Job ID = 16437631 SRX = SRX12261323 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 18415946 spots for SRR15972579/SRR15972579.sra Written 18415946 spots for SRR15972579/SRR15972579.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438030 ("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: 00:11:05 18415946 reads; of these: 18415946 (100.00%) were unpaired; of these: 791945 (4.30%) aligned 0 times 10631133 (57.73%) aligned exactly 1 time 6992868 (37.97%) aligned >1 times 95.70% overall alignment rate Time searching: 00:11:05 Overall time: 00:11:05 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] 3834786 / 17624001 = 0.2176 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 13:18:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12261323/SRX12261323.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12261323/SRX12261323.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12261323/SRX12261323.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12261323/SRX12261323.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 @ Tue, 02 Aug 2022 13:18:08: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:18:08: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:18:15: 1000000 INFO @ Tue, 02 Aug 2022 13:18:21: 2000000 INFO @ Tue, 02 Aug 2022 13:18:27: 3000000 INFO @ Tue, 02 Aug 2022 13:18:33: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 13:18:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12261323/SRX12261323.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12261323/SRX12261323.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12261323/SRX12261323.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12261323/SRX12261323.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 @ Tue, 02 Aug 2022 13:18:38: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:18:38: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:18:39: 5000000 INFO @ Tue, 02 Aug 2022 13:18:45: 1000000 INFO @ Tue, 02 Aug 2022 13:18:46: 6000000 INFO @ Tue, 02 Aug 2022 13:18:52: 2000000 INFO @ Tue, 02 Aug 2022 13:18:53: 7000000 INFO @ Tue, 02 Aug 2022 13:18:58: 3000000 INFO @ Tue, 02 Aug 2022 13:19:00: 8000000 INFO @ Tue, 02 Aug 2022 13:19:05: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 13:19:07: 9000000 INFO @ Tue, 02 Aug 2022 13:19:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12261323/SRX12261323.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12261323/SRX12261323.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12261323/SRX12261323.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12261323/SRX12261323.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 @ Tue, 02 Aug 2022 13:19:08: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:19:08: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:19:12: 5000000 INFO @ Tue, 02 Aug 2022 13:19:14: 10000000 INFO @ Tue, 02 Aug 2022 13:19:15: 1000000 INFO @ Tue, 02 Aug 2022 13:19:19: 6000000 INFO @ Tue, 02 Aug 2022 13:19:21: 11000000 INFO @ Tue, 02 Aug 2022 13:19:22: 2000000 INFO @ Tue, 02 Aug 2022 13:19:26: 7000000 INFO @ Tue, 02 Aug 2022 13:19:27: 12000000 INFO @ Tue, 02 Aug 2022 13:19:29: 3000000 INFO @ Tue, 02 Aug 2022 13:19:33: 8000000 INFO @ Tue, 02 Aug 2022 13:19:34: 13000000 INFO @ Tue, 02 Aug 2022 13:19:36: 4000000 INFO @ Tue, 02 Aug 2022 13:19:40: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:19:40: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:19:40: #1 total tags in treatment: 13789215 INFO @ Tue, 02 Aug 2022 13:19:40: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:19:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 13:19:40: 9000000 INFO @ Tue, 02 Aug 2022 13:19:40: #1 tags after filtering in treatment: 13789215 INFO @ Tue, 02 Aug 2022 13:19:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:19:40: #1 finished! INFO @ Tue, 02 Aug 2022 13:19:40: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:19:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:19:41: #2 number of paired peaks: 104 WARNING @ Tue, 02 Aug 2022 13:19:41: Fewer paired peaks (104) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 104 pairs to build model! INFO @ Tue, 02 Aug 2022 13:19:41: start model_add_line... INFO @ Tue, 02 Aug 2022 13:19:41: start X-correlation... INFO @ Tue, 02 Aug 2022 13:19:41: end of X-cor INFO @ Tue, 02 Aug 2022 13:19:41: #2 finished! INFO @ Tue, 02 Aug 2022 13:19:41: #2 predicted fragment length is 80 bps INFO @ Tue, 02 Aug 2022 13:19:41: #2 alternative fragment length(s) may be 80 bps INFO @ Tue, 02 Aug 2022 13:19:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12261323/SRX12261323.05_model.r WARNING @ Tue, 02 Aug 2022 13:19:41: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:19:41: #2 You may need to consider one of the other alternative d(s): 80 WARNING @ Tue, 02 Aug 2022 13:19:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 13:19:41: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:19:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:19:42: 5000000 INFO @ Tue, 02 Aug 2022 13:19:47: 10000000 INFO @ Tue, 02 Aug 2022 13:19:49: 6000000 INFO @ Tue, 02 Aug 2022 13:19:54: 11000000 INFO @ Tue, 02 Aug 2022 13:19:56: 7000000 INFO @ Tue, 02 Aug 2022 13:20:00: 12000000 INFO @ Tue, 02 Aug 2022 