Job ID = 6457867 SRX = SRX4823783 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:55:06 prefetch.2.10.7: 1) Downloading 'SRR7992741'... 2020-06-21T11:55:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:59:33 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:59:33 prefetch.2.10.7: 1) 'SRR7992741' was downloaded successfully 2020-06-21T11:59:33 prefetch.2.10.7: 'SRR7992741' has 0 unresolved dependencies Read 46627865 spots for SRR7992741/SRR7992741.sra Written 46627865 spots for SRR7992741/SRR7992741.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: 00:12:32 46627865 reads; of these: 46627865 (100.00%) were unpaired; of these: 7266256 (15.58%) aligned 0 times 28311903 (60.72%) aligned exactly 1 time 11049706 (23.70%) aligned >1 times 84.42% overall alignment rate Time searching: 00:12:32 Overall time: 00:12:32 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 20 files... [bam_rmdupse_core] 25865256 / 39361609 = 0.6571 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 21:20:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4823783/SRX4823783.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4823783/SRX4823783.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4823783/SRX4823783.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4823783/SRX4823783.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 21:20:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:20:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:20:40: 1000000 INFO @ Sun, 21 Jun 2020 21:20:46: 2000000 INFO @ Sun, 21 Jun 2020 21:20:51: 3000000 INFO @ Sun, 21 Jun 2020 21:20:57: 4000000 INFO @ Sun, 21 Jun 2020 21:21:02: 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 21:21:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4823783/SRX4823783.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4823783/SRX4823783.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4823783/SRX4823783.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4823783/SRX4823783.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 21:21:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:21:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:21:07: 6000000 INFO @ Sun, 21 Jun 2020 21:21:10: 1000000 INFO @ Sun, 21 Jun 2020 21:21:12: 7000000 INFO @ Sun, 21 Jun 2020 21:21:15: 2000000 INFO @ Sun, 21 Jun 2020 21:21:18: 8000000 INFO @ Sun, 21 Jun 2020 21:21:20: 3000000 INFO @ Sun, 21 Jun 2020 21:21:23: 9000000 INFO @ Sun, 21 Jun 2020 21:21:25: 4000000 INFO @ Sun, 21 Jun 2020 21:21:29: 10000000 INFO @ Sun, 21 Jun 2020 21:21:31: 5000000 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 21:21:34: 11000000 INFO @ Sun, 21 Jun 2020 21:21:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4823783/SRX4823783.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4823783/SRX4823783.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4823783/SRX4823783.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4823783/SRX4823783.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 21:21:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:21:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:21:36: 6000000 INFO @ Sun, 21 Jun 2020 21:21:40: 12000000 INFO @ Sun, 21 Jun 2020 21:21:40: 1000000 INFO @ Sun, 21 Jun 2020 21:21:41: 7000000 INFO @ Sun, 21 Jun 2020 21:21:45: 13000000 INFO @ Sun, 21 Jun 2020 21:21:45: 2000000 INFO @ Sun, 21 Jun 2020 21:21:46: 8000000 INFO @ Sun, 21 Jun 2020 21:21:47: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:21:47: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:21:47: #1 total tags in treatment: 13496353 INFO @ Sun, 21 Jun 2020 21:21:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:21:47: #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 21:21:48: #1 tags after filtering in treatment: 13496287 INFO @ Sun, 21 Jun 2020 21:21:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:21:48: #1 finished! INFO @ Sun, 21 Jun 2020 21:21:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:21:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:21:49: #2 number of paired peaks: 1919 INFO @ Sun, 21 Jun 2020 21:21:49: start model_add_line... INFO @ Sun, 21 Jun 2020 21:21:49: start X-correlation... INFO @ Sun, 21 Jun 2020 21:21:49: end of X-cor INFO @ Sun, 21 Jun 2020 21:21:49: #2 finished! INFO @ Sun, 21 Jun 2020 21:21:49: #2 predicted fragment length is 100 bps INFO @ Sun, 21 Jun 2020 21:21:49: #2 alternative fragment length(s) may be 4,100 bps INFO @ Sun, 21 Jun 2020 21:21:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4823783/SRX4823783.05_model.r WARNING @ Sun, 21 Jun 2020 21:21:49: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:21:49: #2 You may need to consider one of the other alternative d(s): 4,100 WARNING @ Sun, 21 Jun 2020 21:21:49: #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 21:21:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:21:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:21:50: 3000000 INFO @ Sun, 21 Jun 2020 21:21:51: 9000000 INFO @ Sun, 21 Jun 2020 21:21:55: 4000000 INFO @ Sun, 21 Jun 2020 21:21:56: 10000000 INFO @ Sun, 21 Jun 2020 21:22:00: 5000000 INFO @ Sun, 21 Jun 2020 21:22:01: 11000000 INFO @ Sun, 21 Jun 2020 21:22:05: 6000000 INFO @ Sun, 21 Jun 2020 21:22:06: 12000000 