Job ID = 14169541 SRX = SRX8688896 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: 00:01:35 6245607 reads; of these: 6245607 (100.00%) were unpaired; of these: 592142 (9.48%) aligned 0 times 4724066 (75.64%) aligned exactly 1 time 929399 (14.88%) aligned >1 times 90.52% overall alignment rate Time searching: 00:01:35 Overall time: 00:01:35 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] 262273 / 5653465 = 0.0464 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 00:44:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688896/SRX8688896.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688896/SRX8688896.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688896/SRX8688896.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688896/SRX8688896.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 00:44:44: #1 read tag files... INFO @ Sat, 11 Dec 2021 00:44:44: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 00:44:49: 1000000 INFO @ Sat, 11 Dec 2021 00:44:55: 2000000 INFO @ Sat, 11 Dec 2021 00:45:00: 3000000 INFO @ Sat, 11 Dec 2021 00:45:05: 4000000 INFO @ Sat, 11 Dec 2021 00:45:10: 5000000 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 00:45:13: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 00:45:13: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 00:45:13: #1 total tags in treatment: 5391192 INFO @ Sat, 11 Dec 2021 00:45:13: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 00:45:13: #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 00:45:13: #1 tags after filtering in treatment: 5390946 INFO @ Sat, 11 Dec 2021 00:45:13: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 00:45:13: #1 finished! INFO @ Sat, 11 Dec 2021 00:45:13: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 00:45:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 00:45:13: #2 number of paired peaks: 257 WARNING @ Sat, 11 Dec 2021 00:45:13: Fewer paired peaks (257) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 257 pairs to build model! INFO @ Sat, 11 Dec 2021 00:45:13: start model_add_line... INFO @ Sat, 11 Dec 2021 00:45:13: start X-correlation... INFO @ Sat, 11 Dec 2021 00:45:13: end of X-cor INFO @ Sat, 11 Dec 2021 00:45:13: #2 finished! INFO @ Sat, 11 Dec 2021 00:45:13: #2 predicted fragment length is 67 bps INFO @ Sat, 11 Dec 2021 00:45:13: #2 alternative fragment length(s) may be 67 bps INFO @ Sat, 11 Dec 2021 00:45:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688896/SRX8688896.05_model.r WARNING @ Sat, 11 Dec 2021 00:45:13: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 00:45:13: #2 You may need to consider one of the other alternative d(s): 67 WARNING @ Sat, 11 Dec 2021 00:45:13: #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 00:45:13: #3 Call peaks... INFO @ Sat, 11 Dec 2021 00:45:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 00:45:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688896/SRX8688896.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688896/SRX8688896.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688896/SRX8688896.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688896/SRX8688896.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 00:45:14: #1 read tag files... INFO @ Sat, 11 Dec 2021 00:45:14: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 00:45:19: 1000000 INFO @ Sat, 11 Dec 2021 00:45:24: 2000000 INFO @ Sat, 11 Dec 2021 00:45:25: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 00:45:29: 3000000 INFO @ Sat, 11 Dec 2021 00:45:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688896/SRX8688896.05_peaks.xls INFO @ Sat, 11 Dec 2021 00:45:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688896/SRX8688896.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 00:45:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688896/SRX8688896.05_summits.bed INFO @ Sat, 11 Dec 2021 00:45:30: Done! pass1 - making usageList (206 chroms): 1 millis pass2 - checking and writing primary data (558 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 00:45:35: 4000000 INFO @ Sat, 11 Dec 2021 00:45:40: 5000000 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 00:45:43: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 00:45:43: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 00:45:43: #1 total tags in treatment: 5391192 INFO @ Sat, 11 Dec 2021 00:45:43: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 00:45:43: #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 00:45:43: #1 tags after filtering in treatment: 5390946 INFO @ Sat, 11 Dec 2021 00:45:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 00:45:43: #1 finished! INFO @ Sat, 11 Dec 2021 