Job ID = 12265412 SRX = SRX5010736 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:18 23886047 reads; of these: 23886047 (100.00%) were unpaired; of these: 1004658 (4.21%) aligned 0 times 19271602 (80.68%) aligned exactly 1 time 3609787 (15.11%) aligned >1 times 95.79% overall alignment rate Time searching: 00:07:19 Overall time: 00:07:19 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] 14416461 / 22881389 = 0.6301 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 07:06:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5010736/SRX5010736.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5010736/SRX5010736.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5010736/SRX5010736.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5010736/SRX5010736.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 07:06:27: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:06:27: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:06:35: 1000000 INFO @ Sat, 03 Apr 2021 07:06:43: 2000000 INFO @ Sat, 03 Apr 2021 07:06:51: 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 07:06:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5010736/SRX5010736.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5010736/SRX5010736.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5010736/SRX5010736.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5010736/SRX5010736.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 07:06:57: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:06:57: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:06:59: 4000000 INFO @ Sat, 03 Apr 2021 07:07:03: 1000000 INFO @ Sat, 03 Apr 2021 07:07:06: 5000000 INFO @ Sat, 03 Apr 2021 07:07:08: 2000000 INFO @ Sat, 03 Apr 2021 07:07:14: 6000000 INFO @ Sat, 03 Apr 2021 07:07:15: 3000000 INFO @ Sat, 03 Apr 2021 07:07:21: 4000000 INFO @ Sat, 03 Apr 2021 07:07:22: 7000000 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: 5000000 INFO @ Sat, 03 Apr 2021 07:07:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5010736/SRX5010736.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5010736/SRX5010736.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5010736/SRX5010736.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5010736/SRX5010736.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 07:07:27: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:07:27: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:07:30: 8000000 INFO @ Sat, 03 Apr 2021 07:07:32: 6000000 INFO @ Sat, 03 Apr 2021 07:07:33: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:07:33: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:07:33: #1 total tags in treatment: 8464928 INFO @ Sat, 03 Apr 2021 07:07:33: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:07:33: #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 07:07:34: #1 tags after filtering in treatment: 8464817 INFO @ Sat, 03 Apr 2021 07:07:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 07:07:34: #1 finished! INFO @ Sat, 03 Apr 2021 07:07:34: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:07:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:07:35: #2 number of paired peaks: 708 WARNING @ Sat, 03 Apr 2021 07:07:35: Fewer paired peaks (708) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 708 pairs to build model! INFO @ Sat, 03 Apr 2021 07:07:35: start model_add_line... INFO @ Sat, 03 Apr 2021 07:07:35: 1000000 INFO @ Sat, 03 Apr 2021 07:07:35: start X-correlation... INFO @ Sat, 03 Apr 2021 07:07:35: end of X-cor INFO @ Sat, 03 Apr 2021 07:07:35: #2 finished! INFO @ Sat, 03 Apr 2021 07:07:35: #2 predicted fragment length is 56 bps INFO @ Sat, 03 Apr 2021 07:07:35: #2 alternative fragment length(s) may be 56 bps INFO @ Sat, 03 Apr 2021 07:07:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5010736/SRX5010736.05_model.r WARNING @ Sat, 03 Apr 2021 07:07:35: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:07:35: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Sat, 03 Apr 2021 07:07:35: #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 07:07:35: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:07:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:07:39: 7000000 INFO @ Sat, 03 Apr 2021 07:07:42: 2000000 INFO @ Sat, 03 Apr 2021 07:07:45: 8000000 INFO @ Sat, 03 Apr 2021 07:07:48: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:07:48: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:07:48: #1 total tags in treatment: 8464928 INFO @ Sat, 03 Apr 2021 07:07:48: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:07:48: #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 07:07:48: #1 tags after filtering in treatment: 8464817 INFO @ Sat, 03 Apr 2021 07:07:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 07:07:48: #1 finished! INFO @ Sat, 03 Apr 