Job ID = 6454719 SRX = SRX2541752 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:36:25 prefetch.2.10.7: 1) Downloading 'SRR5234226'... 2020-06-21T09:36:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:42:22 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:42:22 prefetch.2.10.7: 1) 'SRR5234226' was downloaded successfully Read 22276144 spots for SRR5234226/SRR5234226.sra Written 22276144 spots for SRR5234226/SRR5234226.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: 00:04:43 22276144 reads; of these: 22276144 (100.00%) were unpaired; of these: 10919801 (49.02%) aligned 0 times 8111414 (36.41%) aligned exactly 1 time 3244929 (14.57%) aligned >1 times 50.98% overall alignment rate Time searching: 00:04:43 Overall time: 00:04:43 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] 1928251 / 11356343 = 0.1698 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 18:51:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2541752/SRX2541752.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2541752/SRX2541752.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2541752/SRX2541752.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2541752/SRX2541752.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 18:51:31: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:51:31: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:51:36: 1000000 INFO @ Sun, 21 Jun 2020 18:51:41: 2000000 INFO @ Sun, 21 Jun 2020 18:51:46: 3000000 INFO @ Sun, 21 Jun 2020 18:51:51: 4000000 INFO @ Sun, 21 Jun 2020 18:51:56: 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 18:52:01: 6000000 INFO @ Sun, 21 Jun 2020 18:52:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2541752/SRX2541752.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2541752/SRX2541752.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2541752/SRX2541752.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2541752/SRX2541752.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 18:52:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:52:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:52:06: 7000000 INFO @ Sun, 21 Jun 2020 18:52:07: 1000000 INFO @ Sun, 21 Jun 2020 18:52:12: 8000000 INFO @ Sun, 21 Jun 2020 18:52:12: 2000000 INFO @ Sun, 21 Jun 2020 18:52:17: 9000000 INFO @ Sun, 21 Jun 2020 18:52:17: 3000000 INFO @ Sun, 21 Jun 2020 18:52:19: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:52:19: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:52:19: #1 total tags in treatment: 9428092 INFO @ Sun, 21 Jun 2020 18:52:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:52:19: #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 18:52:20: #1 tags after filtering in treatment: 9428090 INFO @ Sun, 21 Jun 2020 18:52:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:52:20: #1 finished! INFO @ Sun, 21 Jun 2020 18:52:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:52:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:52:20: #2 number of paired peaks: 1016 INFO @ Sun, 21 Jun 2020 18:52:20: start model_add_line... INFO @ Sun, 21 Jun 2020 18:52:21: start X-correlation... INFO @ Sun, 21 Jun 2020 18:52:21: end of X-cor INFO @ Sun, 21 Jun 2020 18:52:21: #2 finished! INFO @ Sun, 21 Jun 2020 18:52:21: #2 predicted fragment length is 91 bps INFO @ Sun, 21 Jun 2020 18:52:21: #2 alternative fragment length(s) may be 91 bps INFO @ Sun, 21 Jun 2020 18:52:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2541752/SRX2541752.05_model.r WARNING @ Sun, 21 Jun 2020 18:52:21: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:52:21: #2 You may need to consider one of the other alternative d(s): 91 WARNING @ Sun, 21 Jun 2020 18:52:21: #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 18:52:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:52:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:52:22: 4000000 INFO @ Sun, 21 Jun 2020 18:52:27: 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 18:52:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2541752/SRX2541752.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2541752/SRX2541752.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2541752/SRX2541752.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2541752/SRX2541752.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 18:52:31: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:52:31: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:52:32: 6000000 INFO @ Sun, 21 Jun 2020 18:52:37: 1000000 INFO @ Sun, 21 Jun 2020 18:52:37: 7000000 INFO @ Sun, 21 Jun 2020 18:52:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:52:42: 2000000 INFO @ Sun, 21 Jun 2020 18:52:43: 8000000 INFO @ Sun, 21 Jun 2020 18:52:47: 3000000 INFO @ Sun, 21 Jun 2020 18:52:48: 9000000 INFO @ Sun, 21 Jun 2020 18:52:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2541752/SRX2541752.