Job ID = 14170803 SRX = SRX8689018 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: 00:02:26 7306574 reads; of these: 7306574 (100.00%) were unpaired; of these: 388750 (5.32%) aligned 0 times 4782083 (65.45%) aligned exactly 1 time 2135741 (29.23%) aligned >1 times 94.68% overall alignment rate Time searching: 00:02:26 Overall time: 00:02:26 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] 619909 / 6917824 = 0.0896 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 08:52:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689018/SRX8689018.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689018/SRX8689018.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689018/SRX8689018.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689018/SRX8689018.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 08:52:19: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:52:19: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:52:28: 1000000 INFO @ Sat, 11 Dec 2021 08:52:37: 2000000 INFO @ Sat, 11 Dec 2021 08:52:45: 3000000 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 08:52:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689018/SRX8689018.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689018/SRX8689018.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689018/SRX8689018.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689018/SRX8689018.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 08:52:49: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:52:49: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:52:54: 4000000 INFO @ Sat, 11 Dec 2021 08:52:58: 1000000 INFO @ Sat, 11 Dec 2021 08:53:04: 5000000 INFO @ Sat, 11 Dec 2021 08:53:07: 2000000 INFO @ Sat, 11 Dec 2021 08:53:14: 6000000 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 08:53:16: 3000000 INFO @ Sat, 11 Dec 2021 08:53:17: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 08:53:17: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 08:53:17: #1 total tags in treatment: 6297915 INFO @ Sat, 11 Dec 2021 08:53:17: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:53:17: #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 08:53:18: #1 tags after filtering in treatment: 6297907 INFO @ Sat, 11 Dec 2021 08:53:18: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 08:53:18: #1 finished! INFO @ Sat, 11 Dec 2021 08:53:18: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:53:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:53:18: #2 number of paired peaks: 503 WARNING @ Sat, 11 Dec 2021 08:53:18: Fewer paired peaks (503) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 503 pairs to build model! INFO @ Sat, 11 Dec 2021 08:53:18: start model_add_line... INFO @ Sat, 11 Dec 2021 08:53:18: start X-correlation... INFO @ Sat, 11 Dec 2021 08:53:18: end of X-cor INFO @ Sat, 11 Dec 2021 08:53:18: #2 finished! INFO @ Sat, 11 Dec 2021 08:53:18: #2 predicted fragment length is 64 bps INFO @ Sat, 11 Dec 2021 08:53:18: #2 alternative fragment length(s) may be 64 bps INFO @ Sat, 11 Dec 2021 08:53:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689018/SRX8689018.05_model.r WARNING @ Sat, 11 Dec 2021 08:53:18: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:53:18: #2 You may need to consider one of the other alternative d(s): 64 WARNING @ Sat, 11 Dec 2021 08:53:18: #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 08:53:18: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:53:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:53:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689018/SRX8689018.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689018/SRX8689018.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689018/SRX8689018.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689018/SRX8689018.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 08:53:19: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:53:19: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:53:25: 4000000 INFO @ Sat, 11 Dec 2021 08:53:27: 1000000 INFO @ Sat, 11 Dec 2021 08:53:31: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:53:34: 5000000 INFO @ Sat, 11 Dec 2021 08:53:36: 2000000 INFO @ Sat, 11 Dec 2021 08:53:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689018/SRX8689018.05_peaks.xls INFO @ Sat, 11 Dec 2021 08:53:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689018/SRX8689018.