Job ID = 6453041 SRX = SRX101476 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:02:23 prefetch.2.10.7: 1) Downloading 'SRR353680'... 2020-06-21T08:02:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:08:43 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:08:43 prefetch.2.10.7: 1) 'SRR353680' was downloaded successfully Read 34187983 spots for SRR353680/SRR353680.sra Written 34187983 spots for SRR353680/SRR353680.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: 00:05:40 34187983 reads; of these: 34187983 (100.00%) were unpaired; of these: 14016153 (41.00%) aligned 0 times 15083378 (44.12%) aligned exactly 1 time 5088452 (14.88%) aligned >1 times 59.00% overall alignment rate Time searching: 00:05:40 Overall time: 00:05:40 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] 11890272 / 20171830 = 0.5894 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 17:19:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX101476/SRX101476.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX101476/SRX101476.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX101476/SRX101476.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX101476/SRX101476.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 17:19:31: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:19:31: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:19:35: 1000000 INFO @ Sun, 21 Jun 2020 17:19:40: 2000000 INFO @ Sun, 21 Jun 2020 17:19:44: 3000000 INFO @ Sun, 21 Jun 2020 17:19:49: 4000000 INFO @ Sun, 21 Jun 2020 17:19:54: 5000000 INFO @ Sun, 21 Jun 2020 17:19:59: 6000000 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 17:20:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX101476/SRX101476.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX101476/SRX101476.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX101476/SRX101476.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX101476/SRX101476.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 17:20:01: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:20:01: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:20:03: 7000000 INFO @ Sun, 21 Jun 2020 17:20:05: 1000000 INFO @ Sun, 21 Jun 2020 17:20:08: 8000000 INFO @ Sun, 21 Jun 2020 17:20:10: #1 tag size is determined as 41 bps INFO @ Sun, 21 Jun 2020 17:20:10: #1 tag size = 41 INFO @ Sun, 21 Jun 2020 17:20:10: #1 total tags in treatment: 8281558 INFO @ Sun, 21 Jun 2020 17:20:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:20:10: #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 17:20:10: #1 tags after filtering in treatment: 8281479 INFO @ Sun, 21 Jun 2020 17:20:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:20:10: #1 finished! INFO @ Sun, 21 Jun 2020 17:20:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:20:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:20:10: 2000000 INFO @ Sun, 21 Jun 2020 17:20:11: #2 number of paired peaks: 1278 INFO @ Sun, 21 Jun 2020 17:20:11: start model_add_line... INFO @ Sun, 21 Jun 2020 17:20:11: start X-correlation... INFO @ Sun, 21 Jun 2020 17:20:11: end of X-cor INFO @ Sun, 21 Jun 2020 17:20:11: #2 finished! INFO @ Sun, 21 Jun 2020 17:20:11: #2 predicted fragment length is 43 bps INFO @ Sun, 21 Jun 2020 17:20:11: #2 alternative fragment length(s) may be 2,43 bps INFO @ Sun, 21 Jun 2020 17:20:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX101476/SRX101476.05_model.r WARNING @ Sun, 21 Jun 2020 17:20:11: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:20:11: #2 You may need to consider one of the other alternative d(s): 2,43 WARNING @ Sun, 21 Jun 2020 17:20:11: #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 17:20:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:20:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:20:15: 3000000 INFO @ Sun, 21 Jun 2020 17:20:20: 4000000 INFO @ Sun, 21 Jun 2020 17:20:24: 5000000 INFO @ Sun, 21 Jun 2020 17:20:27: #3 Call peaks for each chromosome... 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 17:20:29: 6000000 INFO @ Sun, 21 Jun 2020 17:20:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX101476/SRX101476.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX101476/SRX101476.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX101476/SRX101476.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX101476/SRX101476.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 17:20:31: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:20:31: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:20:34: 7000000 INFO @ Sun, 21 Jun 2020 17:20:35: 1000000 INFO @ Sun, 21 Jun 2020 17:20:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX101476/SRX101476.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:20:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX101476/SRX101476.