Job ID = 14167313 SRX = SRX7723708 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: 00:08:55 28127043 reads; of these: 28127043 (100.00%) were unpaired; of these: 6370008 (22.65%) aligned 0 times 13974579 (49.68%) aligned exactly 1 time 7782456 (27.67%) aligned >1 times 77.35% overall alignment rate Time searching: 00:08:55 Overall time: 00:08:55 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] 8372871 / 21757035 = 0.3848 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 @ Fri, 10 Dec 2021 11:58:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7723708/SRX7723708.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7723708/SRX7723708.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7723708/SRX7723708.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7723708/SRX7723708.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 @ Fri, 10 Dec 2021 11:58:27: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:58:27: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:58:33: 1000000 INFO @ Fri, 10 Dec 2021 11:58:39: 2000000 INFO @ Fri, 10 Dec 2021 11:58:45: 3000000 INFO @ Fri, 10 Dec 2021 11:58:51: 4000000 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 @ Fri, 10 Dec 2021 11:58:56: 5000000 INFO @ Fri, 10 Dec 2021 11:58:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7723708/SRX7723708.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7723708/SRX7723708.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7723708/SRX7723708.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7723708/SRX7723708.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 @ Fri, 10 Dec 2021 11:58:57: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:58:57: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:59:03: 6000000 INFO @ Fri, 10 Dec 2021 11:59:03: 1000000 INFO @ Fri, 10 Dec 2021 11:59:10: 7000000 INFO @ Fri, 10 Dec 2021 11:59:10: 2000000 INFO @ Fri, 10 Dec 2021 11:59:17: 8000000 INFO @ Fri, 10 Dec 2021 11:59:17: 3000000 INFO @ Fri, 10 Dec 2021 11:59:23: 9000000 INFO @ Fri, 10 Dec 2021 11:59:24: 4000000 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 @ Fri, 10 Dec 2021 11:59:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7723708/SRX7723708.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7723708/SRX7723708.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7723708/SRX7723708.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7723708/SRX7723708.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 @ Fri, 10 Dec 2021 11:59:26: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:59:26: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:59:30: 10000000 INFO @ Fri, 10 Dec 2021 11:59:30: 5000000 INFO @ Fri, 10 Dec 2021 11:59:34: 1000000 INFO @ Fri, 10 Dec 2021 11:59:37: 6000000 INFO @ Fri, 10 Dec 2021 11:59:37: 11000000 INFO @ Fri, 10 Dec 2021 11:59:41: 2000000 INFO @ Fri, 10 Dec 2021 11:59:44: 7000000 INFO @ Fri, 10 Dec 2021 11:59:44: 12000000 INFO @ Fri, 10 Dec 2021 11:59:47: 3000000 INFO @ Fri, 10 Dec 2021 11:59:50: 8000000 INFO @ Fri, 10 Dec 2021 11:59:51: 13000000 INFO @ Fri, 10 Dec 2021 11:59:53: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 11:59:53: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 11:59:53: #1 total tags in treatment: 13384164 INFO @ Fri, 10 Dec 2021 11:59:53: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:59:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:59:54: #1 tags after filtering in treatment: 13384043 INFO @ Fri, 10 Dec 2021 11:59:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:59:54: #1 finished! INFO @ Fri, 10 Dec 2021 11:59:54: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:59:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:59:54: 4000000 INFO @ Fri, 10 Dec 2021 11:59:55: #2 number of paired peaks: 3725 INFO @ Fri, 10 Dec 2021 11:59:55: start model_add_line... INFO @ Fri, 10 Dec 2021 11:59:55: start X-correlation... INFO @ Fri, 10 Dec 2021 11:59:55: end of X-cor INFO @ Fri, 10 Dec 2021 11:59:55: #2 finished! INFO @ Fri, 10 Dec 2021 11:59:55: #2 predicted fragment length is 129 bps INFO @ Fri, 10 Dec 2021 11:59:55: #2 alternative fragment length(s) may be 129 bps INFO @ Fri, 10 Dec 2021 11:59:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7723708/SRX7723708.05_model.r WARNING @ Fri, 10 Dec 2021 11:59:55: #2 Since the d (129) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:59:55: #2 You may need to consider one of the other alternative d(s): 129 WARNING @ Fri, 10 Dec 2021 11:59:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 11:59:55: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:59:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:59:57: 9000000 INFO @ Fri, 10 Dec 2021 12:00:01: 5000000 INFO @ Fri, 10 Dec 2021 12:00:04: 10000000 INFO @ Fri, 10 Dec 2021 12:00:08: 6000000 INFO @ Fri, 10 Dec 2021 12:00:11: 11000000 INFO @ Fri, 10 Dec 2021 12:00:14: 7000000 INFO @ Fri, 10 Dec 2021 12:00:18: 12000000 INFO @ Fri, 10 Dec 2021 12:00:21: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 12:00:23: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:00:24: 