Job ID = 6455192 SRX = SRX2831139 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:49:40 prefetch.2.10.7: 1) Downloading 'SRR5572461'... 2020-06-21T09:49:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:53:44 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:53:44 prefetch.2.10.7: 1) 'SRR5572461' was downloaded successfully Read 26735128 spots for SRR5572461/SRR5572461.sra Written 26735128 spots for SRR5572461/SRR5572461.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: 00:07:21 26735128 reads; of these: 26735128 (100.00%) were unpaired; of these: 938850 (3.51%) aligned 0 times 18954798 (70.90%) aligned exactly 1 time 6841480 (25.59%) aligned >1 times 96.49% overall alignment rate Time searching: 00:07:21 Overall time: 00:07:21 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] 3565172 / 25796278 = 0.1382 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 19:08:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2831139/SRX2831139.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2831139/SRX2831139.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2831139/SRX2831139.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2831139/SRX2831139.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 19:08:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:08:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:08:20: 1000000 INFO @ Sun, 21 Jun 2020 19:08:26: 2000000 INFO @ Sun, 21 Jun 2020 19:08:31: 3000000 INFO @ Sun, 21 Jun 2020 19:08:37: 4000000 INFO @ Sun, 21 Jun 2020 19:08:42: 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 19:08:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2831139/SRX2831139.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2831139/SRX2831139.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2831139/SRX2831139.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2831139/SRX2831139.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 19:08:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:08:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:08:48: 6000000 INFO @ Sun, 21 Jun 2020 19:08:51: 1000000 INFO @ Sun, 21 Jun 2020 19:08:54: 7000000 INFO @ Sun, 21 Jun 2020 19:08:57: 2000000 INFO @ Sun, 21 Jun 2020 19:09:00: 8000000 INFO @ Sun, 21 Jun 2020 19:09:03: 3000000 INFO @ Sun, 21 Jun 2020 19:09:06: 9000000 INFO @ Sun, 21 Jun 2020 19:09:09: 4000000 INFO @ Sun, 21 Jun 2020 19:09:12: 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 19:09:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2831139/SRX2831139.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2831139/SRX2831139.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2831139/SRX2831139.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2831139/SRX2831139.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 19:09:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:09:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:09:15: 5000000 INFO @ Sun, 21 Jun 2020 19:09:18: 11000000 INFO @ Sun, 21 Jun 2020 19:09:21: 6000000 INFO @ Sun, 21 Jun 2020 19:09:22: 1000000 INFO @ Sun, 21 Jun 2020 19:09:24: 12000000 INFO @ Sun, 21 Jun 2020 19:09:28: 7000000 INFO @ Sun, 21 Jun 2020 19:09:28: 2000000 INFO @ Sun, 21 Jun 2020 19:09:31: 13000000 INFO @ Sun, 21 Jun 2020 19:09:34: 8000000 INFO @ Sun, 21 Jun 2020 19:09:35: 3000000 INFO @ Sun, 21 Jun 2020 19:09:37: 14000000 INFO @ Sun, 21 Jun 2020 19:09:41: 9000000 INFO @ Sun, 21 Jun 2020 19:09:42: 4000000 INFO @ Sun, 21 Jun 2020 19:09:44: 15000000 INFO @ Sun, 21 Jun 2020 19:09:47: 10000000 INFO @ Sun, 21 Jun 2020 19:09:49: 5000000 INFO @ Sun, 21 Jun 2020 19:09:50: 16000000 INFO @ Sun, 21 Jun 2020 19:09:54: 11000000 INFO @ Sun, 21 Jun 2020 19:09:57: 6000000 INFO @ Sun, 21 Jun 2020 19:09:57: 17000000 INFO @ Sun, 21 Jun 2020 19:10:01: 12000000 INFO @ Sun, 21 Jun 2020 19:10:04: 18000000 INFO @ Sun, 21 Jun 2020 19:10:04: 7000000 INFO @ Sun, 21 Jun 2020 19:10:07: 13000000 INFO @ Sun, 21 Jun 2020 19:10:11: 19000000 INFO @ Sun, 21 Jun 2020 19:10:12: 8000000 INFO @ Sun, 21 Jun 2020 19:10:14: 14000000 INFO @ Sun, 21 Jun 2020 19:10:18: 20000000 INFO @ Sun, 21 Jun 2020 19:10:19: 9000000 INFO @ Sun, 21 Jun 2020 19:10:21: 15000000 INFO @ Sun, 21 Jun 2020 19:10:24: 21000000 INFO @ Sun, 21 Jun 2020 19:10:27: 10000000 INFO @ Sun, 21 Jun 2020 19:10:28: 16000000 INFO @ Sun, 21 Jun 2020 19:10:31: 22000000 INFO @ Sun, 21 Jun 2020 19:10:33: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:10:33: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:10:33: #1 total tags in treatment: 22231106 INFO @ Sun, 21 Jun 2020 19:10:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:10:33: #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 19:10:34: #1 tags after filtering in treatment: 22231037 INFO @ Sun, 21 Jun 2020 19:10:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:10:34: #1 finished! INFO @ Sun, 21 Jun 2020 19:10:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:10:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:10:34: 17000000 INFO @ Sun, 21 Jun 2020 19:10:34: 11000000 INFO @ Sun, 21 Jun 2020 19:10:35: #2 number of paired peaks: 729 WARNING @ Sun, 21 Jun 2020 19:10:35: Fewer paired peaks (729) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 729 pairs to build model! INFO @ Sun, 21 Jun 2020 19:10:35: start model_add_line... INFO @ Sun, 21 Jun 2020 19:10:36: start X-correlation... INFO @ Sun, 21 Jun 2020 19:10:36: end of X-cor INFO @ Sun, 21 Jun 2020 19:10:36: #2 finished! INFO @ Sun, 21 Jun 2020 19:10:36: #2 predicted fragment length is 51 bps INFO @ Sun, 21 Jun 2020 19:10:36: #2 alternative fragment length(s) may be 1,51,563,581 bps INFO @ Sun, 21 Jun 2020 19:10:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2831139/SRX2831139.05_model.r WARNING @ Sun, 21 Jun 2020 19:10:36: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:10:36: #2 You may need to consider one of the other alternative d(s): 1,51,563,581 WARNING @ Sun, 21 Jun 2020 19:10:36: #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 