Job ID = 6459849 SRX = SRX886166 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:52:19 prefetch.2.10.7: 1) Downloading 'SRR1813780'... 2020-06-21T13:52:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:58:00 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:58:00 prefetch.2.10.7: 1) 'SRR1813780' was downloaded successfully Read 43848249 spots for SRR1813780/SRR1813780.sra Written 43848249 spots for SRR1813780/SRR1813780.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: 00:08:30 43848249 reads; of these: 43848249 (100.00%) were unpaired; of these: 13067944 (29.80%) aligned 0 times 23439001 (53.45%) aligned exactly 1 time 7341304 (16.74%) aligned >1 times 70.20% overall alignment rate Time searching: 00:08:30 Overall time: 00:08:30 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 16 files... [bam_rmdupse_core] 24265569 / 30780305 = 0.7883 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 23:13:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX886166/SRX886166.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX886166/SRX886166.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX886166/SRX886166.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX886166/SRX886166.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 23:13:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 23:13:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 23:13:49: 1000000 INFO @ Sun, 21 Jun 2020 23:13:54: 2000000 INFO @ Sun, 21 Jun 2020 23:14:00: 3000000 INFO @ Sun, 21 Jun 2020 23:14:05: 4000000 INFO @ Sun, 21 Jun 2020 23:14:10: 5000000 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 23:14:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX886166/SRX886166.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX886166/SRX886166.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX886166/SRX886166.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX886166/SRX886166.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 23:14:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 23:14:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 23:14:16: 6000000 INFO @ Sun, 21 Jun 2020 23:14:19: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 23:14:19: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 23:14:19: #1 total tags in treatment: 6514736 INFO @ Sun, 21 Jun 2020 23:14:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 23:14:19: #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 23:14:20: #1 tags after filtering in treatment: 6514643 INFO @ Sun, 21 Jun 2020 23:14:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 23:14:20: #1 finished! INFO @ Sun, 21 Jun 2020 23:14:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 23:14:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 23:14:20: #2 number of paired peaks: 4665 INFO @ Sun, 21 Jun 2020 23:14:20: start model_add_line... INFO @ Sun, 21 Jun 2020 23:14:21: start X-correlation... INFO @ Sun, 21 Jun 2020 23:14:21: end of X-cor INFO @ Sun, 21 Jun 2020 23:14:21: #2 finished! INFO @ Sun, 21 Jun 2020 23:14:21: #2 predicted fragment length is 87 bps INFO @ Sun, 21 Jun 2020 23:14:21: #2 alternative fragment length(s) may be 4,87 bps INFO @ Sun, 21 Jun 2020 23:14:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX886166/SRX886166.05_model.r WARNING @ Sun, 21 Jun 2020 23:14:21: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 23:14:21: #2 You may need to consider one of the other alternative d(s): 4,87 WARNING @ Sun, 21 Jun 2020 23:14:21: #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 23:14:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 23:14:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 23:14:21: 1000000 INFO @ Sun, 21 Jun 2020 23:14:27: 2000000 INFO @ Sun, 21 Jun 2020 23:14:33: 3000000 INFO @ Sun, 21 Jun 2020 23:14:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 23:14:40: 4000000 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 23:14:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX886166/SRX886166.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX886166/SRX886166.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX886166/SRX886166.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX886166/SRX886166.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 23:14:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 23:14:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 23:14:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX886166/SRX886166.05_peaks.xls INFO @ Sun, 21 Jun 2020 23:14:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX886166/SRX886166.