Job ID = 6458566 SRX = SRX5343100 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:32:19 prefetch.2.10.7: 1) Downloading 'SRR8540877'... 2020-06-21T12:32:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:35:18 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:35:18 prefetch.2.10.7: 1) 'SRR8540877' was downloaded successfully 2020-06-21T12:35:18 prefetch.2.10.7: 'SRR8540877' has 0 unresolved dependencies Read 23001207 spots for SRR8540877/SRR8540877.sra Written 23001207 spots for SRR8540877/SRR8540877.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: 00:10:47 23001207 reads; of these: 23001207 (100.00%) were unpaired; of these: 1710995 (7.44%) aligned 0 times 8033833 (34.93%) aligned exactly 1 time 13256379 (57.63%) aligned >1 times 92.56% overall alignment rate Time searching: 00:10:47 Overall time: 00:10:47 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] 8683493 / 21290212 = 0.4079 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 21:52:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343100/SRX5343100.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343100/SRX5343100.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343100/SRX5343100.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343100/SRX5343100.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 21:52:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:52:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:52:55: 1000000 INFO @ Sun, 21 Jun 2020 21:53:01: 2000000 INFO @ Sun, 21 Jun 2020 21:53:08: 3000000 INFO @ Sun, 21 Jun 2020 21:53:14: 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 21:53:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343100/SRX5343100.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343100/SRX5343100.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343100/SRX5343100.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343100/SRX5343100.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 21:53:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:53:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:53:20: 5000000 INFO @ Sun, 21 Jun 2020 21:53:26: 1000000 INFO @ Sun, 21 Jun 2020 21:53:27: 6000000 INFO @ Sun, 21 Jun 2020 21:53:33: 2000000 INFO @ Sun, 21 Jun 2020 21:53:34: 7000000 INFO @ Sun, 21 Jun 2020 21:53:40: 3000000 INFO @ Sun, 21 Jun 2020 21:53:41: 8000000 INFO @ Sun, 21 Jun 2020 21:53:47: 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 @ Sun, 21 Jun 2020 21:53:48: 9000000 INFO @ Sun, 21 Jun 2020 21:53:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343100/SRX5343100.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343100/SRX5343100.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343100/SRX5343100.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343100/SRX5343100.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 21:53:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:53:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:53:53: 5000000 INFO @ Sun, 21 Jun 2020 21:53:55: 10000000 INFO @ Sun, 21 Jun 2020 21:53:56: 1000000 INFO @ Sun, 21 Jun 2020 21:54:00: 6000000 INFO @ Sun, 21 Jun 2020 21:54:02: 11000000 INFO @ Sun, 21 Jun 2020 21:54:03: 2000000 INFO @ Sun, 21 Jun 2020 21:54:07: 7000000 INFO @ Sun, 21 Jun 2020 21:54:09: 3000000 INFO @ Sun, 21 Jun 2020 21:54:10: 12000000 INFO @ Sun, 21 Jun 2020 21:54:14: 8000000 INFO @ Sun, 21 Jun 2020 21:54:14: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 21:54:14: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 21:54:14: #1 total tags in treatment: 12606719 INFO @ Sun, 21 Jun 2020 21:54:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:54:14: #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 21:54:15: #1 tags after filtering in treatment: 12606718 INFO @ Sun, 21 Jun 2020 21:54:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:54:15: #1 finished! INFO @ Sun, 21 Jun 2020 21:54:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:54:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:54:16: #2 number of paired peaks: 4449 INFO @ Sun, 21 Jun 2020 21:54:16: start model_add_line... INFO @ Sun, 21 Jun 2020 21:54:16: start X-correlation... INFO @ Sun, 21 Jun 2020 21:54:16: end of X-cor INFO @ Sun, 21 Jun 2020 21:54:16: #2 finished! INFO @ Sun, 21 Jun 2020 21:54:16: #2 predicted fragment length is 76 bps INFO @ Sun, 21 Jun 2020 21:54:16: #2 alternative fragment length(s) may be 3,76 bps INFO @ Sun, 21 Jun 2020 21:54:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343100/SRX5343100.05_model.r WARNING @ Sun, 21 Jun 2020 21:54:16: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:54:16: #2 You may need to consider one of the other alternative d(s): 3,76 WARNING @ Sun, 21 Jun 2020 21:54:16: #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 21:54:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:54:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:54:16: 4000000 INFO @ Sun, 21 Jun 2020 21:54:20: 9000000 INFO @ Sun, 21 Jun 2020 21:54:23: 5000000 INFO @ Sun, 21 Jun 2020 21:54:28: 10000000 INFO @ Sun, 21 Jun 2020 21:54:30: 6000000 INFO @ Sun, 21 Jun 2020 21:54:35: 11000000 INFO @ Sun, 21 Jun 2020 21:54:36: 