00:45:43: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 00:45:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 00:45:43: #2 number of paired peaks: 257 WARNING @ Sat, 11 Dec 2021 00:45:43: Fewer paired peaks (257) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 257 pairs to build model! INFO @ Sat, 11 Dec 2021 00:45:43: start model_add_line... INFO @ Sat, 11 Dec 2021 00:45:43: start X-correlation... INFO @ Sat, 11 Dec 2021 00:45:43: end of X-cor INFO @ Sat, 11 Dec 2021 00:45:43: #2 finished! INFO @ Sat, 11 Dec 2021 00:45:43: #2 predicted fragment length is 67 bps INFO @ Sat, 11 Dec 2021 00:45:43: #2 alternative fragment length(s) may be 67 bps INFO @ Sat, 11 Dec 2021 00:45:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688896/SRX8688896.10_model.r WARNING @ Sat, 11 Dec 2021 00:45:43: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 00:45:43: #2 You may need to consider one of the other alternative d(s): 67 WARNING @ Sat, 11 Dec 2021 00:45:43: #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 00:45:43: #3 Call peaks... INFO @ Sat, 11 Dec 2021 00:45:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 00:45:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688896/SRX8688896.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688896/SRX8688896.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688896/SRX8688896.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688896/SRX8688896.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 00:45:44: #1 read tag files... INFO @ Sat, 11 Dec 2021 00:45:44: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 00:45:49: 1000000 INFO @ Sat, 11 Dec 2021 00:45:54: 2000000 INFO @ Sat, 11 Dec 2021 00:45:55: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 00:45:59: 3000000 INFO @ Sat, 11 Dec 2021 00:46:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688896/SRX8688896.10_peaks.xls INFO @ Sat, 11 Dec 2021 00:46:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688896/SRX8688896.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 00:46:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688896/SRX8688896.10_summits.bed INFO @ Sat, 11 Dec 2021 00:46:01: Done! pass1 - making usageList (128 chroms): 0 millis pass2 - checking and writing primary data (246 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 00:46:05: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 00:46:10: 5000000 INFO @ Sat, 11 Dec 2021 00:46:12: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 00:46:12: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 00:46:12: #1 total tags in treatment: 5391192 INFO @ Sat, 11 Dec 2021 00:46:12: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 00:46:12: #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 00:46:13: #1 tags after filtering in treatment: 5390946 INFO @ Sat, 11 Dec 2021 00:46:13: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 00:46:13: #1 finished! INFO @ Sat, 11 Dec 2021 00:46:13: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 00:46:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 00:46:13: #2 number of paired peaks: 257 WARNING @ Sat, 11 Dec 2021 00:46:13: Fewer paired peaks (257) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 257 pairs to build model! INFO @ Sat, 11 Dec 2021 00:46:13: start model_add_line... INFO @ Sat, 11 Dec 2021 00:46:13: start X-correlation... INFO @ Sat, 11 Dec 2021 00:46:13: end of X-cor INFO @ Sat, 11 Dec 2021 00:46:13: #2 finished! INFO @ Sat, 11 Dec 2021 00:46:13: #2 predicted fragment length is 67 bps INFO @ Sat, 11 Dec 2021 00:46:13: #2 alternative fragment length(s) may be 67 bps INFO @ Sat, 11 Dec 2021 00:46:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688896/SRX8688896.20_model.r WARNING @ Sat, 11 Dec 2021 00:46:13: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 00:46:13: #2 You may need to consider one of the other alternative d(s): 67 WARNING @ Sat, 11 Dec 2021 00:46:13: #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 00:46:13: #3 Call peaks... INFO @ Sat, 11 Dec 2021 00:46:13: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 00:46:25: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 00:46:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688896/SRX8688896.20_peaks.xls INFO @ Sat, 11 Dec 2021 00:46:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688896/SRX8688896.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 00:46:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688896/SRX8688896.20_summits.bed INFO @ Sat, 11 Dec 2021 00:46:30: Done! pass1 - making usageList (54 chroms): 1 millis pass2 - checking and writing primary data (92 records, 4 fields): 3 millis CompletedMACS2peakCalling