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:53:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689018/SRX8689018.05_summits.bed INFO @ Sat, 11 Dec 2021 08:53:38: Done! pass1 - making usageList (534 chroms): 2 millis pass2 - checking and writing primary data (1452 records, 4 fields): 35 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 08:53:44: 3000000 INFO @ Sat, 11 Dec 2021 08:53:45: 6000000 INFO @ Sat, 11 Dec 2021 08:53:48: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 08:53:48: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 08:53:48: #1 total tags in treatment: 6297915 INFO @ Sat, 11 Dec 2021 08:53:48: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:53:48: #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 08:53:49: #1 tags after filtering in treatment: 6297907 INFO @ Sat, 11 Dec 2021 08:53:49: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 08:53:49: #1 finished! INFO @ Sat, 11 Dec 2021 08:53:49: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:53:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:53:49: #2 number of paired peaks: 503 WARNING @ Sat, 11 Dec 2021 08:53:49: Fewer paired peaks (503) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 503 pairs to build model! INFO @ Sat, 11 Dec 2021 08:53:49: start model_add_line... INFO @ Sat, 11 Dec 2021 08:53:49: start X-correlation... INFO @ Sat, 11 Dec 2021 08:53:49: end of X-cor INFO @ Sat, 11 Dec 2021 08:53:49: #2 finished! INFO @ Sat, 11 Dec 2021 08:53:49: #2 predicted fragment length is 64 bps INFO @ Sat, 11 Dec 2021 08:53:49: #2 alternative fragment length(s) may be 64 bps INFO @ Sat, 11 Dec 2021 08:53:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689018/SRX8689018.10_model.r WARNING @ Sat, 11 Dec 2021 08:53:49: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:53:49: #2 You may need to consider one of the other alternative d(s): 64 WARNING @ Sat, 11 Dec 2021 08:53:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 08:53:49: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:53:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:53:52: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 08:54:00: 5000000 INFO @ Sat, 11 Dec 2021 08:54:02: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:54:09: 6000000 INFO @ Sat, 11 Dec 2021 08:54:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689018/SRX8689018.10_peaks.xls INFO @ Sat, 11 Dec 2021 08:54:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689018/SRX8689018.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:54:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689018/SRX8689018.10_summits.bed INFO @ Sat, 11 Dec 2021 08:54:09: Done! pass1 - making usageList (283 chroms): 1 millis pass2 - checking and writing primary data (584 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 08:54:12: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 08:54:12: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 08:54:12: #1 total tags in treatment: 6297915 INFO @ Sat, 11 Dec 2021 08:54:12: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:54:12: #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 08:54:13: #1 tags after filtering in treatment: 6297907 INFO @ Sat, 11 Dec 2021 08:54:13: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 08:54:13: #1 finished! INFO @ Sat, 11 Dec 2021 08:54:13: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:54:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:54:13: #2 number of paired peaks: 503 WARNING @ Sat, 11 Dec 2021 08:54:13: Fewer paired peaks (503) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 503 pairs to build model! INFO @ Sat, 11 Dec 2021 08:54:13: start model_add_line... INFO @ Sat, 11 Dec 2021 08:54:13: start X-correlation... INFO @ Sat, 11 Dec 2021 08:54:13: end of X-cor INFO @ Sat, 11 Dec 2021 08:54:13: #2 finished! INFO @ Sat, 11 Dec 2021 08:54:13: #2 predicted fragment length is 64 bps INFO @ Sat, 11 Dec 2021 08:54:13: #2 alternative fragment length(s) may be 64 bps INFO @ Sat, 11 Dec 2021 08:54:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689018/SRX8689018.20_model.r WARNING @ Sat, 11 Dec 2021 08:54:13: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:54:13: #2 You may need to consider one of the other alternative d(s): 64 WARNING @ Sat, 11 Dec 2021 08:54:13: #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 08:54:13: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:54:13: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 08:54:26: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:54:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689018/SRX8689018.20_peaks.xls INFO @ Sat, 11 Dec 2021 08:54:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689018/SRX8689018.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:54:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689018/SRX8689018.20_summits.bed INFO @ Sat, 11 Dec 2021 08:54:33: Done! pass1 - making usageList (120 chroms): 2 millis pass2 - checking and writing primary data (223 records, 4 fields): 18 millis CompletedMACS2peakCalling