2021 07:07:48: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:07:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:07:48: 3000000 INFO @ Sat, 03 Apr 2021 07:07:49: #2 number of paired peaks: 708 WARNING @ Sat, 03 Apr 2021 07:07:49: Fewer paired peaks (708) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 708 pairs to build model! INFO @ Sat, 03 Apr 2021 07:07:49: start model_add_line... INFO @ Sat, 03 Apr 2021 07:07:49: start X-correlation... INFO @ Sat, 03 Apr 2021 07:07:49: end of X-cor INFO @ Sat, 03 Apr 2021 07:07:49: #2 finished! INFO @ Sat, 03 Apr 2021 07:07:49: #2 predicted fragment length is 56 bps INFO @ Sat, 03 Apr 2021 07:07:49: #2 alternative fragment length(s) may be 56 bps INFO @ Sat, 03 Apr 2021 07:07:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5010736/SRX5010736.10_model.r WARNING @ Sat, 03 Apr 2021 07:07:49: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:07:49: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Sat, 03 Apr 2021 07:07:49: #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 07:07:49: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:07:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:07:51: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:07:55: 4000000 INFO @ Sat, 03 Apr 2021 07:08:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5010736/SRX5010736.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:08:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5010736/SRX5010736.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:08:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5010736/SRX5010736.05_summits.bed INFO @ Sat, 03 Apr 2021 07:08:00: Done! pass1 - making usageList (368 chroms): 1 millis pass2 - checking and writing primary data (3467 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:08:01: 5000000 INFO @ Sat, 03 Apr 2021 07:08:06: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:08:07: 6000000 INFO @ Sat, 03 Apr 2021 07:08:15: 7000000 INFO @ Sat, 03 Apr 2021 07:08:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5010736/SRX5010736.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:08:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5010736/SRX5010736.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:08:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5010736/SRX5010736.10_summits.bed INFO @ Sat, 03 Apr 2021 07:08:15: Done! pass1 - making usageList (185 chroms): 2 millis pass2 - checking and writing primary data (1509 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:08:21: 8000000 INFO @ Sat, 03 Apr 2021 07:08:24: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:08:24: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:08:24: #1 total tags in treatment: 8464928 INFO @ Sat, 03 Apr 2021 07:08:24: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:08:24: #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 07:08:25: #1 tags after filtering in treatment: 8464817 INFO @ Sat, 03 Apr 2021 07:08:25: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 07:08:25: #1 finished! INFO @ Sat, 03 Apr 2021 07:08:25: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:08:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:08:26: #2 number of paired peaks: 708 WARNING @ Sat, 03 Apr 2021 07:08:26: Fewer paired peaks (708) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 708 pairs to build model! INFO @ Sat, 03 Apr 2021 07:08:26: start model_add_line... INFO @ Sat, 03 Apr 2021 07:08:26: start X-correlation... INFO @ Sat, 03 Apr 2021 07:08:26: end of X-cor INFO @ Sat, 03 Apr 2021 07:08:26: #2 finished! INFO @ Sat, 03 Apr 2021 07:08:26: #2 predicted fragment length is 56 bps INFO @ Sat, 03 Apr 2021 07:08:26: #2 alternative fragment length(s) may be 56 bps INFO @ Sat, 03 Apr 2021 07:08:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5010736/SRX5010736.20_model.r WARNING @ Sat, 03 Apr 2021 07:08:26: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:08:26: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Sat, 03 Apr 2021 07:08:26: #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 07:08:26: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:08:26: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 07:08:42: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:08:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5010736/SRX5010736.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:08:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5010736/SRX5010736.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:08:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5010736/SRX5010736.20_summits.bed INFO @ Sat, 03 Apr 2021 07:08:51: Done! pass1 - making usageList (107 chroms): 2 millis pass2 - checking and writing primary data (430 records, 4 fields): 8 millis CompletedMACS2peakCalling