287881/SRX287881.10_peaks.xls INFO @ Mon, 29 Jun 2020 23:13:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287881/SRX287881.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:13:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287881/SRX287881.10_summits.bed INFO @ Mon, 29 Jun 2020 23:13:02: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1878 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:13:15: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:13:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287881/SRX287881.20_peaks.xls INFO @ Mon, 29 Jun 2020 23:13:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287881/SRX287881.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:13:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287881/SRX287881.20_summits.bed INFO @ Mon, 29 Jun 2020 23:13:31: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1447 records, 4 fields): 3 millis CompletedMACS2peakCalling