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:52:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2541752/SRX2541752.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:52:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2541752/SRX2541752.05_summits.bed INFO @ Sun, 21 Jun 2020 18:52:50: Done! INFO @ Sun, 21 Jun 2020 18:52:50: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:52:50: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:52:50: #1 total tags in treatment: 9428092 INFO @ Sun, 21 Jun 2020 18:52:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:52:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (603 chroms): 1 millis pass2 - checking and writing primary data (2412 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:52:50: #1 tags after filtering in treatment: 9428090 INFO @ Sun, 21 Jun 2020 18:52:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:52:50: #1 finished! INFO @ Sun, 21 Jun 2020 18:52:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:52:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:52:51: #2 number of paired peaks: 1016 INFO @ Sun, 21 Jun 2020 18:52:51: start model_add_line... INFO @ Sun, 21 Jun 2020 18:52:51: start X-correlation... INFO @ Sun, 21 Jun 2020 18:52:51: end of X-cor INFO @ Sun, 21 Jun 2020 18:52:51: #2 finished! INFO @ Sun, 21 Jun 2020 18:52:51: #2 predicted fragment length is 91 bps INFO @ Sun, 21 Jun 2020 18:52:51: #2 alternative fragment length(s) may be 91 bps INFO @ Sun, 21 Jun 2020 18:52:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2541752/SRX2541752.10_model.r WARNING @ Sun, 21 Jun 2020 18:52:51: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:52:51: #2 You may need to consider one of the other alternative d(s): 91 WARNING @ Sun, 21 Jun 2020 18:52:51: #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 18:52:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:52:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:52:52: 4000000 INFO @ Sun, 21 Jun 2020 18:52:56: 5000000 INFO @ Sun, 21 Jun 2020 18:53:01: 6000000 INFO @ Sun, 21 Jun 2020 18:53:06: 7000000 INFO @ Sun, 21 Jun 2020 18:53:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:53:12: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:53:16: 9000000 INFO @ Sun, 21 Jun 2020 18:53:19: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:53:19: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:53:19: #1 total tags in treatment: 9428092 INFO @ Sun, 21 Jun 2020 18:53:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:53:19: #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 18:53:19: #1 tags after filtering in treatment: 9428090 INFO @ Sun, 21 Jun 2020 18:53:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:53:19: #1 finished! INFO @ Sun, 21 Jun 2020 18:53:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:53:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:53:20: #2 number of paired peaks: 1016 INFO @ Sun, 21 Jun 2020 18:53:20: start model_add_line... INFO @ Sun, 21 Jun 2020 18:53:20: start X-correlation... INFO @ Sun, 21 Jun 2020 18:53:20: end of X-cor INFO @ Sun, 21 Jun 2020 18:53:20: #2 finished! INFO @ Sun, 21 Jun 2020 18:53:20: #2 predicted fragment length is 91 bps INFO @ Sun, 21 Jun 2020 18:53:20: #2 alternative fragment length(s) may be 91 bps INFO @ Sun, 21 Jun 2020 18:53:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2541752/SRX2541752.20_model.r WARNING @ Sun, 21 Jun 2020 18:53:20: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:53:20: #2 You may need to consider one of the other alternative d(s): 91 WARNING @ Sun, 21 Jun 2020 18:53:20: #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 18:53:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:53:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:53:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2541752/SRX2541752.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:53:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2541752/SRX2541752.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:53:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2541752/SRX2541752.10_summits.bed INFO @ Sun, 21 Jun 2020 18:53:21: Done! pass1 - making usageList (490 chroms): 1 millis pass2 - checking and writing primary data (1760 records, 4 fields): 14 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:53:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:53:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2541752/SRX2541752.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:53:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2541752/SRX2541752.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:53:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2541752/SRX2541752.20_summits.bed INFO @ Sun, 21 Jun 2020 18:53:49: Done! pass1 - making usageList (384 chroms): 1 millis pass2 - checking and writing primary data (1053 records, 4 fields): 11 millis CompletedMACS2peakCalling