Job ID = 16438085 SRX = SRX12261330 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:12:26 26995928 reads; of these: 26995928 (100.00%) were unpaired; of these: 1739673 (6.44%) aligned 0 times 15327981 (56.78%) aligned exactly 1 time 9928274 (36.78%) aligned >1 times 93.56% overall alignment rate Time searching: 00:12:26 Overall time: 00:12:26 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 12 files... [bam_rmdupse_core] 18265135 / 25256255 = 0.7232 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 13:51:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX12261330/SRX12261330.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX12261330/SRX12261330.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX12261330/SRX12261330.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX12261330/SRX12261330.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 13:51:01: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:51:01: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:51:07: 1000000 INFO @ Tue, 02 Aug 2022 13:51:12: 2000000 INFO @ Tue, 02 Aug 2022 13:51:18: 3000000 INFO @ Tue, 02 Aug 2022 13:51:24: 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 13:51:29: 5000000 INFO @ Tue, 02 Aug 2022 13:51:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX12261330/SRX12261330.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX12261330/SRX12261330.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX12261330/SRX12261330.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX12261330/SRX12261330.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 13:51:30: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:51:30: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:51:36: 6000000 INFO @ Tue, 02 Aug 2022 13:51:36: 1000000 INFO @ Tue, 02 Aug 2022 13:51:42: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:51:42: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:51:42: #1 total tags in treatment: 6991120 INFO @ Tue, 02 Aug 2022 13:51:42: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:51:42: #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 13:51:42: #1 tags after filtering in treatment: 6991118 INFO @ Tue, 02 Aug 2022 13:51:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:51:42: #1 finished! INFO @ Tue, 02 Aug 2022 13:51:42: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:51:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:51:43: 2000000 INFO @ Tue, 02 Aug 2022 13:51:43: #2 number of paired peaks: 2018 INFO @ Tue, 02 Aug 2022 13:51:43: start model_add_line... INFO @ Tue, 02 Aug 2022 13:51:43: start X-correlation... INFO @ Tue, 02 Aug 2022 13:51:43: end of X-cor INFO @ Tue, 02 Aug 2022 13:51:43: #2 finished! INFO @ Tue, 02 Aug 2022 13:51:43: #2 predicted fragment length is 80 bps INFO @ Tue, 02 Aug 2022 13:51:43: #2 alternative fragment length(s) may be 80 bps INFO @ Tue, 02 Aug 2022 13:51:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX12261330/SRX12261330.05_model.r WARNING @ Tue, 02 Aug 2022 13:51:43: #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 13:51:43: #2 You may need to consider one of the other alternative d(s): 80 WARNING @ Tue, 02 Aug 2022 13:51:43: #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 13:51:43: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:51:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:51:48: 3000000 INFO @ Tue, 02 Aug 2022 13:51:54: 4000000 INFO @ Tue, 02 Aug 2022 13:51:58: #3 Call peaks for each chromosome... 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 13:52:00: 5000000 INFO @ Tue, 02 Aug 2022 13:52:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX12261330/SRX12261330.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX12261330/SRX12261330.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX12261330/SRX12261330.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX12261330/SRX12261330.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 13:52:00: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:52:00: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:52:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX12261330/SRX12261330.05_peaks.xls INFO @ Tue, 02 Aug 2022 13:52:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX12261330/SRX12261330.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:52:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX12261330/SRX12261330.05_summits.bed INFO @ Tue, 02 Aug 2022 13:52:05: Done! pass1 - making usageList (900 chroms): 2 millis pass2 - checking and writing primary data (3671 records, 4 fields): 54 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:52:07: 6000000 INFO @ Tue, 02 Aug 2022 13:52:07: 1000000 INFO @ Tue, 02 Aug 2022 13:52:13: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:52:13: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:52:13: #1 total tags in treatment: 6991120 INFO @ Tue, 02 Aug 2022 13:52:13: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:52:13: #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 13:52:14: #1 tags after filtering in treatment: 6991118 INFO @ Tue, 02 Aug 2022 13:52:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:52:14: #1 finished! INFO @ Tue, 02 Aug 2022 13:52:14: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:52:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:52:14: 2000000 INFO @ Tue, 02 Aug 2022 13:52:14: #2 number of paired peaks: 2018 INFO @ Tue, 02 Aug 2022 13:52:14: start model_add_line... INFO @ Tue, 02 Aug 2022 13:52:15: start X-correlation... INFO @ Tue, 02 Aug 2022 13:52:15: end of X-cor INFO @ Tue, 02 Aug 2022 13:52:15: #2 finished! INFO @ Tue, 02 Aug 2022 13:52:15: #2 predicted fragment length is 80 bps INFO @ Tue, 02 Aug 2022 13:52:15: #2 alternative fragment length(s) may be 80 bps INFO @ Tue, 02 Aug 2022 13:52:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX12261330/SRX12261330.10_model.r WARNING @ Tue, 02 Aug 2022 13:52:15: #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 13:52:15: #2 You may need to consider one of the other alternative d(s): 80 WARNING @ Tue, 02 Aug 2022 13:52:15: #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 13:52:15: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:52:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:52:21: 3000000 INFO @ Tue, 02 Aug 2022 13:52:28: 4000000 INFO @ Tue, 02 Aug 2022 13:52:29: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 13:52:35: 5000000 INFO @ Tue, 02 Aug 2022 13:52:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX12261330/SRX12261330.10_peaks.xls INFO @ Tue, 02 Aug 2022 13:52:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX12261330/SRX12261330.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:52:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX12261330/SRX12261330.10_summits.bed INFO @ Tue, 02 Aug 2022 13:52:37: Done! pass1 - making usageList (685 chroms): 2 millis pass2 - checking and writing primary data (2007 records, 4 fields): 32 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:52:42: 6000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 13:52:48: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:52:48: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:52:48: #1 total tags in treatment: 6991120 INFO @ Tue, 02 Aug 2022 13:52:48: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:52:48: #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 13:52:49: #1 tags after filtering in treatment: 6991118 INFO @ Tue, 02 Aug 2022 13:52:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:52:49: #1 finished! INFO @ Tue, 02 Aug 2022 13:52:49: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:52:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:52:49: #2 number of paired peaks: 2018 INFO @ Tue, 02 Aug 2022 13:52:49: start model_add_line... INFO @ Tue, 02 Aug 2022 13:52:49: start X-correlation... INFO @ Tue, 02 Aug 2022 13:52:49: end of X-cor INFO @ Tue, 02 Aug 2022 13:52:49: #2 finished! INFO @ Tue, 02 Aug 2022 13:52:49: #2 predicted fragment length is 80 bps INFO @ Tue, 02 Aug 2022 13:52:49: #2 alternative fragment length(s) may be 80 bps INFO @ Tue, 02 Aug 2022 13:52:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX12261330/SRX12261330.20_model.r WARNING @ Tue, 02 Aug 2022 13:52:49: #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 13:52:49: #2 You may need to consider one of the other alternative d(s): 80 WARNING @ Tue, 02 Aug 2022 13:52:49: #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 13:52:49: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:52:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:53:04: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:53:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX12261330/SRX12261330.20_peaks.xls INFO @ Tue, 02 Aug 2022 13:53:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX12261330/SRX12261330.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:53:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX12261330/SRX12261330.20_summits.bed INFO @ Tue, 02 Aug 2022 13:53:11: Done! pass1 - making usageList (526 chroms): 1 millis pass2 - checking and writing primary data (1402 records, 4 fields): 52 millis CompletedMACS2peakCalling