7000000 INFO @ Sun, 21 Jun 2020 21:54:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:54:42: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:54:43: 8000000 INFO @ Sun, 21 Jun 2020 21:54:46: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 21:54:46: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 21:54:46: #1 total tags in treatment: 12606719 INFO @ Sun, 21 Jun 2020 21:54:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:54:46: #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 21:54:47: #1 tags after filtering in treatment: 12606718 INFO @ Sun, 21 Jun 2020 21:54:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:54:47: #1 finished! INFO @ Sun, 21 Jun 2020 21:54:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:54:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:54:48: #2 number of paired peaks: 4449 INFO @ Sun, 21 Jun 2020 21:54:48: start model_add_line... INFO @ Sun, 21 Jun 2020 21:54:48: start X-correlation... INFO @ Sun, 21 Jun 2020 21:54:48: end of X-cor INFO @ Sun, 21 Jun 2020 21:54:48: #2 finished! INFO @ Sun, 21 Jun 2020 21:54:48: #2 predicted fragment length is 76 bps INFO @ Sun, 21 Jun 2020 21:54:48: #2 alternative fragment length(s) may be 3,76 bps INFO @ Sun, 21 Jun 2020 21:54:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343100/SRX5343100.10_model.r WARNING @ Sun, 21 Jun 2020 21:54:48: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:54:48: #2 You may need to consider one of the other alternative d(s): 3,76 WARNING @ Sun, 21 Jun 2020 21:54:48: #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 21:54:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:54:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:54:49: 9000000 INFO @ Sun, 21 Jun 2020 21:54:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343100/SRX5343100.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:54:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343100/SRX5343100.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:54:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343100/SRX5343100.05_summits.bed INFO @ Sun, 21 Jun 2020 21:54:55: Done! pass1 - making usageList (1264 chroms): 2 millis pass2 - checking and writing primary data (7211 records, 4 fields): 37 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:54:56: 10000000 INFO @ Sun, 21 Jun 2020 21:55:03: 11000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:55:10: 12000000 INFO @ Sun, 21 Jun 2020 21:55:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:55:14: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 21:55:14: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 21:55:14: #1 total tags in treatment: 12606719 INFO @ Sun, 21 Jun 2020 21:55:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:55:14: #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 21:55:14: #1 tags after filtering in treatment: 12606718 INFO @ Sun, 21 Jun 2020 21:55:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:55:14: #1 finished! INFO @ Sun, 21 Jun 2020 21:55:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:55:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:55:15: #2 number of paired peaks: 4449 INFO @ Sun, 21 Jun 2020 21:55:15: start model_add_line... INFO @ Sun, 21 Jun 2020 21:55:15: start X-correlation... INFO @ Sun, 21 Jun 2020 21:55:15: end of X-cor INFO @ Sun, 21 Jun 2020 21:55:15: #2 finished! INFO @ Sun, 21 Jun 2020 21:55:15: #2 predicted fragment length is 76 bps INFO @ Sun, 21 Jun 2020 21:55:15: #2 alternative fragment length(s) may be 3,76 bps INFO @ Sun, 21 Jun 2020 21:55:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343100/SRX5343100.20_model.r WARNING @ Sun, 21 Jun 2020 21:55:15: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:55:15: #2 You may need to consider one of the other alternative d(s): 3,76 WARNING @ Sun, 21 Jun 2020 21:55:15: #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 21:55:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:55:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:55:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343100/SRX5343100.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:55:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343100/SRX5343100.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:55:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343100/SRX5343100.10_summits.bed INFO @ Sun, 21 Jun 2020 21:55:25: Done! pass1 - making usageList (961 chroms): 2 millis pass2 - checking and writing primary data (3306 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:55:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:55:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343100/SRX5343100.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:55:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343100/SRX5343100.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:55:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343100/SRX5343100.20_summits.bed INFO @ Sun, 21 Jun 2020 21:55:53: Done! pass1 - making usageList (642 chroms): 1 millis pass2 - checking and writing primary data (1564 records, 4 fields): 18 millis CompletedMACS2peakCalling