Job ID = 6458186 SRX = SRX495296 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:15:21 prefetch.2.10.7: 1) Downloading 'SRR1198801'... 2020-06-21T12:15:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:17:31 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:17:31 prefetch.2.10.7: 1) 'SRR1198801' was downloaded successfully Read 17643933 spots for SRR1198801/SRR1198801.sra Written 17643933 spots for SRR1198801/SRR1198801.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: 00:05:21 17643933 reads; of these: 17643933 (100.00%) were unpaired; of these: 1075730 (6.10%) aligned 0 times 11626983 (65.90%) aligned exactly 1 time 4941220 (28.01%) aligned >1 times 93.90% overall alignment rate Time searching: 00:05:21 Overall time: 00:05:21 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 8 files... [bam_rmdupse_core] 4020659 / 16568203 = 0.2427 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 21:27:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495296/SRX495296.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495296/SRX495296.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495296/SRX495296.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495296/SRX495296.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 21:27:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:27:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:27:46: 1000000 INFO @ Sun, 21 Jun 2020 21:27:52: 2000000 INFO @ Sun, 21 Jun 2020 21:27:58: 3000000 INFO @ Sun, 21 Jun 2020 21:28:05: 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 21:28:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495296/SRX495296.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495296/SRX495296.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495296/SRX495296.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495296/SRX495296.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 21:28:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:28:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:28:11: 5000000 INFO @ Sun, 21 Jun 2020 21:28:18: 1000000 INFO @ Sun, 21 Jun 2020 21:28:19: 6000000 INFO @ Sun, 21 Jun 2020 21:28:26: 2000000 INFO @ Sun, 21 Jun 2020 21:28:27: 7000000 INFO @ Sun, 21 Jun 2020 21:28:35: 8000000 INFO @ Sun, 21 Jun 2020 21:28:35: 3000000 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 21:28:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495296/SRX495296.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495296/SRX495296.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495296/SRX495296.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495296/SRX495296.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 21:28:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:28:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:28:43: 9000000 INFO @ Sun, 21 Jun 2020 21:28:44: 4000000 INFO @ Sun, 21 Jun 2020 21:28:49: 1000000 INFO @ Sun, 21 Jun 2020 21:28:51: 10000000 INFO @ Sun, 21 Jun 2020 21:28:52: 5000000 INFO @ Sun, 21 Jun 2020 21:28:58: 2000000 INFO @ Sun, 21 Jun 2020 21:28:59: 11000000 INFO @ Sun, 21 Jun 2020 21:29:01: 6000000 INFO @ Sun, 21 Jun 2020 21:29:07: 3000000 INFO @ Sun, 21 Jun 2020 21:29:07: 12000000 INFO @ Sun, 21 Jun 2020 21:29:09: 7000000 INFO @ Sun, 21 Jun 2020 21:29:11: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:29:11: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:29:11: #1 total tags in treatment: 12547544 INFO @ Sun, 21 Jun 2020 21:29:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:29:11: #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 21:29:12: #1 tags after filtering in treatment: 12547473 INFO @ Sun, 21 Jun 2020 21:29:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:29:12: #1 finished! INFO @ Sun, 21 Jun 2020 21:29:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:29:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:29:13: #2 number of paired peaks: 225 WARNING @ Sun, 21 Jun 2020 21:29:13: Fewer paired peaks (225) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 225 pairs to build model! INFO @ Sun, 21 Jun 2020 21:29:13: start model_add_line... INFO @ Sun, 21 Jun 2020 21:29:13: start X-correlation... INFO @ Sun, 21 Jun 2020 21:29:13: end of X-cor INFO @ Sun, 21 Jun 2020 21:29:13: #2 finished! INFO @ Sun, 21 Jun 2020 21:29:13: #2 predicted fragment length is 48 bps INFO @ Sun, 21 Jun 2020 21:29:13: #2 alternative fragment length(s) may be 3,48,537,576 bps INFO @ Sun, 21 Jun 2020 21:29:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495296/SRX495296.05_model.r WARNING @ Sun, 21 Jun 2020 21:29:13: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:29:13: #2 You may need to consider one of the other alternative d(s): 3,48,537,576 WARNING @ Sun, 21 Jun 2020 21:29:13: #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 21:29:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:29:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:29:15: 4000000 INFO @ Sun, 21 Jun 2020 21:29:18: 8000000 INFO @ Sun, 21 Jun 2020 21:29:24: 5000000 INFO @ Sun, 21 Jun 2020 21:29:26: 9000000 INFO @ Sun, 21 Jun 2020 21:29:32: 6000000 INFO @ Sun, 21 Jun 2020 21:29:35: 10000000 INFO @ Sun, 21 Jun 2020 21:29:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:29:41: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:29:43: 11000000 INFO @ Sun, 21 Jun 2020 21:29:49: 8000000 INFO @ Sun, 21 Jun 2020 21:29:51: 12000000 INFO @ Sun, 21 Jun 2020 21:29:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495296/SRX495296.