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 23:14:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX886166/SRX886166.05_summits.bed INFO @ Sun, 21 Jun 2020 23:14:45: Done! pass1 - making usageList (700 chroms): 2 millis pass2 - checking and writing primary data (8930 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 23:14:46: 5000000 INFO @ Sun, 21 Jun 2020 23:14:50: 1000000 INFO @ Sun, 21 Jun 2020 23:14:53: 6000000 INFO @ Sun, 21 Jun 2020 23:14:56: 2000000 INFO @ Sun, 21 Jun 2020 23:14:57: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 23:14:57: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 23:14:57: #1 total tags in treatment: 6514736 INFO @ Sun, 21 Jun 2020 23:14:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 23:14:57: #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 23:14:57: #1 tags after filtering in treatment: 6514643 INFO @ Sun, 21 Jun 2020 23:14:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 23:14:57: #1 finished! INFO @ Sun, 21 Jun 2020 23:14:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 23:14:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 23:14:58: #2 number of paired peaks: 4665 INFO @ Sun, 21 Jun 2020 23:14:58: start model_add_line... INFO @ Sun, 21 Jun 2020 23:14:58: start X-correlation... INFO @ Sun, 21 Jun 2020 23:14:58: end of X-cor INFO @ Sun, 21 Jun 2020 23:14:58: #2 finished! INFO @ Sun, 21 Jun 2020 23:14:58: #2 predicted fragment length is 87 bps INFO @ Sun, 21 Jun 2020 23:14:58: #2 alternative fragment length(s) may be 4,87 bps INFO @ Sun, 21 Jun 2020 23:14:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX886166/SRX886166.10_model.r WARNING @ Sun, 21 Jun 2020 23:14:58: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 23:14:58: #2 You may need to consider one of the other alternative d(s): 4,87 WARNING @ Sun, 21 Jun 2020 23:14:58: #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 23:14:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 23:14:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 23:15:01: 3000000 INFO @ Sun, 21 Jun 2020 23:15:07: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 23:15:13: 5000000 INFO @ Sun, 21 Jun 2020 23:15:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 23:15:18: 6000000 INFO @ Sun, 21 Jun 2020 23:15:21: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 23:15:21: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 23:15:21: #1 total tags in treatment: 6514736 INFO @ Sun, 21 Jun 2020 23:15:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 23:15:21: #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 23:15:21: #1 tags after filtering in treatment: 6514643 INFO @ Sun, 21 Jun 2020 23:15:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 23:15:21: #1 finished! INFO @ Sun, 21 Jun 2020 23:15:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 23:15:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 23:15:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX886166/SRX886166.10_peaks.xls INFO @ Sun, 21 Jun 2020 23:15:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX886166/SRX886166.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 23:15:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX886166/SRX886166.10_summits.bed INFO @ Sun, 21 Jun 2020 23:15:22: Done! INFO @ Sun, 21 Jun 2020 23:15:22: #2 number of paired peaks: 4665 INFO @ Sun, 21 Jun 2020 23:15:22: start model_add_line... INFO @ Sun, 21 Jun 2020 23:15:22: start X-correlation... INFO @ Sun, 21 Jun 2020 23:15:22: end of X-cor INFO @ Sun, 21 Jun 2020 23:15:22: #2 finished! INFO @ Sun, 21 Jun 2020 23:15:22: #2 predicted fragment length is 87 bps INFO @ Sun, 21 Jun 2020 23:15:22: #2 alternative fragment length(s) may be 4,87 bps INFO @ Sun, 21 Jun 2020 23:15:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX886166/SRX886166.20_model.r WARNING @ Sun, 21 Jun 2020 23:15:22: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 23:15:22: #2 You may need to consider one of the other alternative d(s): 4,87 WARNING @ Sun, 21 Jun 2020 23:15:22: #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 23:15:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 23:15:22: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (613 chroms): 2 millis pass2 - checking and writing primary data (5698 records, 4 fields): 21 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 23:15:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 23:15:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX886166/SRX886166.20_peaks.xls INFO @ Sun, 21 Jun 2020 23:15:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX886166/SRX886166.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 23:15:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX886166/SRX886166.20_summits.bed INFO @ Sun, 21 Jun 2020 23:15:45: Done! pass1 - making usageList (366 chroms): 1 millis pass2 - checking and writing primary data (2564 records, 4 fields): 12 millis CompletedMACS2peakCalling