Job ID = 6453669 SRX = SRX135531 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:35:39 prefetch.2.10.7: 1) Downloading 'SRR453256'... 2020-06-21T08:35:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:51:41 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:51:41 prefetch.2.10.7: 1) 'SRR453256' was downloaded successfully Read 82193180 spots for SRR453256/SRR453256.sra Written 82193180 spots for SRR453256/SRR453256.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: 00:12:19 82193180 reads; of these: 82193180 (100.00%) were unpaired; of these: 65388808 (79.56%) aligned 0 times 12119538 (14.75%) aligned exactly 1 time 4684834 (5.70%) aligned >1 times 20.44% overall alignment rate Time searching: 00:12:19 Overall time: 00:12:19 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 8 files... [bam_rmdupse_core] 12011658 / 16804372 = 0.7148 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 18:11:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX135531/SRX135531.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX135531/SRX135531.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX135531/SRX135531.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX135531/SRX135531.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 18:11:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:11:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:11:59: 1000000 INFO @ Sun, 21 Jun 2020 18:12:04: 2000000 INFO @ Sun, 21 Jun 2020 18:12:09: 3000000 INFO @ Sun, 21 Jun 2020 18:12:15: 4000000 INFO @ Sun, 21 Jun 2020 18:12:19: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:12:19: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:12:19: #1 total tags in treatment: 4792714 INFO @ Sun, 21 Jun 2020 18:12:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:12:19: #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 18:12:19: #1 tags after filtering in treatment: 4792701 INFO @ Sun, 21 Jun 2020 18:12:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:12:19: #1 finished! INFO @ Sun, 21 Jun 2020 18:12:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:12:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:12:20: #2 number of paired peaks: 1561 INFO @ Sun, 21 Jun 2020 18:12:20: start model_add_line... INFO @ Sun, 21 Jun 2020 18:12:20: start X-correlation... INFO @ Sun, 21 Jun 2020 18:12:20: end of X-cor INFO @ Sun, 21 Jun 2020 18:12:20: #2 finished! INFO @ Sun, 21 Jun 2020 18:12:20: #2 predicted fragment length is 92 bps INFO @ Sun, 21 Jun 2020 18:12:20: #2 alternative fragment length(s) may be 3,92 bps INFO @ Sun, 21 Jun 2020 18:12:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX135531/SRX135531.05_model.r WARNING @ Sun, 21 Jun 2020 18:12:20: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:12:20: #2 You may need to consider one of the other alternative d(s): 3,92 WARNING @ Sun, 21 Jun 2020 18:12:20: #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 18:12:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:12:20: #3 Pre-compute pvalue-qvalue table... 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 18:12:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX135531/SRX135531.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX135531/SRX135531.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX135531/SRX135531.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX135531/SRX135531.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 18:12:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:12:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:12:29: 1000000 INFO @ Sun, 21 Jun 2020 18:12:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:12:34: 2000000 INFO @ Sun, 21 Jun 2020 18:12:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX135531/SRX135531.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:12:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX135531/SRX135531.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:12:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX135531/SRX135531.05_summits.bed INFO @ Sun, 21 Jun 2020 18:12:38: Done! pass1 - making usageList (735 chroms): 2 millis pass2 - checking and writing primary data (2277 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:12:39: 3000000 INFO @ Sun, 21 Jun 2020 18:12:45: 4000000 INFO @ Sun, 21 Jun 2020 18:12:49: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:12:49: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:12:49: #1 total tags in treatment: 4792714 INFO @ Sun, 21 Jun 2020 18:12:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:12:49: #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 18:12:49: #1 tags after filtering in treatment: 4792701 INFO @ Sun, 21 Jun 2020 18:12:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:12:49: #1 finished! INFO @ Sun, 21 Jun 2020 18:12:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:12:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:12:50: #2 number of paired peaks: 1561 INFO @ Sun, 21 Jun 2020 18:12:50: start model_add_line... INFO @ Sun, 21 Jun 2020 18:12:50: start X-correlation... INFO @ Sun, 21 Jun 2020 18:12:50: end of X-cor INFO @ Sun, 21 Jun 2020 18:12:50: #2 finished! INFO @ Sun, 21 Jun 2020 18:12:50: #2 predicted fragment length is 92 bps INFO @ Sun, 21 Jun 2020 18:12:50: #2 alternative fragment length(s) may be 3,92 bps INFO @ Sun, 21 Jun 2020 18:12:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX135531/SRX135531.10_model.r WARNING @ Sun, 21 Jun 2020 18:12:50: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:12:50: #2 You may need to consider one of the other alternative d(s): 3,92 WARNING @ Sun, 21 Jun 2020 18:12:50: #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 18:12:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:12:50: #3 Pre-compute pvalue-qvalue table... 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 18:12:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX135531/SRX135531.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX135531/SRX135531.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX135531/SRX135531.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX135531/SRX135531.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 18:12:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:12:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:13:00: 1000000 INFO @ Sun, 21 Jun 2020 18:13:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:13:06: 2000000 INFO @ Sun, 21 Jun 2020 18:13:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX135531/SRX135531.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:13:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX135531/SRX135531.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:13:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX135531/SRX135531.10_summits.bed INFO @ Sun, 21 Jun 2020 18:13:08: Done! pass1 - making usageList (463 chroms): 1 millis pass2 - checking and writing primary data (944 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:13:12: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:13:18: 4000000 INFO @ Sun, 21 Jun 2020 18:13:23: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:13:23: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:13:23: #1 total tags in treatment: 4792714 INFO @ Sun, 21 Jun 2020 18:13:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:13:23: #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 18:13:23: #1 tags after filtering in treatment: 4792701 INFO @ Sun, 21 Jun 2020 18:13:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:13:23: #1 finished! INFO @ Sun, 21 Jun 2020 18:13:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:13:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:13:24: #2 number of paired peaks: 1561 INFO @ Sun, 21 Jun 2020 18:13:24: start model_add_line... INFO @ Sun, 21 Jun 2020 18:13:24: start X-correlation... INFO @ Sun, 21 Jun 2020 18:13:24: end of X-cor INFO @ Sun, 21 Jun 2020 18:13:24: #2 finished! INFO @ Sun, 21 Jun 2020 18:13:24: #2 predicted fragment length is 92 bps INFO @ Sun, 21 Jun 2020 18:13:24: #2 alternative fragment length(s) may be 3,92 bps INFO @ Sun, 21 Jun 2020 18:13:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX135531/SRX135531.20_model.r WARNING @ Sun, 21 Jun 2020 18:13:24: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:13:24: #2 You may need to consider one of the other alternative d(s): 3,92 WARNING @ Sun, 21 Jun 2020 18:13:24: #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 18:13:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:13:24: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:13:36: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:13:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX135531/SRX135531.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:13:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX135531/SRX135531.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:13:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX135531/SRX135531.20_summits.bed INFO @ Sun, 21 Jun 2020 18:13:42: Done! pass1 - making usageList (165 chroms): 1 millis pass2 - checking and writing primary data (284 records, 4 fields): 7 millis CompletedMACS2peakCalling