Job ID = 12265268 SRX = SRX5010728 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 18496695 spots for SRR8191153/SRR8191153.sra Written 18496695 spots for SRR8191153/SRR8191153.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265400 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:07 18496695 reads; of these: 18496695 (100.00%) were unpaired; of these: 669021 (3.62%) aligned 0 times 8576296 (46.37%) aligned exactly 1 time 9251378 (50.02%) aligned >1 times 96.38% overall alignment rate Time searching: 00:05:07 Overall time: 00:05:07 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] 9293013 / 17827674 = 0.5213 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 06:29:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5010728/SRX5010728.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5010728/SRX5010728.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5010728/SRX5010728.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5010728/SRX5010728.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 06:29:29: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:29:29: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:29:36: 1000000 INFO @ Sat, 03 Apr 2021 06:29:42: 2000000 INFO @ Sat, 03 Apr 2021 06:29:48: 3000000 INFO @ Sat, 03 Apr 2021 06:29:54: 4000000 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 06:29:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5010728/SRX5010728.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5010728/SRX5010728.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5010728/SRX5010728.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5010728/SRX5010728.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 06:29:59: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:29:59: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:29:59: 5000000 INFO @ Sat, 03 Apr 2021 06:30:05: 1000000 INFO @ Sat, 03 Apr 2021 06:30:06: 6000000 INFO @ Sat, 03 Apr 2021 06:30:12: 2000000 INFO @ Sat, 03 Apr 2021 06:30:12: 7000000 INFO @ Sat, 03 Apr 2021 06:30:18: 3000000 INFO @ Sat, 03 Apr 2021 06:30:18: 8000000 INFO @ Sat, 03 Apr 2021 06:30:22: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:30:22: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:30:22: #1 total tags in treatment: 8534661 INFO @ Sat, 03 Apr 2021 06:30:22: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:30:22: #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 06:30:22: #1 tags after filtering in treatment: 8534661 INFO @ Sat, 03 Apr 2021 06:30:22: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:30:22: #1 finished! INFO @ Sat, 03 Apr 2021 06:30:22: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:30:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:30:22: #2 number of paired peaks: 304 WARNING @ Sat, 03 Apr 2021 06:30:22: Fewer paired peaks (304) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 304 pairs to build model! INFO @ Sat, 03 Apr 2021 06:30:22: start model_add_line... INFO @ Sat, 03 Apr 2021 06:30:22: start X-correlation... INFO @ Sat, 03 Apr 2021 06:30:22: end of X-cor INFO @ Sat, 03 Apr 2021 06:30:22: #2 finished! INFO @ Sat, 03 Apr 2021 06:30:22: #2 predicted fragment length is 61 bps INFO @ Sat, 03 Apr 2021 06:30:22: #2 alternative fragment length(s) may be 61 bps INFO @ Sat, 03 Apr 2021 06:30:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5010728/SRX5010728.05_model.r WARNING @ Sat, 03 Apr 2021 06:30:22: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:30:22: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Sat, 03 Apr 2021 06:30:22: #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 06:30:22: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:30:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:30:24: 4000000 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 06:30:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5010728/SRX5010728.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5010728/SRX5010728.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5010728/SRX5010728.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5010728/SRX5010728.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 06:30:29: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:30:29: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:30:30: 5000000 INFO @ Sat, 03 Apr 2021 06:30:35: 1000000 INFO @ Sat, 03 Apr 2021 06:30:37: 6000000 INFO @ Sat, 03 Apr 2021 06:30:41: 2000000 INFO @ Sat, 03 Apr 2021 06:30:42: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:30:43: 7000000 INFO @ Sat, 03 Apr 2021 06:30:48: 3000000 INFO @ Sat, 03 Apr 2021 06:30:49: 8000000 INFO @ Sat, 03 Apr 2021 06:30:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5010728/SRX5010728.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:30:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5010728/SRX5010728.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:30:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5010728/SRX5010728.05_summits.bed INFO @ Sat, 03 Apr 2021 06:30:52: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4663 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:30:52: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:30:52: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:30:52: #1 total tags in treatment: 8534661 INFO @ Sat, 03 Apr 2021 06:30:52: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:30:52: #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 06:30:53: #1 tags after filtering in treatment: 8534661 INFO @ Sat, 03 Apr 2021 06:30:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:30:53: #1 finished! INFO @ Sat, 03 Apr 2021 06:30:53: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:30:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:30:53: #2 number of paired peaks: 304 WARNING @ Sat, 03 Apr 2021 06:30:53: Fewer paired peaks (304) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 304 pairs to build model! INFO @ Sat, 03 Apr 2021 06:30:53: start model_add_line... INFO @ Sat, 03 Apr 2021 06:30:53: start X-correlation... INFO @ Sat, 03 Apr 2021 06:30:53: end of X-cor INFO @ Sat, 03 Apr 2021 06:30:53: #2 finished! INFO @ Sat, 03 Apr 2021 06:30:53: #2 predicted fragment length is 61 bps INFO @ Sat, 03 Apr 2021 06:30:53: #2 alternative fragment length(s) may be 61 bps INFO @ Sat, 03 Apr 2021 06:30:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5010728/SRX5010728.10_model.r WARNING @ Sat, 03 Apr 2021 06:30:53: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:30:53: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Sat, 03 Apr 2021 06:30:53: #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 06:30:53: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:30:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:30:54: 4000000 INFO @ Sat, 03 Apr 2021 06:31:00: 5000000 INFO @ Sat, 03 Apr 2021 06:31:05: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:31:11: 7000000 INFO @ Sat, 03 Apr 2021 06:31:12: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:31:17: 8000000 INFO @ Sat, 03 Apr 2021 06:31:20: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:31:20: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:31:20: #1 total tags in treatment: 8534661 INFO @ Sat, 03 Apr 2021 06:31:20: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:31:20: #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 06:31:20: #1 tags after filtering in treatment: 8534661 INFO @ Sat, 03 Apr 2021 06:31:20: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:31:20: #1 finished! INFO @ Sat, 03 Apr 2021 06:31:20: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:31:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:31:21: #2 number of paired peaks: 304 WARNING @ Sat, 03 Apr 2021 06:31:21: Fewer paired peaks (304) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 304 pairs to build model! INFO @ Sat, 03 Apr 2021 06:31:21: start model_add_line... INFO @ Sat, 03 Apr 2021 06:31:21: start X-correlation... INFO @ Sat, 03 Apr 2021 06:31:21: end of X-cor INFO @ Sat, 03 Apr 2021 06:31:21: #2 finished! INFO @ Sat, 03 Apr 2021 06:31:21: #2 predicted fragment length is 61 bps INFO @ Sat, 03 Apr 2021 06:31:21: #2 alternative fragment length(s) may be 61 bps INFO @ Sat, 03 Apr 2021 06:31:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5010728/SRX5010728.20_model.r WARNING @ Sat, 03 Apr 2021 06:31:21: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:31:21: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Sat, 03 Apr 2021 06:31:21: #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 06:31:21: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:31:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:31:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5010728/SRX5010728.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:31:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5010728/SRX5010728.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:31:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5010728/SRX5010728.10_summits.bed INFO @ Sat, 03 Apr 2021 06:31:21: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1605 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:31:40: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:31:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5010728/SRX5010728.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:31:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5010728/SRX5010728.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:31:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5010728/SRX5010728.20_summits.bed INFO @ Sat, 03 Apr 2021 06:31:49: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (280 records, 4 fields): 1 millis CompletedMACS2peakCalling