Job ID = 12265419 SRX = SRX5010740 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: 00:05:38 18888376 reads; of these: 18888376 (100.00%) were unpaired; of these: 616361 (3.26%) aligned 0 times 15695983 (83.10%) aligned exactly 1 time 2576032 (13.64%) aligned >1 times 96.74% overall alignment rate Time searching: 00:05:38 Overall time: 00:05:38 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 8 files... [bam_rmdupse_core] 11873595 / 18272015 = 0.6498 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:06:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5010740/SRX5010740.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5010740/SRX5010740.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5010740/SRX5010740.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5010740/SRX5010740.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, 03 Apr 2021 07:06:26: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:06:26: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:06:34: 1000000 INFO @ Sat, 03 Apr 2021 07:06:41: 2000000 INFO @ Sat, 03 Apr 2021 07:06:48: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:06:56: 4000000 INFO @ Sat, 03 Apr 2021 07:06:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5010740/SRX5010740.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5010740/SRX5010740.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5010740/SRX5010740.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5010740/SRX5010740.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, 03 Apr 2021 07:06:56: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:06:56: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:07:03: 5000000 INFO @ Sat, 03 Apr 2021 07:07:04: 1000000 INFO @ Sat, 03 Apr 2021 07:07:11: 6000000 INFO @ Sat, 03 Apr 2021 07:07:12: 2000000 INFO @ Sat, 03 Apr 2021 07:07:15: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:07:15: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:07:15: #1 total tags in treatment: 6398420 INFO @ Sat, 03 Apr 2021 07:07:15: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:07:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:07:15: #1 tags after filtering in treatment: 6398281 INFO @ Sat, 03 Apr 2021 07:07:15: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 07:07:15: #1 finished! INFO @ Sat, 03 Apr 2021 07:07:15: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:07:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:07:16: #2 number of paired peaks: 1744 INFO @ Sat, 03 Apr 2021 07:07:16: start model_add_line... INFO @ Sat, 03 Apr 2021 07:07:16: start X-correlation... INFO @ Sat, 03 Apr 2021 07:07:16: end of X-cor INFO @ Sat, 03 Apr 2021 07:07:16: #2 finished! INFO @ Sat, 03 Apr 2021 07:07:16: #2 predicted fragment length is 85 bps INFO @ Sat, 03 Apr 2021 07:07:16: #2 alternative fragment length(s) may be 85 bps INFO @ Sat, 03 Apr 2021 07:07:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5010740/SRX5010740.05_model.r WARNING @ Sat, 03 Apr 2021 07:07:16: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:07:16: #2 You may need to consider one of the other alternative d(s): 85 WARNING @ Sat, 03 Apr 2021 07:07:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:07:16: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:07:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:07:19: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:07:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5010740/SRX5010740.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5010740/SRX5010740.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5010740/SRX5010740.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5010740/SRX5010740.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, 03 Apr 2021 07:07:26: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:07:26: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:07:27: 4000000 INFO @ Sat, 03 Apr 2021 07:07:30: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:07:34: 1000000 INFO @ Sat, 03 Apr 2021 07:07:35: 5000000 INFO @ Sat, 03 Apr 2021 07:07:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5010740/SRX5010740.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:07:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5010740/SRX5010740.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:07:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5010740/SRX5010740.05_summits.bed INFO @ Sat, 03 Apr 2021 07:07:39: Done! pass1 - making usageList (360 chroms): 3 millis pass2 - checking and writing primary data (8998 records, 4 fields): 53 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:07:42: 2000000 INFO @ Sat, 03 Apr 2021 07:07:44: 6000000 INFO @ Sat, 03 Apr 2021 07:07:47: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:07:47: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:07:47: #1 total tags in treatment: 6398420 INFO @ Sat, 03 Apr 2021 07:07:47: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:07:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:07:47: #1 tags after filtering in treatment: 6398281 INFO @ Sat, 03 Apr 2021 07:07:47: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 07:07:47: #1 finished! INFO @ Sat, 03 Apr 2021 07:07:47: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:07:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:07:48: #2 number of paired peaks: 1744 INFO @ Sat, 03 Apr 2021 07:07:48: start model_add_line... INFO @ Sat, 03 Apr 2021 07:07:48: start X-correlation... INFO @ Sat, 03 Apr 2021 07:07:48: end of X-cor INFO @ Sat, 03 Apr 2021 07:07:48: #2 finished! INFO @ Sat, 03 Apr 2021 07:07:48: #2 predicted fragment length is 85 bps INFO @ Sat, 03 Apr 2021 07:07:48: #2 alternative fragment length(s) may be 85 bps INFO @ Sat, 03 Apr 2021 07:07:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5010740/SRX5010740.10_model.r WARNING @ Sat, 03 Apr 2021 07:07:48: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:07:48: #2 You may need to consider one of the other alternative d(s): 85 WARNING @ Sat, 03 Apr 2021 07:07:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:07:48: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:07:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:07:50: 3000000 INFO @ Sat, 03 Apr 2021 07:07:57: 4000000 INFO @ Sat, 03 Apr 2021 07:08:02: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:08:04: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:08:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5010740/SRX5010740.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:08:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5010740/SRX5010740.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:08:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5010740/SRX5010740.10_summits.bed INFO @ Sat, 03 Apr 2021 07:08:10: Done! pass1 - making usageList (175 chroms): 2 millis pass2 - checking and writing primary data (4174 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:08:11: 6000000 INFO @ Sat, 03 Apr 2021 07:08:14: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:08:14: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:08:14: #1 total tags in treatment: 6398420 INFO @ Sat, 03 Apr 2021 07:08:14: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:08:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:08:14: #1 tags after filtering in treatment: 6398281 INFO @ Sat, 03 Apr 2021 07:08:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 07:08:14: #1 finished! INFO @ Sat, 03 Apr 2021 07:08:14: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:08:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:08:15: #2 number of paired peaks: 1744 INFO @ Sat, 03 Apr 2021 07:08:15: start model_add_line... INFO @ Sat, 03 Apr 2021 07:08:15: start X-correlation... INFO @ Sat, 03 Apr 2021 07:08:15: end of X-cor INFO @ Sat, 03 Apr 2021 07:08:15: #2 finished! INFO @ Sat, 03 Apr 2021 07:08:15: #2 predicted fragment length is 85 bps INFO @ Sat, 03 Apr 2021 07:08:15: #2 alternative fragment length(s) may be 85 bps INFO @ Sat, 03 Apr 2021 07:08:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5010740/SRX5010740.20_model.r WARNING @ Sat, 03 Apr 2021 07:08:15: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:08:15: #2 You may need to consider one of the other alternative d(s): 85 WARNING @ Sat, 03 Apr 2021 07:08:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:08:15: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:08:15: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 07:08:29: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:08:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5010740/SRX5010740.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:08:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5010740/SRX5010740.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:08:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5010740/SRX5010740.20_summits.bed INFO @ Sat, 03 Apr 2021 07:08:37: Done! pass1 - making usageList (115 chroms): 2 millis pass2 - checking and writing primary data (1213 records, 4 fields): 9 millis CompletedMACS2peakCalling