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:20:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX101476/SRX101476.05_summits.bed INFO @ Sun, 21 Jun 2020 17:20:36: Done! pass1 - making usageList (630 chroms): 1 millis pass2 - checking and writing primary data (2514 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:20:39: 8000000 INFO @ Sun, 21 Jun 2020 17:20:40: 2000000 INFO @ Sun, 21 Jun 2020 17:20:41: #1 tag size is determined as 41 bps INFO @ Sun, 21 Jun 2020 17:20:41: #1 tag size = 41 INFO @ Sun, 21 Jun 2020 17:20:41: #1 total tags in treatment: 8281558 INFO @ Sun, 21 Jun 2020 17:20:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:20:41: #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 17:20:41: #1 tags after filtering in treatment: 8281479 INFO @ Sun, 21 Jun 2020 17:20:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:20:41: #1 finished! INFO @ Sun, 21 Jun 2020 17:20:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:20:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:20:42: #2 number of paired peaks: 1278 INFO @ Sun, 21 Jun 2020 17:20:42: start model_add_line... INFO @ Sun, 21 Jun 2020 17:20:42: start X-correlation... INFO @ Sun, 21 Jun 2020 17:20:42: end of X-cor INFO @ Sun, 21 Jun 2020 17:20:42: #2 finished! INFO @ Sun, 21 Jun 2020 17:20:42: #2 predicted fragment length is 43 bps INFO @ Sun, 21 Jun 2020 17:20:42: #2 alternative fragment length(s) may be 2,43 bps INFO @ Sun, 21 Jun 2020 17:20:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX101476/SRX101476.10_model.r WARNING @ Sun, 21 Jun 2020 17:20:42: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:20:42: #2 You may need to consider one of the other alternative d(s): 2,43 WARNING @ Sun, 21 Jun 2020 17:20:42: #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 17:20:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:20:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:20:45: 3000000 INFO @ Sun, 21 Jun 2020 17:20:50: 4000000 INFO @ Sun, 21 Jun 2020 17:20:54: 5000000 INFO @ Sun, 21 Jun 2020 17:20:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:20:59: 6000000 INFO @ Sun, 21 Jun 2020 17:21:04: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:21:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX101476/SRX101476.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:21:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX101476/SRX101476.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:21:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX101476/SRX101476.10_summits.bed INFO @ Sun, 21 Jun 2020 17:21:07: Done! pass1 - making usageList (532 chroms): 1 millis pass2 - checking and writing primary data (1877 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:21:09: 8000000 INFO @ Sun, 21 Jun 2020 17:21:10: #1 tag size is determined as 41 bps INFO @ Sun, 21 Jun 2020 17:21:10: #1 tag size = 41 INFO @ Sun, 21 Jun 2020 17:21:10: #1 total tags in treatment: 8281558 INFO @ Sun, 21 Jun 2020 17:21:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:21:10: #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 17:21:11: #1 tags after filtering in treatment: 8281479 INFO @ Sun, 21 Jun 2020 17:21:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:21:11: #1 finished! INFO @ Sun, 21 Jun 2020 17:21:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:21:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:21:11: #2 number of paired peaks: 1278 INFO @ Sun, 21 Jun 2020 17:21:11: start model_add_line... INFO @ Sun, 21 Jun 2020 17:21:12: start X-correlation... INFO @ Sun, 21 Jun 2020 17:21:12: end of X-cor INFO @ Sun, 21 Jun 2020 17:21:12: #2 finished! INFO @ Sun, 21 Jun 2020 17:21:12: #2 predicted fragment length is 43 bps INFO @ Sun, 21 Jun 2020 17:21:12: #2 alternative fragment length(s) may be 2,43 bps INFO @ Sun, 21 Jun 2020 17:21:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX101476/SRX101476.20_model.r WARNING @ Sun, 21 Jun 2020 17:21:12: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:21:12: #2 You may need to consider one of the other alternative d(s): 2,43 WARNING @ Sun, 21 Jun 2020 17:21:12: #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 17:21:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:21:12: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:21:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:21:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX101476/SRX101476.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:21:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX101476/SRX101476.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:21:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX101476/SRX101476.20_summits.bed INFO @ Sun, 21 Jun 2020 17:21:36: Done! pass1 - making usageList (413 chroms): 1 millis pass2 - checking and writing primary data (1703 records, 4 fields): 12 millis CompletedMACS2peakCalling