INFO @ Sun, 21 Jun 2020 21:22:10: 7000000 INFO @ Sun, 21 Jun 2020 21:22:11: 13000000 INFO @ Sun, 21 Jun 2020 21:22:14: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:22:14: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:22:14: #1 total tags in treatment: 13496353 INFO @ Sun, 21 Jun 2020 21:22:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:22:14: #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 21:22:14: #1 tags after filtering in treatment: 13496287 INFO @ Sun, 21 Jun 2020 21:22:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:22:14: #1 finished! INFO @ Sun, 21 Jun 2020 21:22:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:22:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:22:15: 8000000 INFO @ Sun, 21 Jun 2020 21:22:15: #2 number of paired peaks: 1919 INFO @ Sun, 21 Jun 2020 21:22:15: start model_add_line... INFO @ Sun, 21 Jun 2020 21:22:16: start X-correlation... INFO @ Sun, 21 Jun 2020 21:22:16: end of X-cor INFO @ Sun, 21 Jun 2020 21:22:16: #2 finished! INFO @ Sun, 21 Jun 2020 21:22:16: #2 predicted fragment length is 100 bps INFO @ Sun, 21 Jun 2020 21:22:16: #2 alternative fragment length(s) may be 4,100 bps INFO @ Sun, 21 Jun 2020 21:22:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4823783/SRX4823783.10_model.r WARNING @ Sun, 21 Jun 2020 21:22:16: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:22:16: #2 You may need to consider one of the other alternative d(s): 4,100 WARNING @ Sun, 21 Jun 2020 21:22:16: #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 21:22:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:22:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:22:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:22:20: 9000000 INFO @ Sun, 21 Jun 2020 21:22:25: 10000000 INFO @ Sun, 21 Jun 2020 21:22:30: 11000000 INFO @ Sun, 21 Jun 2020 21:22:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4823783/SRX4823783.05_peaks.xls BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:22:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4823783/SRX4823783.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:22:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4823783/SRX4823783.05_summits.bed INFO @ Sun, 21 Jun 2020 21:22:32: Done! pass1 - making usageList (847 chroms): 2 millis pass2 - checking and writing primary data (13218 records, 4 fields): 32 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:22:34: 12000000 INFO @ Sun, 21 Jun 2020 21:22:39: 13000000 INFO @ Sun, 21 Jun 2020 21:22:42: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:22:42: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:22:42: #1 total tags in treatment: 13496353 INFO @ Sun, 21 Jun 2020 21:22:42: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:22:42: #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 21:22:42: #1 tags after filtering in treatment: 13496287 INFO @ Sun, 21 Jun 2020 21:22:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:22:42: #1 finished! INFO @ Sun, 21 Jun 2020 21:22:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:22:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:22:43: #2 number of paired peaks: 1919 INFO @ Sun, 21 Jun 2020 21:22:43: start model_add_line... INFO @ Sun, 21 Jun 2020 21:22:43: start X-correlation... INFO @ Sun, 21 Jun 2020 21:22:43: end of X-cor INFO @ Sun, 21 Jun 2020 21:22:43: #2 finished! INFO @ Sun, 21 Jun 2020 21:22:43: #2 predicted fragment length is 100 bps INFO @ Sun, 21 Jun 2020 21:22:43: #2 alternative fragment length(s) may be 4,100 bps INFO @ Sun, 21 Jun 2020 21:22:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4823783/SRX4823783.20_model.r WARNING @ Sun, 21 Jun 2020 21:22:43: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:22:43: #2 You may need to consider one of the other alternative d(s): 4,100 WARNING @ Sun, 21 Jun 2020 21:22:43: #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 21:22:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:22:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:22:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:22:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4823783/SRX4823783.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:22:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4823783/SRX4823783.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:22:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4823783/SRX4823783.10_summits.bed INFO @ Sun, 21 Jun 2020 21:22:58: Done! pass1 - making usageList (722 chroms): 2 millis pass2 - checking and writing primary data (7110 records, 4 fields): 24 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:23:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:23:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4823783/SRX4823783.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:23:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4823783/SRX4823783.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:23:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4823783/SRX4823783.20_summits.bed INFO @ Sun, 21 Jun 2020 21:23:26: Done! pass1 - making usageList (619 chroms): 1 millis pass2 - checking and writing primary data (3171 records, 4 fields): 18 millis CompletedMACS2peakCalling