Job ID = 6454501 SRX = SRX2165285 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:18:39 prefetch.2.10.7: 1) Downloading 'SRR4244799'... 2020-06-21T09:18:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:21:21 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:21:22 prefetch.2.10.7: 'SRR4244799' is valid 2020-06-21T09:21:22 prefetch.2.10.7: 1) 'SRR4244799' was downloaded successfully Read 13782519 spots for SRR4244799/SRR4244799.sra Written 13782519 spots for SRR4244799/SRR4244799.sra 2020-06-21T09:22:12 prefetch.2.10.7: 1) Downloading 'SRR4244800'... 2020-06-21T09:22:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:26:42 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:26:42 prefetch.2.10.7: 1) 'SRR4244800' was downloaded successfully Read 27169910 spots for SRR4244800/SRR4244800.sra Written 27169910 spots for SRR4244800/SRR4244800.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: 00:14:19 40952429 reads; of these: 40952429 (100.00%) were unpaired; of these: 4837782 (11.81%) aligned 0 times 26294263 (64.21%) aligned exactly 1 time 9820384 (23.98%) aligned >1 times 88.19% overall alignment rate Time searching: 00:14:19 Overall time: 00:14:19 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 16 files... [bam_rmdupse_core] 21444941 / 36114647 = 0.5938 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 18:49:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2165285/SRX2165285.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2165285/SRX2165285.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2165285/SRX2165285.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2165285/SRX2165285.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 18:49:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:49:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:49:58: 1000000 INFO @ Sun, 21 Jun 2020 18:50:04: 2000000 INFO @ Sun, 21 Jun 2020 18:50:09: 3000000 INFO @ Sun, 21 Jun 2020 18:50:14: 4000000 INFO @ Sun, 21 Jun 2020 18:50:19: 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 18:50:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2165285/SRX2165285.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2165285/SRX2165285.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2165285/SRX2165285.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2165285/SRX2165285.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 18:50:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:50:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:50:25: 6000000 INFO @ Sun, 21 Jun 2020 18:50:30: 1000000 INFO @ Sun, 21 Jun 2020 18:50:30: 7000000 INFO @ Sun, 21 Jun 2020 18:50:36: 8000000 INFO @ Sun, 21 Jun 2020 18:50:36: 2000000 INFO @ Sun, 21 Jun 2020 18:50:42: 9000000 INFO @ Sun, 21 Jun 2020 18:50:43: 3000000 INFO @ Sun, 21 Jun 2020 18:50:47: 10000000 INFO @ Sun, 21 Jun 2020 18:50:50: 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 18:50:53: 11000000 INFO @ Sun, 21 Jun 2020 18:50:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2165285/SRX2165285.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2165285/SRX2165285.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2165285/SRX2165285.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2165285/SRX2165285.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 18:50:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:50:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:50:56: 5000000 INFO @ Sun, 21 Jun 2020 18:50:59: 12000000 INFO @ Sun, 21 Jun 2020 18:51:00: 1000000 INFO @ Sun, 21 Jun 2020 18:51:03: 6000000 INFO @ Sun, 21 Jun 2020 18:51:05: 13000000 INFO @ Sun, 21 Jun 2020 18:51:07: 2000000 INFO @ Sun, 21 Jun 2020 18:51:09: 7000000 INFO @ Sun, 21 Jun 2020 18:51:10: 14000000 INFO @ Sun, 21 Jun 2020 18:51:14: 3000000 INFO @ Sun, 21 Jun 2020 18:51:14: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 18:51:14: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 18:51:14: #1 total tags in treatment: 14669706 INFO @ Sun, 21 Jun 2020 18:51:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:51:14: #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 18:51:15: #1 tags after filtering in treatment: 14669706 INFO @ Sun, 21 Jun 2020 18:51:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:51:15: #1 finished! INFO @ Sun, 21 Jun 2020 18:51:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:51:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:51:15: 8000000 INFO @ Sun, 21 Jun 2020 18:51:16: #2 number of paired peaks: 1041 INFO @ Sun, 21 Jun 2020 18:51:16: start model_add_line... INFO @ Sun, 21 Jun 2020 18:51:16: start X-correlation... INFO @ Sun, 21 Jun 2020 18:51:16: end of X-cor INFO @ Sun, 21 Jun 2020 18:51:16: #2 finished! INFO @ Sun, 21 Jun 2020 18:51:16: #2 predicted fragment length is 72 bps INFO @ Sun, 21 Jun 2020 18:51:16: #2 alternative fragment length(s) may be 4,72 bps INFO @ Sun, 21 Jun 2020 18:51:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2165285/SRX2165285.05_model.r WARNING @ Sun, 21 Jun 2020 18:51:16: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:51:16: #2 You may need to consider one of the other alternative d(s): 4,72 WARNING @ Sun, 21 Jun 2020 18:51:16: #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 18:51:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:51:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:51:20: 4000000 INFO @ Sun, 21 Jun 2020 18:51:22: 9000000 INFO @ Sun, 21 Jun 2020 18:51:27: 