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:29:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495296/SRX495296.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:29:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495296/SRX495296.05_summits.bed INFO @ Sun, 21 Jun 2020 21:29:53: Done! pass1 - making usageList (514 chroms): 1 millis pass2 - checking and writing primary data (1840 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:29:56: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:29:56: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:29:56: #1 total tags in treatment: 12547544 INFO @ Sun, 21 Jun 2020 21:29:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:29:56: #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 21:29:57: #1 tags after filtering in treatment: 12547473 INFO @ Sun, 21 Jun 2020 21:29:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:29:57: #1 finished! INFO @ Sun, 21 Jun 2020 21:29:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:29:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:29:57: 9000000 INFO @ Sun, 21 Jun 2020 21:29:57: #2 number of paired peaks: 225 WARNING @ Sun, 21 Jun 2020 21:29:57: Fewer paired peaks (225) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 225 pairs to build model! INFO @ Sun, 21 Jun 2020 21:29:57: start model_add_line... INFO @ Sun, 21 Jun 2020 21:29:57: start X-correlation... INFO @ Sun, 21 Jun 2020 21:29:58: end of X-cor INFO @ Sun, 21 Jun 2020 21:29:58: #2 finished! INFO @ Sun, 21 Jun 2020 21:29:58: #2 predicted fragment length is 48 bps INFO @ Sun, 21 Jun 2020 21:29:58: #2 alternative fragment length(s) may be 3,48,537,576 bps INFO @ Sun, 21 Jun 2020 21:29:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495296/SRX495296.10_model.r WARNING @ Sun, 21 Jun 2020 21:29:58: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:29:58: #2 You may need to consider one of the other alternative d(s): 3,48,537,576 WARNING @ Sun, 21 Jun 2020 21:29:58: #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 21:29:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:29:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:30:06: 10000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:30:14: 11000000 INFO @ Sun, 21 Jun 2020 21:30:22: 12000000 INFO @ Sun, 21 Jun 2020 21:30:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:30:26: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:30:26: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:30:26: #1 total tags in treatment: 12547544 INFO @ Sun, 21 Jun 2020 21:30:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:30:26: #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 21:30:27: #1 tags after filtering in treatment: 12547473 INFO @ Sun, 21 Jun 2020 21:30:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:30:27: #1 finished! INFO @ Sun, 21 Jun 2020 21:30:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:30:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:30:27: #2 number of paired peaks: 225 WARNING @ Sun, 21 Jun 2020 21:30:27: Fewer paired peaks (225) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 225 pairs to build model! INFO @ Sun, 21 Jun 2020 21:30:27: start model_add_line... INFO @ Sun, 21 Jun 2020 21:30:28: start X-correlation... INFO @ Sun, 21 Jun 2020 21:30:28: end of X-cor INFO @ Sun, 21 Jun 2020 21:30:28: #2 finished! INFO @ Sun, 21 Jun 2020 21:30:28: #2 predicted fragment length is 48 bps INFO @ Sun, 21 Jun 2020 21:30:28: #2 alternative fragment length(s) may be 3,48,537,576 bps INFO @ Sun, 21 Jun 2020 21:30:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495296/SRX495296.20_model.r WARNING @ Sun, 21 Jun 2020 21:30:28: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:30:28: #2 You may need to consider one of the other alternative d(s): 3,48,537,576 WARNING @ Sun, 21 Jun 2020 21:30:28: #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 21:30:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:30:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:30:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495296/SRX495296.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:30:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495296/SRX495296.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:30:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495296/SRX495296.10_summits.bed INFO @ Sun, 21 Jun 2020 21:30:36: Done! pass1 - making usageList (272 chroms): 1 millis pass2 - checking and writing primary data (598 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:30:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:31:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495296/SRX495296.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:31:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495296/SRX495296.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:31:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495296/SRX495296.20_summits.bed INFO @ Sun, 21 Jun 2020 21:31:08: Done! pass1 - making usageList (81 chroms): 1 millis pass2 - checking and writing primary data (155 records, 4 fields): 3 millis CompletedMACS2peakCalling