Job ID = 6456423 SRX = SRX3404017 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:55:01 prefetch.2.10.7: 1) Downloading 'SRR6303494'... 2020-06-21T10:55:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:55:47 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:55:47 prefetch.2.10.7: 'SRR6303494' is valid 2020-06-21T10:55:47 prefetch.2.10.7: 1) 'SRR6303494' was downloaded successfully 2020-06-21T10:55:47 prefetch.2.10.7: 'SRR6303494' has 0 unresolved dependencies Read 6702486 spots for SRR6303494/SRR6303494.sra Written 6702486 spots for SRR6303494/SRR6303494.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: 00:04:02 6702486 reads; of these: 6702486 (100.00%) were unpaired; of these: 962018 (14.35%) aligned 0 times 2166836 (32.33%) aligned exactly 1 time 3573632 (53.32%) aligned >1 times 85.65% overall alignment rate Time searching: 00:04:02 Overall time: 00:04:02 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_rmdupse_core] 2849066 / 5740468 = 0.4963 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 20:01:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3404017/SRX3404017.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3404017/SRX3404017.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3404017/SRX3404017.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3404017/SRX3404017.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 20:01:54: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:01:54: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:02:00: 1000000 INFO @ Sun, 21 Jun 2020 20:02:06: 2000000 INFO @ Sun, 21 Jun 2020 20:02:12: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:02:12: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:02:12: #1 total tags in treatment: 2891402 INFO @ Sun, 21 Jun 2020 20:02:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:02:12: #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 20:02:12: #1 tags after filtering in treatment: 2891176 INFO @ Sun, 21 Jun 2020 20:02:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:02:12: #1 finished! INFO @ Sun, 21 Jun 2020 20:02:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:02:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:02:13: #2 number of paired peaks: 1776 INFO @ Sun, 21 Jun 2020 20:02:13: start model_add_line... INFO @ Sun, 21 Jun 2020 20:02:13: start X-correlation... INFO @ Sun, 21 Jun 2020 20:02:13: end of X-cor INFO @ Sun, 21 Jun 2020 20:02:13: #2 finished! INFO @ Sun, 21 Jun 2020 20:02:13: #2 predicted fragment length is 56 bps INFO @ Sun, 21 Jun 2020 20:02:13: #2 alternative fragment length(s) may be 56 bps INFO @ Sun, 21 Jun 2020 20:02:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3404017/SRX3404017.05_model.r WARNING @ Sun, 21 Jun 2020 20:02:13: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:02:13: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Sun, 21 Jun 2020 20:02:13: #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 20:02:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:02:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:02:19: #3 Call peaks for each chromosome... 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 20:02:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3404017/SRX3404017.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:02:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3404017/SRX3404017.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:02:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3404017/SRX3404017.05_summits.bed INFO @ Sun, 21 Jun 2020 20:02:23: Done! pass1 - making usageList (452 chroms): 1 millis pass2 - checking and writing primary data (1475 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:02:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3404017/SRX3404017.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3404017/SRX3404017.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3404017/SRX3404017.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3404017/SRX3404017.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 20:02:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:02:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:02:30: 1000000 INFO @ Sun, 21 Jun 2020 20:02:35: 2000000 INFO @ Sun, 21 Jun 2020 20:02:41: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:02:41: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:02:41: #1 total tags in treatment: 2891402 INFO @ Sun, 21 Jun 2020 20:02:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:02:41: #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 20:02:41: #1 tags after filtering in treatment: 2891176 INFO @ Sun, 21 Jun 2020 20:02:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:02:41: #1 finished! INFO @ Sun, 21 Jun 2020 20:02:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:02:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:02:42: #2 number of paired peaks: 1776 INFO @ Sun, 21 Jun 2020 20:02:42: start model_add_line... INFO @ Sun, 21 Jun 2020 20:02:42: start X-correlation... INFO @ Sun, 21 Jun 2020 20:02:42: end of X-cor INFO @ Sun, 21 Jun 2020 20:02:42: #2 finished! INFO @ Sun, 21 Jun 2020 20:02:42: #2 predicted fragment length is 56 bps INFO @ Sun, 21 Jun 2020 20:02:42: #2 alternative fragment length(s) may be 56 bps INFO @ Sun, 21 Jun 2020 20:02:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3404017/SRX3404017.10_model.r WARNING @ Sun, 21 Jun 2020 20:02:42: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:02:42: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Sun, 21 Jun 2020 20:02:42: #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 20:02:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:02:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:02:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:02:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3404017/SRX3404017.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:02:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3404017/SRX3404017.10_peaks.narrowPeak BedGraph に変換中... INFO @ Sun, 21 Jun 2020 20:02:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3404017/SRX3404017.10_summits.bed INFO @ Sun, 21 Jun 2020 20:02:52: Done! 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 pass1 - making usageList (231 chroms): 1 millis pass2 - checking and writing primary data (612 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:02:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3404017/SRX3404017.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3404017/SRX3404017.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3404017/SRX3404017.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3404017/SRX3404017.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 20:02:54: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:02:54: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:03:00: 1000000 INFO @ Sun, 21 Jun 2020 20:03:07: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:03:14: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:03:14: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:03:14: #1 total tags in treatment: 2891402 INFO @ Sun, 21 Jun 2020 20:03:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:03:14: #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 20:03:14: #1 tags after filtering in treatment: 2891176 INFO @ Sun, 21 Jun 2020 20:03:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:03:14: #1 finished! INFO @ Sun, 21 Jun 2020 20:03:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:03:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:03:14: #2 number of paired peaks: 1776 INFO @ Sun, 21 Jun 2020 20:03:14: start model_add_line... INFO @ Sun, 21 Jun 2020 20:03:14: start X-correlation... INFO @ Sun, 21 Jun 2020 20:03:14: end of X-cor INFO @ Sun, 21 Jun 2020 20:03:14: #2 finished! INFO @ Sun, 21 Jun 2020 20:03:14: #2 predicted fragment length is 56 bps INFO @ Sun, 21 Jun 2020 20:03:14: #2 alternative fragment length(s) may be 56 bps INFO @ Sun, 21 Jun 2020 20:03:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3404017/SRX3404017.20_model.r WARNING @ Sun, 21 Jun 2020 20:03:14: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:03:14: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Sun, 21 Jun 2020 20:03:14: #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 20:03:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:03:14: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:03:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:03:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3404017/SRX3404017.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:03:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3404017/SRX3404017.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:03:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3404017/SRX3404017.20_summits.bed INFO @ Sun, 21 Jun 2020 20:03:24: Done! pass1 - making usageList (135 chroms): 1 millis pass2 - checking and writing primary data (290 records, 4 fields): 6 millis CompletedMACS2peakCalling