13:20:03: 8000000 INFO @ Tue, 02 Aug 2022 13:20:07: 13000000 INFO @ Tue, 02 Aug 2022 13:20:08: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:20:10: 9000000 INFO @ Tue, 02 Aug 2022 13:20:13: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:20:13: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:20:13: #1 total tags in treatment: 13789215 INFO @ Tue, 02 Aug 2022 13:20:13: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:20:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 13:20:13: #1 tags after filtering in treatment: 13789215 INFO @ Tue, 02 Aug 2022 13:20:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:20:13: #1 finished! INFO @ Tue, 02 Aug 2022 13:20:13: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:20:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:20:14: #2 number of paired peaks: 104 WARNING @ Tue, 02 Aug 2022 13:20:14: Fewer paired peaks (104) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 104 pairs to build model! INFO @ Tue, 02 Aug 2022 13:20:14: start model_add_line... INFO @ Tue, 02 Aug 2022 13:20:14: start X-correlation... INFO @ Tue, 02 Aug 2022 13:20:14: end of X-cor INFO @ Tue, 02 Aug 2022 13:20:14: #2 finished! INFO @ Tue, 02 Aug 2022 13:20:14: #2 predicted fragment length is 80 bps INFO @ Tue, 02 Aug 2022 13:20:14: #2 alternative fragment length(s) may be 80 bps INFO @ Tue, 02 Aug 2022 13:20:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12261323/SRX12261323.10_model.r WARNING @ Tue, 02 Aug 2022 13:20:14: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:20:14: #2 You may need to consider one of the other alternative d(s): 80 WARNING @ Tue, 02 Aug 2022 13:20:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 13:20:14: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:20:14: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 13:20:16: 10000000 INFO @ Tue, 02 Aug 2022 13:20:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12261323/SRX12261323.05_peaks.xls INFO @ Tue, 02 Aug 2022 13:20:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12261323/SRX12261323.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:20:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12261323/SRX12261323.05_summits.bed INFO @ Tue, 02 Aug 2022 13:20:21: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4730 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:20:23: 11000000 INFO @ Tue, 02 Aug 2022 13:20:29: 12000000 INFO @ Tue, 02 Aug 2022 13:20:35: 13000000 INFO @ Tue, 02 Aug 2022 13:20:40: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:20:40: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:20:40: #1 total tags in treatment: 13789215 INFO @ Tue, 02 Aug 2022 13:20:40: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:20:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 13:20:40: #1 tags after filtering in treatment: 13789215 INFO @ Tue, 02 Aug 2022 13:20:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:20:40: #1 finished! INFO @ Tue, 02 Aug 2022 13:20:40: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:20:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:20:41: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:20:41: #2 number of paired peaks: 104 WARNING @ Tue, 02 Aug 2022 13:20:41: Fewer paired peaks (104) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 104 pairs to build model! INFO @ Tue, 02 Aug 2022 13:20:41: start model_add_line... INFO @ Tue, 02 Aug 2022 13:20:41: start X-correlation... INFO @ Tue, 02 Aug 2022 13:20:41: end of X-cor INFO @ Tue, 02 Aug 2022 13:20:41: #2 finished! INFO @ Tue, 02 Aug 2022 13:20:41: #2 predicted fragment length is 80 bps INFO @ Tue, 02 Aug 2022 13:20:41: #2 alternative fragment length(s) may be 80 bps INFO @ Tue, 02 Aug 2022 13:20:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12261323/SRX12261323.20_model.r WARNING @ Tue, 02 Aug 2022 13:20:41: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:20:41: #2 You may need to consider one of the other alternative d(s): 80 WARNING @ Tue, 02 Aug 2022 13:20:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 13:20:41: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:20:41: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 13:20:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12261323/SRX12261323.10_peaks.xls INFO @ Tue, 02 Aug 2022 13:20:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12261323/SRX12261323.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:20:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12261323/SRX12261323.10_summits.bed INFO @ Tue, 02 Aug 2022 13:20:54: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1697 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:21:07: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:21:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12261323/SRX12261323.20_peaks.xls INFO @ Tue, 02 Aug 2022 13:21:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12261323/SRX12261323.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:21:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12261323/SRX12261323.20_summits.bed INFO @ Tue, 02 Aug 2022 13:21:20: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (569 records, 4 fields): 49 millis CompletedMACS2peakCalling