13000000 INFO @ Fri, 10 Dec 2021 12:00:27: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 12:00:27: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 12:00:27: #1 total tags in treatment: 13384164 INFO @ Fri, 10 Dec 2021 12:00:27: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:00:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 12:00:27: #1 tags after filtering in treatment: 13384043 INFO @ Fri, 10 Dec 2021 12:00:27: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:00:27: #1 finished! INFO @ Fri, 10 Dec 2021 12:00:27: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:00:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:00:28: 9000000 INFO @ Fri, 10 Dec 2021 12:00:28: #2 number of paired peaks: 3725 INFO @ Fri, 10 Dec 2021 12:00:28: start model_add_line... INFO @ Fri, 10 Dec 2021 12:00:29: start X-correlation... INFO @ Fri, 10 Dec 2021 12:00:29: end of X-cor INFO @ Fri, 10 Dec 2021 12:00:29: #2 finished! INFO @ Fri, 10 Dec 2021 12:00:29: #2 predicted fragment length is 129 bps INFO @ Fri, 10 Dec 2021 12:00:29: #2 alternative fragment length(s) may be 129 bps INFO @ Fri, 10 Dec 2021 12:00:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7723708/SRX7723708.10_model.r WARNING @ Fri, 10 Dec 2021 12:00:29: #2 Since the d (129) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:00:29: #2 You may need to consider one of the other alternative d(s): 129 WARNING @ Fri, 10 Dec 2021 12:00:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 12:00:29: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:00:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:00:34: 10000000 INFO @ Fri, 10 Dec 2021 12:00:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7723708/SRX7723708.05_peaks.xls INFO @ Fri, 10 Dec 2021 12:00:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7723708/SRX7723708.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:00:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7723708/SRX7723708.05_summits.bed INFO @ Fri, 10 Dec 2021 12:00:37: Done! pass1 - making usageList (860 chroms): 3 millis pass2 - checking and writing primary data (12889 records, 4 fields): 63 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 12:00:41: 11000000 INFO @ Fri, 10 Dec 2021 12:00:47: 12000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 12:00:53: 13000000 INFO @ Fri, 10 Dec 2021 12:00:56: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 12:00:56: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 12:00:56: #1 total tags in treatment: 13384164 INFO @ Fri, 10 Dec 2021 12:00:56: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:00:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 12:00:56: #1 tags after filtering in treatment: 13384043 INFO @ Fri, 10 Dec 2021 12:00:56: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:00:56: #1 finished! INFO @ Fri, 10 Dec 2021 12:00:56: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:00:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:00:57: #2 number of paired peaks: 3725 INFO @ Fri, 10 Dec 2021 12:00:57: start model_add_line... INFO @ Fri, 10 Dec 2021 12:00:57: start X-correlation... INFO @ Fri, 10 Dec 2021 12:00:57: end of X-cor INFO @ Fri, 10 Dec 2021 12:00:57: #2 finished! INFO @ Fri, 10 Dec 2021 12:00:57: #2 predicted fragment length is 129 bps INFO @ Fri, 10 Dec 2021 12:00:57: #2 alternative fragment length(s) may be 129 bps INFO @ Fri, 10 Dec 2021 12:00:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7723708/SRX7723708.20_model.r WARNING @ Fri, 10 Dec 2021 12:00:57: #2 Since the d (129) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:00:57: #2 You may need to consider one of the other alternative d(s): 129 WARNING @ Fri, 10 Dec 2021 12:00:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 12:00:57: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:00:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:00:58: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:01:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7723708/SRX7723708.10_peaks.xls INFO @ Fri, 10 Dec 2021 12:01:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7723708/SRX7723708.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:01:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7723708/SRX7723708.10_summits.bed INFO @ Fri, 10 Dec 2021 12:01:12: Done! pass1 - making usageList (729 chroms): 2 millis pass2 - checking and writing primary data (5981 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 12:01:25: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:01:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7723708/SRX7723708.20_peaks.xls INFO @ Fri, 10 Dec 2021 12:01:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7723708/SRX7723708.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:01:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7723708/SRX7723708.20_summits.bed INFO @ Fri, 10 Dec 2021 12:01:39: Done! pass1 - making usageList (533 chroms): 2 millis pass2 - checking and writing primary data (2005 records, 4 fields): 23 millis CompletedMACS2peakCalling