Job ID = 14172515 SRX = SRX10089755 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: 00:04:09 30454379 reads; of these: 30454379 (100.00%) were unpaired; of these: 26445765 (86.84%) aligned 0 times 3445680 (11.31%) aligned exactly 1 time 562934 (1.85%) aligned >1 times 13.16% overall alignment rate Time searching: 00:04:09 Overall time: 00:04:09 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_rmdupse_core] 517955 / 4008614 = 0.1292 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 15:51:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX10089755/SRX10089755.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX10089755/SRX10089755.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX10089755/SRX10089755.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX10089755/SRX10089755.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, 11 Dec 2021 15:51:20: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:51:20: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:51:26: 1000000 INFO @ Sat, 11 Dec 2021 15:51:33: 2000000 INFO @ Sat, 11 Dec 2021 15:51:40: 3000000 INFO @ Sat, 11 Dec 2021 15:51:44: #1 tag size is determined as 74 bps INFO @ Sat, 11 Dec 2021 15:51:44: #1 tag size = 74 INFO @ Sat, 11 Dec 2021 15:51:44: #1 total tags in treatment: 3490659 INFO @ Sat, 11 Dec 2021 15:51:44: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:51:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 15:51:44: #1 tags after filtering in treatment: 3490426 INFO @ Sat, 11 Dec 2021 15:51:44: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 15:51:44: #1 finished! INFO @ Sat, 11 Dec 2021 15:51:44: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:51:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:51:44: #2 number of paired peaks: 2904 INFO @ Sat, 11 Dec 2021 15:51:44: start model_add_line... INFO @ Sat, 11 Dec 2021 15:51:44: start X-correlation... INFO @ Sat, 11 Dec 2021 15:51:44: end of X-cor INFO @ Sat, 11 Dec 2021 15:51:44: #2 finished! INFO @ Sat, 11 Dec 2021 15:51:44: #2 predicted fragment length is 142 bps INFO @ Sat, 11 Dec 2021 15:51:44: #2 alternative fragment length(s) may be 142 bps INFO @ Sat, 11 Dec 2021 15:51:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX10089755/SRX10089755.05_model.r WARNING @ Sat, 11 Dec 2021 15:51:44: #2 Since the d (142) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 15:51:44: #2 You may need to consider one of the other alternative d(s): 142 WARNING @ Sat, 11 Dec 2021 15:51:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 15:51:44: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:51:44: #3 Pre-compute pvalue-qvalue table... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 15:51:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX10089755/SRX10089755.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX10089755/SRX10089755.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX10089755/SRX10089755.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX10089755/SRX10089755.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, 11 Dec 2021 15:51:49: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:51:49: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:51:53: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:51:54: 1000000 INFO @ Sat, 11 Dec 2021 15:51:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX10089755/SRX10089755.05_peaks.xls INFO @ Sat, 11 Dec 2021 15:51:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX10089755/SRX10089755.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:51:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX10089755/SRX10089755.05_summits.bed INFO @ Sat, 11 Dec 2021 15:51:57: Done! pass1 - making usageList (235 chroms): 1 millis pass2 - checking and writing primary data (4845 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:52:00: 2000000 INFO @ Sat, 11 Dec 2021 15:52:06: 3000000 INFO @ Sat, 11 Dec 2021 15:52:08: #1 tag size is determined as 74 bps INFO @ Sat, 11 Dec 2021 15:52:08: #1 tag size = 74 INFO @ Sat, 11 Dec 2021 15:52:08: #1 total tags in treatment: 3490659 INFO @ Sat, 11 Dec 2021 15:52:08: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:52:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 15:52:09: #1 tags after filtering in treatment: 3490426 INFO @ Sat, 11 Dec 2021 15:52:09: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 15:52:09: #1 finished! INFO @ Sat, 11 Dec 2021 15:52:09: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:52:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:52:09: #2 number of paired peaks: 2904 INFO @ Sat, 11 Dec 2021 15:52:09: start model_add_line... INFO @ Sat, 11 Dec 2021 15:52:09: start X-correlation... INFO @ Sat, 11 Dec 2021 15:52:09: end of X-cor INFO @ Sat, 11 Dec 2021 15:52:09: #2 finished! INFO @ Sat, 11 Dec 2021 15:52:09: #2 predicted fragment length is 142 bps INFO @ Sat, 11 Dec 2021 15:52:09: #2 alternative fragment length(s) may be 142 bps INFO @ Sat, 11 Dec 2021 15:52:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX10089755/SRX10089755.10_model.r WARNING @ Sat, 11 Dec 2021 15:52:09: #2 Since the d (142) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 15:52:09: #2 You may need to consider one of the other alternative d(s): 142 WARNING @ Sat, 11 Dec 2021 15:52:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 15:52:09: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:52:09: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 15:52:17: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:52:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX10089755/SRX10089755.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX10089755/SRX10089755.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX10089755/SRX10089755.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX10089755/SRX10089755.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, 11 Dec 2021 15:52:19: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:52:19: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:52:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX10089755/SRX10089755.10_peaks.xls INFO @ Sat, 11 Dec 2021 15:52:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX10089755/SRX10089755.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:52:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX10089755/SRX10089755.10_summits.bed INFO @ Sat, 11 Dec 2021 15:52:21: Done! pass1 - making usageList (104 chroms): 1 millis pass2 - checking and writing primary data (2569 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:52:26: 1000000 INFO @ Sat, 11 Dec 2021 15:52:33: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 15:52:40: 3000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 15:52:44: #1 tag size is determined as 74 bps INFO @ Sat, 11 Dec 2021 15:52:44: #1 tag size = 74 INFO @ Sat, 11 Dec 2021 15:52:44: #1 total tags in treatment: 3490659 INFO @ Sat, 11 Dec 2021 15:52:44: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:52:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 15:52:44: #1 tags after filtering in treatment: 3490426 INFO @ Sat, 11 Dec 2021 15:52:44: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 15:52:44: #1 finished! INFO @ Sat, 11 Dec 2021 15:52:44: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:52:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:52:44: #2 number of paired peaks: 2904 INFO @ Sat, 11 Dec 2021 15:52:44: start model_add_line... INFO @ Sat, 11 Dec 2021 15:52:44: start X-correlation... INFO @ Sat, 11 Dec 2021 15:52:44: end of X-cor INFO @ Sat, 11 Dec 2021 15:52:44: #2 finished! INFO @ Sat, 11 Dec 2021 15:52:44: #2 predicted fragment length is 142 bps INFO @ Sat, 11 Dec 2021 15:52:44: #2 alternative fragment length(s) may be 142 bps INFO @ Sat, 11 Dec 2021 15:52:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX10089755/SRX10089755.20_model.r WARNING @ Sat, 11 Dec 2021 15:52:44: #2 Since the d (142) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 15:52:44: #2 You may need to consider one of the other alternative d(s): 142 WARNING @ Sat, 11 Dec 2021 15:52:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 15:52:44: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:52:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:52:53: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:52:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX10089755/SRX10089755.20_peaks.xls INFO @ Sat, 11 Dec 2021 15:52:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX10089755/SRX10089755.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:52:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX10089755/SRX10089755.20_summits.bed INFO @ Sat, 11 Dec 2021 15:52:57: Done! pass1 - making usageList (61 chroms): 0 millis pass2 - checking and writing primary data (1133 records, 4 fields): 5 millis CompletedMACS2peakCalling