19:10:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:10:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:10:41: 18000000 INFO @ Sun, 21 Jun 2020 19:10:42: 12000000 INFO @ Sun, 21 Jun 2020 19:10:48: 19000000 INFO @ Sun, 21 Jun 2020 19:10:49: 13000000 INFO @ Sun, 21 Jun 2020 19:10:55: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:10:57: 14000000 INFO @ Sun, 21 Jun 2020 19:11:02: 21000000 INFO @ Sun, 21 Jun 2020 19:11:04: 15000000 INFO @ Sun, 21 Jun 2020 19:11:08: 22000000 INFO @ Sun, 21 Jun 2020 19:11:10: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:11:10: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:11:10: #1 total tags in treatment: 22231106 INFO @ Sun, 21 Jun 2020 19:11:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:11:10: #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 19:11:10: 16000000 INFO @ Sun, 21 Jun 2020 19:11:11: #1 tags after filtering in treatment: 22231037 INFO @ Sun, 21 Jun 2020 19:11:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:11:11: #1 finished! INFO @ Sun, 21 Jun 2020 19:11:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:11:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:11:12: #2 number of paired peaks: 729 WARNING @ Sun, 21 Jun 2020 19:11:12: Fewer paired peaks (729) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 729 pairs to build model! INFO @ Sun, 21 Jun 2020 19:11:12: start model_add_line... INFO @ Sun, 21 Jun 2020 19:11:13: start X-correlation... INFO @ Sun, 21 Jun 2020 19:11:13: end of X-cor INFO @ Sun, 21 Jun 2020 19:11:13: #2 finished! INFO @ Sun, 21 Jun 2020 19:11:13: #2 predicted fragment length is 51 bps INFO @ Sun, 21 Jun 2020 19:11:13: #2 alternative fragment length(s) may be 1,51,563,581 bps INFO @ Sun, 21 Jun 2020 19:11:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2831139/SRX2831139.10_model.r WARNING @ Sun, 21 Jun 2020 19:11:13: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:11:13: #2 You may need to consider one of the other alternative d(s): 1,51,563,581 WARNING @ Sun, 21 Jun 2020 19:11:13: #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 19:11:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:11:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:11:17: 17000000 INFO @ Sun, 21 Jun 2020 19:11:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:11:23: 18000000 INFO @ Sun, 21 Jun 2020 19:11:30: 19000000 INFO @ Sun, 21 Jun 2020 19:11:37: 20000000 INFO @ Sun, 21 Jun 2020 19:11:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2831139/SRX2831139.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:11:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2831139/SRX2831139.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:11:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2831139/SRX2831139.05_summits.bed INFO @ Sun, 21 Jun 2020 19:11:41: Done! pass1 - making usageList (606 chroms): 1 millis pass2 - checking and writing primary data (3317 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:11:43: 21000000 INFO @ Sun, 21 Jun 2020 19:11:50: 22000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:11:51: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:11:51: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:11:51: #1 total tags in treatment: 22231106 INFO @ Sun, 21 Jun 2020 19:11:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:11:51: #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 19:11:52: #1 tags after filtering in treatment: 22231037 INFO @ Sun, 21 Jun 2020 19:11:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:11:52: #1 finished! INFO @ Sun, 21 Jun 2020 19:11:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:11:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:11:53: #2 number of paired peaks: 729 WARNING @ Sun, 21 Jun 2020 19:11:53: Fewer paired peaks (729) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 729 pairs to build model! INFO @ Sun, 21 Jun 2020 19:11:53: start model_add_line... INFO @ Sun, 21 Jun 2020 19:11:54: start X-correlation... INFO @ Sun, 21 Jun 2020 19:11:54: end of X-cor INFO @ Sun, 21 Jun 2020 19:11:54: #2 finished! INFO @ Sun, 21 Jun 2020 19:11:54: #2 predicted fragment length is 51 bps INFO @ Sun, 21 Jun 2020 19:11:54: #2 alternative fragment length(s) may be 1,51,563,581 bps INFO @ Sun, 21 Jun 2020 19:11:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2831139/SRX2831139.20_model.r WARNING @ Sun, 21 Jun 2020 19:11:54: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:11:54: #2 You may need to consider one of the other alternative d(s): 1,51,563,581 WARNING @ Sun, 21 Jun 2020 19:11:54: #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 19:11:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:11:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:11:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:12:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2831139/SRX2831139.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:12:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2831139/SRX2831139.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:12:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2831139/SRX2831139.10_summits.bed INFO @ Sun, 21 Jun 2020 19:12:17: Done! pass1 - making usageList (504 chroms): 1 millis pass2 - checking and writing primary data (2139 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:12:34: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:12:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2831139/SRX2831139.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:12:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2831139/SRX2831139.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:12:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2831139/SRX2831139.20_summits.bed INFO @ Sun, 21 Jun 2020 19:12:55: Done! pass1 - making usageList (334 chroms): 1 millis pass2 - checking and writing primary data (826 records, 4 fields): 10 millis CompletedMACS2peakCalling