Job ID = 12264873 SRX = SRX3032272 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 21255567 spots for SRR5863962/SRR5863962.sra Written 21255567 spots for SRR5863962/SRR5863962.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265096 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:06:05 21255567 reads; of these: 21255567 (100.00%) were unpaired; of these: 2196506 (10.33%) aligned 0 times 15996453 (75.26%) aligned exactly 1 time 3062608 (14.41%) aligned >1 times 89.67% overall alignment rate Time searching: 00:06:06 Overall time: 00:06:06 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 10087739 / 19059061 = 0.5293 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:05:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032272/SRX3032272.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032272/SRX3032272.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032272/SRX3032272.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032272/SRX3032272.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 @ Sat, 03 Apr 2021 06:05:32: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:05:32: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:05:40: 1000000 INFO @ Sat, 03 Apr 2021 06:05:47: 2000000 INFO @ Sat, 03 Apr 2021 06:05:54: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:06:00: 4000000 INFO @ Sat, 03 Apr 2021 06:06:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032272/SRX3032272.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032272/SRX3032272.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032272/SRX3032272.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032272/SRX3032272.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 @ Sat, 03 Apr 2021 06:06:02: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:06:02: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:06:07: 5000000 INFO @ Sat, 03 Apr 2021 06:06:11: 1000000 INFO @ Sat, 03 Apr 2021 06:06:15: 6000000 INFO @ Sat, 03 Apr 2021 06:06:19: 2000000 INFO @ Sat, 03 Apr 2021 06:06:23: 7000000 INFO @ Sat, 03 Apr 2021 06:06:28: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:06:30: 8000000 INFO @ Sat, 03 Apr 2021 06:06:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032272/SRX3032272.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032272/SRX3032272.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032272/SRX3032272.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032272/SRX3032272.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 @ Sat, 03 Apr 2021 06:06:33: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:06:33: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:06:37: 4000000 INFO @ Sat, 03 Apr 2021 06:06:38: #1 tag size is determined as 51 bps INFO @ Sat, 03 Apr 2021 06:06:38: #1 tag size = 51 INFO @ Sat, 03 Apr 2021 06:06:38: #1 total tags in treatment: 8971322 INFO @ Sat, 03 Apr 2021 06:06:38: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:06:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:06:38: #1 tags after filtering in treatment: 8971322 INFO @ Sat, 03 Apr 2021 06:06:38: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:06:38: #1 finished! INFO @ Sat, 03 Apr 2021 06:06:38: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:06:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:06:39: #2 number of paired peaks: 5181 INFO @ Sat, 03 Apr 2021 06:06:39: start model_add_line... INFO @ Sat, 03 Apr 2021 06:06:39: start X-correlation... INFO @ Sat, 03 Apr 2021 06:06:39: end of X-cor INFO @ Sat, 03 Apr 2021 06:06:39: #2 finished! INFO @ Sat, 03 Apr 2021 06:06:39: #2 predicted fragment length is 84 bps INFO @ Sat, 03 Apr 2021 06:06:39: #2 alternative fragment length(s) may be 84 bps INFO @ Sat, 03 Apr 2021 06:06:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032272/SRX3032272.05_model.r WARNING @ Sat, 03 Apr 2021 06:06:39: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:06:39: #2 You may need to consider one of the other alternative d(s): 84 WARNING @ Sat, 03 Apr 2021 06:06:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:06:39: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:06:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:06:40: 1000000 INFO @ Sat, 03 Apr 2021 06:06:46: 5000000 INFO @ Sat, 03 Apr 2021 06:06:48: 2000000 INFO @ Sat, 03 Apr 2021 06:06:53: 6000000 INFO @ Sat, 03 Apr 2021 06:06:55: 3000000 INFO @ Sat, 03 Apr 2021 06:06:59: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:07:02: 7000000 INFO @ Sat, 03 Apr 2021 06:07:03: 4000000 INFO @ Sat, 03 Apr 2021 06:07:10: 5000000 INFO @ Sat, 03 Apr 2021 06:07:11: 8000000 INFO @ Sat, 03 Apr 2021 06:07:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032272/SRX3032272.