5000000 INFO @ Sun, 21 Jun 2020 18:51:29: 10000000 INFO @ Sun, 21 Jun 2020 18:51:34: 6000000 INFO @ Sun, 21 Jun 2020 18:51:35: 11000000 INFO @ Sun, 21 Jun 2020 18:51:40: 7000000 INFO @ Sun, 21 Jun 2020 18:51:42: 12000000 INFO @ Sun, 21 Jun 2020 18:51:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:51:47: 8000000 INFO @ Sun, 21 Jun 2020 18:51:48: 13000000 INFO @ Sun, 21 Jun 2020 18:51:53: 9000000 INFO @ Sun, 21 Jun 2020 18:51:54: 14000000 INFO @ Sun, 21 Jun 2020 18:51:59: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 18:51:59: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 18:51:59: #1 total tags in treatment: 14669706 INFO @ Sun, 21 Jun 2020 18:51:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:51:59: #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 18:51:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2165285/SRX2165285.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:51:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2165285/SRX2165285.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:51:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2165285/SRX2165285.05_summits.bed INFO @ Sun, 21 Jun 2020 18:51:59: Done! INFO @ Sun, 21 Jun 2020 18:51:59: #1 tags after filtering in treatment: 14669706 INFO @ Sun, 21 Jun 2020 18:51:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:51:59: #1 finished! INFO @ Sun, 21 Jun 2020 18:51:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:51:59: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (871 chroms): 2 millis pass2 - checking and writing primary data (3296 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:52:00: 10000000 INFO @ Sun, 21 Jun 2020 18:52:00: #2 number of paired peaks: 1041 INFO @ Sun, 21 Jun 2020 18:52:00: start model_add_line... INFO @ Sun, 21 Jun 2020 18:52:01: start X-correlation... INFO @ Sun, 21 Jun 2020 18:52:01: end of X-cor INFO @ Sun, 21 Jun 2020 18:52:01: #2 finished! INFO @ Sun, 21 Jun 2020 18:52:01: #2 predicted fragment length is 72 bps INFO @ Sun, 21 Jun 2020 18:52:01: #2 alternative fragment length(s) may be 4,72 bps INFO @ Sun, 21 Jun 2020 18:52:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2165285/SRX2165285.10_model.r WARNING @ Sun, 21 Jun 2020 18:52:01: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:52:01: #2 You may need to consider one of the other alternative d(s): 4,72 WARNING @ Sun, 21 Jun 2020 18:52:01: #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 18:52:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:52:01: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:52:06: 11000000 INFO @ Sun, 21 Jun 2020 18:52:13: 12000000 INFO @ Sun, 21 Jun 2020 18:52:19: 13000000 INFO @ Sun, 21 Jun 2020 18:52:26: 14000000 INFO @ Sun, 21 Jun 2020 18:52:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:52:30: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 18:52:30: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 18:52:30: #1 total tags in treatment: 14669706 INFO @ Sun, 21 Jun 2020 18:52:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:52:30: #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 18:52:30: #1 tags after filtering in treatment: 14669706 INFO @ Sun, 21 Jun 2020 18:52:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:52:30: #1 finished! INFO @ Sun, 21 Jun 2020 18:52:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:52:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:52:31: #2 number of paired peaks: 1041 INFO @ Sun, 21 Jun 2020 18:52:31: start model_add_line... INFO @ Sun, 21 Jun 2020 18:52:31: start X-correlation... INFO @ Sun, 21 Jun 2020 18:52:31: end of X-cor INFO @ Sun, 21 Jun 2020 18:52:31: #2 finished! INFO @ Sun, 21 Jun 2020 18:52:31: #2 predicted fragment length is 72 bps INFO @ Sun, 21 Jun 2020 18:52:31: #2 alternative fragment length(s) may be 4,72 bps INFO @ Sun, 21 Jun 2020 18:52:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2165285/SRX2165285.20_model.r WARNING @ Sun, 21 Jun 2020 18:52:31: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:52:31: #2 You may need to consider one of the other alternative d(s): 4,72 WARNING @ Sun, 21 Jun 2020 18:52:31: #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 18:52:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:52:31: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:52:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2165285/SRX2165285.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:52:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2165285/SRX2165285.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:52:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2165285/SRX2165285.10_summits.bed INFO @ Sun, 21 Jun 2020 18:52:44: Done! pass1 - making usageList (689 chroms): 1 millis pass2 - checking and writing primary data (2195 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:53:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:53:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2165285/SRX2165285.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:53:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2165285/SRX2165285.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:53:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2165285/SRX2165285.20_summits.bed INFO @ Sun, 21 Jun 2020 18:53:15: Done! pass1 - making usageList (555 chroms): 1 millis pass2 - checking and writing primary data (1498 records, 4 fields): 15 millis CompletedMACS2peakCalling