Job ID = 6455289 SRX = SRX287666 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:57:55 prefetch.2.10.7: 1) Downloading 'SRR869854'... 2020-06-21T09:57:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:59:38 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:59:38 prefetch.2.10.7: 'SRR869854' is valid 2020-06-21T09:59:38 prefetch.2.10.7: 1) 'SRR869854' was downloaded successfully Read 12148753 spots for SRR869854/SRR869854.sra Written 12148753 spots for SRR869854/SRR869854.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: 00:03:43 12148753 reads; of these: 12148753 (100.00%) were unpaired; of these: 741194 (6.10%) aligned 0 times 7741832 (63.73%) aligned exactly 1 time 3665727 (30.17%) aligned >1 times 93.90% overall alignment rate Time searching: 00:03:43 Overall time: 00:03:43 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] 2231674 / 11407559 = 0.1956 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 19:07:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287666/SRX287666.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287666/SRX287666.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287666/SRX287666.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287666/SRX287666.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 19:07:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:07:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:07:24: 1000000 INFO @ Sun, 21 Jun 2020 19:07:30: 2000000 INFO @ Sun, 21 Jun 2020 19:07:36: 3000000 INFO @ Sun, 21 Jun 2020 19:07:43: 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 19:07:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287666/SRX287666.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287666/SRX287666.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287666/SRX287666.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287666/SRX287666.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 19:07:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:07:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:07:49: 5000000 INFO @ Sun, 21 Jun 2020 19:07:56: 6000000 INFO @ Sun, 21 Jun 2020 19:07:56: 1000000 INFO @ Sun, 21 Jun 2020 19:08:04: 7000000 INFO @ Sun, 21 Jun 2020 19:08:05: 2000000 INFO @ Sun, 21 Jun 2020 19:08:12: 8000000 INFO @ Sun, 21 Jun 2020 19:08:13: 3000000 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 19:08:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287666/SRX287666.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287666/SRX287666.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287666/SRX287666.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287666/SRX287666.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 19:08:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:08:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:08:19: 9000000 INFO @ Sun, 21 Jun 2020 19:08:21: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:08:21: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:08:21: #1 total tags in treatment: 9175885 INFO @ Sun, 21 Jun 2020 19:08:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:08:21: #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 19:08:21: #1 tags after filtering in treatment: 9175885 INFO @ Sun, 21 Jun 2020 19:08:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:08:21: #1 finished! INFO @ Sun, 21 Jun 2020 19:08:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:08:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:08:21: 4000000 INFO @ Sun, 21 Jun 2020 19:08:22: #2 number of paired peaks: 889 WARNING @ Sun, 21 Jun 2020 19:08:22: Fewer paired peaks (889) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 889 pairs to build model! INFO @ Sun, 21 Jun 2020 19:08:22: start model_add_line... INFO @ Sun, 21 Jun 2020 19:08:22: start X-correlation... INFO @ Sun, 21 Jun 2020 19:08:22: end of X-cor INFO @ Sun, 21 Jun 2020 19:08:22: #2 finished! INFO @ Sun, 21 Jun 2020 19:08:22: #2 predicted fragment length is 43 bps INFO @ Sun, 21 Jun 2020 19:08:22: #2 alternative fragment length(s) may be 4,43 bps INFO @ Sun, 21 Jun 2020 19:08:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287666/SRX287666.05_model.r WARNING @ Sun, 21 Jun 2020 19:08:22: #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 19:08:22: #2 You may need to consider one of the other alternative d(s): 4,43 WARNING @ Sun, 21 Jun 2020 19:08:22: #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 19:08:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:08:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:08:26: 1000000 INFO @ Sun, 21 Jun 2020 19:08:29: 5000000 INFO @ Sun, 21 Jun 2020 19:08:34: 2000000 INFO @ Sun, 21 Jun 2020 19:08:38: 6000000 INFO @ Sun, 21 Jun 2020 19:08:42: 3000000 INFO @ Sun, 21 Jun 2020 19:08:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:08:46: 7000000 INFO @ Sun, 21 Jun 2020 19:08:50: 4000000 INFO @ Sun, 21 Jun 2020 19:08:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287666/SRX287666.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:08:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287666/SRX287666.