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:07:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032272/SRX3032272.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:07:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032272/SRX3032272.05_summits.bed INFO @ Sat, 03 Apr 2021 06:07:11: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (21694 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:07:17: 6000000 INFO @ Sat, 03 Apr 2021 06:07:19: #1 tag size is determined as 51 bps INFO @ Sat, 03 Apr 2021 06:07:19: #1 tag size = 51 INFO @ Sat, 03 Apr 2021 06:07:19: #1 total tags in treatment: 8971322 INFO @ Sat, 03 Apr 2021 06:07:19: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:07:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:07:19: #1 tags after filtering in treatment: 8971322 INFO @ Sat, 03 Apr 2021 06:07:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:07:19: #1 finished! INFO @ Sat, 03 Apr 2021 06:07:19: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:07:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:07:20: #2 number of paired peaks: 5181 INFO @ Sat, 03 Apr 2021 06:07:20: start model_add_line... INFO @ Sat, 03 Apr 2021 06:07:20: start X-correlation... INFO @ Sat, 03 Apr 2021 06:07:20: end of X-cor INFO @ Sat, 03 Apr 2021 06:07:20: #2 finished! INFO @ Sat, 03 Apr 2021 06:07:20: #2 predicted fragment length is 84 bps INFO @ Sat, 03 Apr 2021 06:07:20: #2 alternative fragment length(s) may be 84 bps INFO @ Sat, 03 Apr 2021 06:07:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032272/SRX3032272.10_model.r WARNING @ Sat, 03 Apr 2021 06:07:20: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:07:20: #2 You may need to consider one of the other alternative d(s): 84 WARNING @ Sat, 03 Apr 2021 06:07:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:07:20: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:07:20: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:07:24: 7000000 INFO @ Sat, 03 Apr 2021 06:07:31: 8000000 INFO @ Sat, 03 Apr 2021 06:07:37: #1 tag size is determined as 51 bps INFO @ Sat, 03 Apr 2021 06:07:37: #1 tag size = 51 INFO @ Sat, 03 Apr 2021 06:07:37: #1 total tags in treatment: 8971322 INFO @ Sat, 03 Apr 2021 06:07:37: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:07:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:07:37: #1 tags after filtering in treatment: 8971322 INFO @ Sat, 03 Apr 2021 06:07:37: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:07:37: #1 finished! INFO @ Sat, 03 Apr 2021 06:07:37: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:07:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:07:38: #2 number of paired peaks: 5181 INFO @ Sat, 03 Apr 2021 06:07:38: start model_add_line... INFO @ Sat, 03 Apr 2021 06:07:38: start X-correlation... INFO @ Sat, 03 Apr 2021 06:07:38: end of X-cor INFO @ Sat, 03 Apr 2021 06:07:38: #2 finished! INFO @ Sat, 03 Apr 2021 06:07:38: #2 predicted fragment length is 84 bps INFO @ Sat, 03 Apr 2021 06:07:38: #2 alternative fragment length(s) may be 84 bps INFO @ Sat, 03 Apr 2021 06:07:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032272/SRX3032272.20_model.r WARNING @ Sat, 03 Apr 2021 06:07:38: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:07:38: #2 You may need to consider one of the other alternative d(s): 84 WARNING @ Sat, 03 Apr 2021 06:07:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:07:38: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:07:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:07:39: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:07:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032272/SRX3032272.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:07:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032272/SRX3032272.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:07:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032272/SRX3032272.10_summits.bed INFO @ Sat, 03 Apr 2021 06:07:50: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (14424 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:07:57: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:08:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032272/SRX3032272.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:08:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032272/SRX3032272.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:08:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032272/SRX3032272.20_summits.bed INFO @ Sat, 03 Apr 2021 06:08:07: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (6392 records, 4 fields): 9 millis CompletedMACS2peakCalling