Job ID = 6456489 SRX = SRX3511940 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:52:01 prefetch.2.10.7: 1) Downloading 'SRR6418925'... 2020-06-21T10:52:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:55:11 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:55:11 prefetch.2.10.7: 1) 'SRR6418925' was downloaded successfully 2020-06-21T10:55:11 prefetch.2.10.7: 'SRR6418925' has 0 unresolved dependencies Read 11884963 spots for SRR6418925/SRR6418925.sra Written 11884963 spots for SRR6418925/SRR6418925.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: 00:04:49 11884963 reads; of these: 11884963 (100.00%) were unpaired; of these: 2298700 (19.34%) aligned 0 times 7816115 (65.76%) aligned exactly 1 time 1770148 (14.89%) aligned >1 times 80.66% overall alignment rate Time searching: 00:04:49 Overall time: 00:04:49 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] 855581 / 9586263 = 0.0893 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 20:05:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3511940/SRX3511940.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3511940/SRX3511940.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3511940/SRX3511940.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3511940/SRX3511940.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 20:05:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:05:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:06:00: 1000000 INFO @ Sun, 21 Jun 2020 20:06:07: 2000000 INFO @ Sun, 21 Jun 2020 20:06:14: 3000000 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 20:06:22: 4000000 INFO @ Sun, 21 Jun 2020 20:06:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3511940/SRX3511940.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3511940/SRX3511940.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3511940/SRX3511940.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3511940/SRX3511940.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 20:06:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:06:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:06:31: 5000000 INFO @ Sun, 21 Jun 2020 20:06:33: 1000000 INFO @ Sun, 21 Jun 2020 20:06:40: 6000000 INFO @ Sun, 21 Jun 2020 20:06:43: 2000000 INFO @ Sun, 21 Jun 2020 20:06:49: 7000000 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 20:06:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3511940/SRX3511940.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3511940/SRX3511940.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3511940/SRX3511940.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3511940/SRX3511940.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 20:06:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:06:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:06:53: 3000000 INFO @ Sun, 21 Jun 2020 20:06:58: 8000000 INFO @ Sun, 21 Jun 2020 20:07:03: 4000000 INFO @ Sun, 21 Jun 2020 20:07:03: 1000000 INFO @ Sun, 21 Jun 2020 20:07:05: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 20:07:05: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 20:07:05: #1 total tags in treatment: 8730682 INFO @ Sun, 21 Jun 2020 20:07:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:07:05: #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 20:07:06: #1 tags after filtering in treatment: 8730639 INFO @ Sun, 21 Jun 2020 20:07:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:07:06: #1 finished! INFO @ Sun, 21 Jun 2020 20:07:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:07:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:07:07: #2 number of paired peaks: 2924 INFO @ Sun, 21 Jun 2020 20:07:07: start model_add_line... INFO @ Sun, 21 Jun 2020 20:07:07: start X-correlation... INFO @ Sun, 21 Jun 2020 20:07:07: end of X-cor INFO @ Sun, 21 Jun 2020 20:07:07: #2 finished! INFO @ Sun, 21 Jun 2020 20:07:07: #2 predicted fragment length is 176 bps INFO @ Sun, 21 Jun 2020 20:07:07: #2 alternative fragment length(s) may be 176 bps INFO @ Sun, 21 Jun 2020 20:07:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3511940/SRX3511940.05_model.r WARNING @ Sun, 21 Jun 2020 20:07:07: #2 Since the d (176) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:07:07: #2 You may need to consider one of the other alternative d(s): 176 WARNING @ Sun, 21 Jun 2020 20:07:07: #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 20:07:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:07:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:07:12: 5000000 INFO @ Sun, 21 Jun 2020 20:07:13: 2000000 INFO @ Sun, 21 Jun 2020 20:07:22: 6000000 INFO @ Sun, 21 Jun 2020 20:07:23: 3000000 INFO @ Sun, 21 Jun 2020 20:07:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:07:32: 7000000 INFO @ Sun, 21 Jun 2020 20:07:33: 4000000 INFO @ Sun, 21 Jun 2020 20:07:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3511940/SRX3511940.