Job ID = 14171520 SRX = SRX10000680 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: 00:12:06 64365296 reads; of these: 64365296 (100.00%) were unpaired; of these: 61044736 (94.84%) aligned 0 times 2650543 (4.12%) aligned exactly 1 time 670017 (1.04%) aligned >1 times 5.16% overall alignment rate Time searching: 00:12:06 Overall time: 00:12:06 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] 402711 / 3320560 = 0.1213 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 12:07:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX10000680/SRX10000680.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX10000680/SRX10000680.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX10000680/SRX10000680.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX10000680/SRX10000680.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 12:07:02: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:07:02: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:07:09: 1000000 INFO @ Sat, 11 Dec 2021 12:07:15: 2000000 INFO @ Sat, 11 Dec 2021 12:07:21: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 12:07:21: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 12:07:21: #1 total tags in treatment: 2917849 INFO @ Sat, 11 Dec 2021 12:07:21: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:07:21: #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 12:07:21: #1 tags after filtering in treatment: 2917518 INFO @ Sat, 11 Dec 2021 12:07:21: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 12:07:21: #1 finished! INFO @ Sat, 11 Dec 2021 12:07:21: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:07:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:07:21: #2 number of paired peaks: 1648 INFO @ Sat, 11 Dec 2021 12:07:21: start model_add_line... INFO @ Sat, 11 Dec 2021 12:07:21: start X-correlation... INFO @ Sat, 11 Dec 2021 12:07:21: end of X-cor INFO @ Sat, 11 Dec 2021 12:07:21: #2 finished! INFO @ Sat, 11 Dec 2021 12:07:21: #2 predicted fragment length is 106 bps INFO @ Sat, 11 Dec 2021 12:07:21: #2 alternative fragment length(s) may be 106,557,571,578 bps INFO @ Sat, 11 Dec 2021 12:07:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX10000680/SRX10000680.05_model.r WARNING @ Sat, 11 Dec 2021 12:07:21: #2 Since the d (106) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:07:21: #2 You may need to consider one of the other alternative d(s): 106,557,571,578 WARNING @ Sat, 11 Dec 2021 12:07:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 12:07:21: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:07:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:07:28: #3 Call peaks for each chromosome... 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 12:07:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX10000680/SRX10000680.05_peaks.xls INFO @ Sat, 11 Dec 2021 12:07:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX10000680/SRX10000680.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:07:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX10000680/SRX10000680.05_summits.bed INFO @ Sat, 11 Dec 2021 12:07:32: Done! pass1 - making usageList (257 chroms): 1 millis pass2 - checking and writing primary data (708 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:07:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX10000680/SRX10000680.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX10000680/SRX10000680.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX10000680/SRX10000680.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX10000680/SRX10000680.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 12:07:32: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:07:32: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:07:39: 1000000 INFO @ Sat, 11 Dec 2021 12:07:46: 2000000 INFO @ Sat, 11 Dec 2021 12:07:53: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 12:07:53: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 12:07:53: #1 total tags in treatment: 2917849 INFO @ Sat, 11 Dec 2021 12:07:53: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:07:53: #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 12:07:54: #1 tags after filtering in treatment: 2917518 INFO @ Sat, 11 Dec 2021 12:07:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 12:07:54: #1 finished! INFO @ Sat, 11 Dec 2021 12:07:54: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:07:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:07:54: #2 number of paired peaks: 1648 INFO @ Sat, 11 Dec 2021 12:07:54: start model_add_line... INFO @ Sat, 11 Dec 2021 12:07:54: start X-correlation... INFO @ Sat, 11 Dec 2021 12:07:54: end of X-cor INFO @ Sat, 11 Dec 2021 12:07:54: #2 finished! INFO @ Sat, 11 Dec 2021 12:07:54: #2 predicted fragment length is 106 bps INFO @ Sat, 11 Dec 2021 12:07:54: #2 alternative fragment length(s) may be 106,557,571,578 bps INFO @ Sat, 11 Dec 2021 12:07:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX10000680/SRX10000680.10_model.r WARNING @ Sat, 11 Dec 2021 12:07:54: #2 Since the d (106) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:07:54: #2 You may need to consider one of the other alternative d(s): 106,557,571,578 WARNING @ Sat, 11 Dec 2021 12:07:54: #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 12:07:54: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:07:54: #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 12:08:01: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:08:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX10000680/SRX10000680.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX10000680/SRX10000680.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX10000680/SRX10000680.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX10000680/SRX10000680.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 12:08:02: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:08:02: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:08:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX10000680/SRX10000680.10_peaks.xls INFO @ Sat, 11 Dec 2021 12:08:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX10000680/SRX10000680.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:08:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX10000680/SRX10000680.10_summits.bed INFO @ Sat, 11 Dec 2021 12:08:04: Done! pass1 - making usageList (138 chroms): 1 millis pass2 - checking and writing primary data (309 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:08:08: 1000000 INFO @ Sat, 11 Dec 2021 12:08:14: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 12:08:20: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 12:08:20: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 12:08:20: #1 total tags in treatment: 2917849 INFO @ Sat, 11 Dec 2021 12:08:20: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:08:20: #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 12:08:20: #1 tags after filtering in treatment: 2917518 INFO @ Sat, 11 Dec 2021 12:08:20: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 12:08:20: #1 finished! INFO @ Sat, 11 Dec 2021 12:08:20: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:08:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:08:20: #2 number of paired peaks: 1648 INFO @ Sat, 11 Dec 2021 12:08:20: start model_add_line... INFO @ Sat, 11 Dec 2021 12:08:20: start X-correlation... INFO @ Sat, 11 Dec 2021 12:08:20: end of X-cor INFO @ Sat, 11 Dec 2021 12:08:20: #2 finished! INFO @ Sat, 11 Dec 2021 12:08:20: #2 predicted fragment length is 106 bps INFO @ Sat, 11 Dec 2021 12:08:20: #2 alternative fragment length(s) may be 106,557,571,578 bps INFO @ Sat, 11 Dec 2021 12:08:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX10000680/SRX10000680.20_model.r WARNING @ Sat, 11 Dec 2021 12:08:20: #2 Since the d (106) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:08:20: #2 You may need to consider one of the other alternative d(s): 106,557,571,578 WARNING @ Sat, 11 Dec 2021 12:08:20: #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 12:08:20: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:08:20: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 12:08:27: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:08:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX10000680/SRX10000680.20_peaks.xls INFO @ Sat, 11 Dec 2021 12:08:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX10000680/SRX10000680.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:08:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX10000680/SRX10000680.20_summits.bed INFO @ Sat, 11 Dec 2021 12:08:30: Done! pass1 - making usageList (70 chroms): 1 millis pass2 - checking and writing primary data (131 records, 4 fields): 3 millis CompletedMACS2peakCalling