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:08:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287666/SRX287666.05_summits.bed INFO @ Sun, 21 Jun 2020 19:08:53: Done! pass1 - making usageList (620 chroms): 2 millis pass2 - checking and writing primary data (2294 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:08:55: 8000000 INFO @ Sun, 21 Jun 2020 19:08:58: 5000000 INFO @ Sun, 21 Jun 2020 19:09:03: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:09:04: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:09:04: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:09:04: #1 total tags in treatment: 9175885 INFO @ Sun, 21 Jun 2020 19:09:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:09:04: #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 19:09:05: #1 tags after filtering in treatment: 9175885 INFO @ Sun, 21 Jun 2020 19:09:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:09:05: #1 finished! INFO @ Sun, 21 Jun 2020 19:09:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:09:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:09:06: #2 number of paired peaks: 889 WARNING @ Sun, 21 Jun 2020 19:09:06: Fewer paired peaks (889) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 889 pairs to build model! INFO @ Sun, 21 Jun 2020 19:09:06: start model_add_line... INFO @ Sun, 21 Jun 2020 19:09:06: start X-correlation... INFO @ Sun, 21 Jun 2020 19:09:06: end of X-cor INFO @ Sun, 21 Jun 2020 19:09:06: #2 finished! INFO @ Sun, 21 Jun 2020 19:09:06: #2 predicted fragment length is 43 bps INFO @ Sun, 21 Jun 2020 19:09:06: #2 alternative fragment length(s) may be 4,43 bps INFO @ Sun, 21 Jun 2020 19:09:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287666/SRX287666.10_model.r WARNING @ Sun, 21 Jun 2020 19:09:06: #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 19:09:06: #2 You may need to consider one of the other alternative d(s): 4,43 WARNING @ Sun, 21 Jun 2020 19:09:06: #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 19:09:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:09:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:09:06: 6000000 INFO @ Sun, 21 Jun 2020 19:09:12: 7000000 INFO @ Sun, 21 Jun 2020 19:09:19: 8000000 INFO @ Sun, 21 Jun 2020 19:09:25: 9000000 INFO @ Sun, 21 Jun 2020 19:09:26: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:09:26: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:09:26: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:09:26: #1 total tags in treatment: 9175885 INFO @ Sun, 21 Jun 2020 19:09:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:09:26: #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 19:09:26: #1 tags after filtering in treatment: 9175885 INFO @ Sun, 21 Jun 2020 19:09:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:09:26: #1 finished! INFO @ Sun, 21 Jun 2020 19:09:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:09:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:09:27: #2 number of paired peaks: 889 WARNING @ Sun, 21 Jun 2020 19:09:27: Fewer paired peaks (889) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 889 pairs to build model! INFO @ Sun, 21 Jun 2020 19:09:27: start model_add_line... INFO @ Sun, 21 Jun 2020 19:09:27: start X-correlation... INFO @ Sun, 21 Jun 2020 19:09:27: end of X-cor INFO @ Sun, 21 Jun 2020 19:09:27: #2 finished! INFO @ Sun, 21 Jun 2020 19:09:27: #2 predicted fragment length is 43 bps INFO @ Sun, 21 Jun 2020 19:09:27: #2 alternative fragment length(s) may be 4,43 bps INFO @ Sun, 21 Jun 2020 19:09:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287666/SRX287666.20_model.r WARNING @ Sun, 21 Jun 2020 19:09:27: #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 19:09:27: #2 You may need to consider one of the other alternative d(s): 4,43 WARNING @ Sun, 21 Jun 2020 19:09:27: #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 19:09:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:09:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:09:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287666/SRX287666.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:09:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287666/SRX287666.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:09:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287666/SRX287666.10_summits.bed INFO @ Sun, 21 Jun 2020 19:09:35: Done! pass1 - making usageList (498 chroms): 1 millis pass2 - checking and writing primary data (1842 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:09:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:09:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287666/SRX287666.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:09:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287666/SRX287666.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:09:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287666/SRX287666.20_summits.bed INFO @ Sun, 21 Jun 2020 19:09:55: Done! pass1 - making usageList (341 chroms): 1 millis pass2 - checking and writing primary data (741 records, 4 fields): 10 millis CompletedMACS2peakCalling