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:07:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3511940/SRX3511940.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:07:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3511940/SRX3511940.05_summits.bed INFO @ Sun, 21 Jun 2020 20:07:37: Done! pass1 - making usageList (376 chroms): 1 millis pass2 - checking and writing primary data (1991 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:07:42: 8000000 INFO @ Sun, 21 Jun 2020 20:07:43: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:07:49: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 20:07:49: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 20:07:49: #1 total tags in treatment: 8730682 INFO @ Sun, 21 Jun 2020 20:07:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:07:49: #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 20:07:50: #1 tags after filtering in treatment: 8730639 INFO @ Sun, 21 Jun 2020 20:07:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:07:50: #1 finished! INFO @ Sun, 21 Jun 2020 20:07:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:07:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:07:50: #2 number of paired peaks: 2924 INFO @ Sun, 21 Jun 2020 20:07:50: start model_add_line... INFO @ Sun, 21 Jun 2020 20:07:50: start X-correlation... INFO @ Sun, 21 Jun 2020 20:07:50: end of X-cor INFO @ Sun, 21 Jun 2020 20:07:50: #2 finished! INFO @ Sun, 21 Jun 2020 20:07:50: #2 predicted fragment length is 176 bps INFO @ Sun, 21 Jun 2020 20:07:50: #2 alternative fragment length(s) may be 176 bps INFO @ Sun, 21 Jun 2020 20:07:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3511940/SRX3511940.10_model.r WARNING @ Sun, 21 Jun 2020 20:07:50: #2 Since the d (176) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:07:50: #2 You may need to consider one of the other alternative d(s): 176 WARNING @ Sun, 21 Jun 2020 20:07:50: #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 20:07:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:07:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:07:53: 6000000 INFO @ Sun, 21 Jun 2020 20:08:02: 7000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:08:11: 8000000 INFO @ Sun, 21 Jun 2020 20:08:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:08:18: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 20:08:18: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 20:08:18: #1 total tags in treatment: 8730682 INFO @ Sun, 21 Jun 2020 20:08:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:08:18: #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 20:08:18: #1 tags after filtering in treatment: 8730639 INFO @ Sun, 21 Jun 2020 20:08:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:08:18: #1 finished! INFO @ Sun, 21 Jun 2020 20:08:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:08:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:08:19: #2 number of paired peaks: 2924 INFO @ Sun, 21 Jun 2020 20:08:19: start model_add_line... INFO @ Sun, 21 Jun 2020 20:08:19: start X-correlation... INFO @ Sun, 21 Jun 2020 20:08:19: end of X-cor INFO @ Sun, 21 Jun 2020 20:08:19: #2 finished! INFO @ Sun, 21 Jun 2020 20:08:19: #2 predicted fragment length is 176 bps INFO @ Sun, 21 Jun 2020 20:08:19: #2 alternative fragment length(s) may be 176 bps INFO @ Sun, 21 Jun 2020 20:08:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3511940/SRX3511940.20_model.r WARNING @ Sun, 21 Jun 2020 20:08:19: #2 Since the d (176) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:08:19: #2 You may need to consider one of the other alternative d(s): 176 WARNING @ Sun, 21 Jun 2020 20:08:19: #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 20:08:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:08:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:08:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3511940/SRX3511940.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:08:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3511940/SRX3511940.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:08:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3511940/SRX3511940.10_summits.bed INFO @ Sun, 21 Jun 2020 20:08:21: Done! pass1 - making usageList (290 chroms): 1 millis pass2 - checking and writing primary data (908 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:08:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:08:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3511940/SRX3511940.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:08:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3511940/SRX3511940.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:08:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3511940/SRX3511940.20_summits.bed INFO @ Sun, 21 Jun 2020 20:08:50: Done! pass1 - making usageList (188 chroms): 1 millis pass2 - checking and writing primary data (378 records, 4 fields): 7 millis CompletedMACS2peakCalling