Job ID = 14170906 SRX = SRX8689042 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: 00:05:04 17797151 reads; of these: 17797151 (100.00%) were unpaired; of these: 746830 (4.20%) aligned 0 times 11480393 (64.51%) aligned exactly 1 time 5569928 (31.30%) aligned >1 times 95.80% overall alignment rate Time searching: 00:05:04 Overall time: 00:05:04 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] 2135186 / 17050321 = 0.1252 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 09:08:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689042/SRX8689042.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689042/SRX8689042.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689042/SRX8689042.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689042/SRX8689042.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 09:08:00: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:08:00: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:08:05: 1000000 INFO @ Sat, 11 Dec 2021 09:08:11: 2000000 INFO @ Sat, 11 Dec 2021 09:08:18: 3000000 INFO @ Sat, 11 Dec 2021 09:08:24: 4000000 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 09:08:30: 5000000 INFO @ Sat, 11 Dec 2021 09:08:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689042/SRX8689042.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689042/SRX8689042.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689042/SRX8689042.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689042/SRX8689042.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 09:08:30: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:08:30: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:08:36: 6000000 INFO @ Sat, 11 Dec 2021 09:08:36: 1000000 INFO @ Sat, 11 Dec 2021 09:08:42: 7000000 INFO @ Sat, 11 Dec 2021 09:08:42: 2000000 INFO @ Sat, 11 Dec 2021 09:08:48: 8000000 INFO @ Sat, 11 Dec 2021 09:08:48: 3000000 INFO @ Sat, 11 Dec 2021 09:08:54: 9000000 INFO @ Sat, 11 Dec 2021 09:08:55: 4000000 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 09:09:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689042/SRX8689042.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689042/SRX8689042.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689042/SRX8689042.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689042/SRX8689042.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 09:09:00: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:09:00: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:09:00: 10000000 INFO @ Sat, 11 Dec 2021 09:09:01: 5000000 INFO @ Sat, 11 Dec 2021 09:09:05: 1000000 INFO @ Sat, 11 Dec 2021 09:09:06: 11000000 INFO @ Sat, 11 Dec 2021 09:09:07: 6000000 INFO @ Sat, 11 Dec 2021 09:09:11: 2000000 INFO @ Sat, 11 Dec 2021 09:09:12: 12000000 INFO @ Sat, 11 Dec 2021 09:09:13: 7000000 INFO @ Sat, 11 Dec 2021 09:09:16: 3000000 INFO @ Sat, 11 Dec 2021 09:09:19: 13000000 INFO @ Sat, 11 Dec 2021 09:09:19: 8000000 INFO @ Sat, 11 Dec 2021 09:09:21: 4000000 INFO @ Sat, 11 Dec 2021 09:09:25: 14000000 INFO @ Sat, 11 Dec 2021 09:09:26: 9000000 INFO @ Sat, 11 Dec 2021 09:09:26: 5000000 INFO @ Sat, 11 Dec 2021 09:09:31: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:09:31: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:09:31: #1 total tags in treatment: 14915135 INFO @ Sat, 11 Dec 2021 09:09:31: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:09:31: #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 09:09:31: #1 tags after filtering in treatment: 14915135 INFO @ Sat, 11 Dec 2021 09:09:31: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:09:31: #1 finished! INFO @ Sat, 11 Dec 2021 09:09:31: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:09:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:09:32: 6000000 INFO @ Sat, 11 Dec 2021 09:09:32: 10000000 INFO @ Sat, 11 Dec 2021 09:09:33: #2 number of paired peaks: 413 WARNING @ Sat, 11 Dec 2021 09:09:33: Fewer paired peaks (413) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 413 pairs to build model! INFO @ Sat, 11 Dec 2021 09:09:33: start model_add_line... INFO @ Sat, 11 Dec 2021 09:09:33: start X-correlation... INFO @ Sat, 11 Dec 2021 09:09:33: end of X-cor INFO @ Sat, 11 Dec 2021 09:09:33: #2 finished! INFO @ Sat, 11 Dec 2021 09:09:33: #2 predicted fragment length is 57 bps INFO @ Sat, 11 Dec 2021 09:09:33: #2 alternative fragment length(s) may be 4,57,558 bps INFO @ Sat, 11 Dec 2021 09:09:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689042/SRX8689042.05_model.r WARNING @ Sat, 11 Dec 2021 09:09:33: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:09:33: #2 You may need to consider one of the other alternative d(s): 4,57,558 WARNING @ Sat, 11 Dec 2021 09:09:33: #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 09:09:33: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:09:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:09:37: 7000000 INFO @ Sat, 11 Dec 2021 09:09:38: 11000000 INFO @ Sat, 11 Dec 2021 09:09:42: 8000000 INFO @ Sat, 11 Dec 2021 09:09:44: 12000000 INFO @ Sat, 11 Dec 2021 09:09:47: 9000000 INFO @ Sat, 11 Dec 2021 09:09:50: 13000000 INFO @ Sat, 11 Dec 2021 09:09:52: 10000000 INFO @ Sat, 11 Dec 2021 09:09:57: 14000000 INFO @ Sat, 11 Dec 2021 09:09:57: 11000000 INFO @ Sat, 11 Dec 2021 09:10:02: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:10:02: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:10:02: #1 total tags in treatment: 14915135 INFO @ Sat, 11 Dec 2021 09:10:02: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:10:02: #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 09:10:03: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:10:03: 12000000 INFO @ Sat, 11 Dec 2021 09:10:03: #1 tags after filtering in treatment: 14915135 INFO @ Sat, 11 Dec 2021 09:10:03: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:10:03: #1 finished! INFO @ Sat, 11 Dec 2021 09:10:03: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:10:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:10:04: #2 number of paired peaks: 413 WARNING @ Sat, 11 Dec 2021 09:10:04: Fewer paired peaks (413) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 413 pairs to build model! INFO @ Sat, 11 Dec 2021 09:10:04: start model_add_line... INFO @ Sat, 11 Dec 2021 09:10:04: start X-correlation... INFO @ Sat, 11 Dec 2021 09:10:04: end of X-cor INFO @ Sat, 11 Dec 2021 09:10:04: #2 finished! INFO @ Sat, 11 Dec 2021 09:10:04: #2 predicted fragment length is 57 bps INFO @ Sat, 11 Dec 2021 09:10:04: #2 alternative fragment length(s) may be 4,57,558 bps INFO @ Sat, 11 Dec 2021 09:10:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689042/SRX8689042.10_model.r WARNING @ Sat, 11 Dec 2021 09:10:04: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:10:04: #2 You may need to consider one of the other alternative d(s): 4,57,558 WARNING @ Sat, 11 Dec 2021 09:10:04: #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 09:10:04: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:10:04: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 09:10:08: 13000000 INFO @ Sat, 11 Dec 2021 09:10:13: 14000000 INFO @ Sat, 11 Dec 2021 09:10:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689042/SRX8689042.05_peaks.xls INFO @ Sat, 11 Dec 2021 09:10:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689042/SRX8689042.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:10:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689042/SRX8689042.05_summits.bed INFO @ Sat, 11 Dec 2021 09:10:17: Done! pass1 - making usageList (862 chroms): 2 millis pass2 - checking and writing primary data (3533 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:10:18: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:10:18: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:10:18: #1 total tags in treatment: 14915135 INFO @ Sat, 11 Dec 2021 09:10:18: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:10:18: #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 09:10:18: #1 tags after filtering in treatment: 14915135 INFO @ Sat, 11 Dec 2021 09:10:18: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:10:18: #1 finished! INFO @ Sat, 11 Dec 2021 09:10:18: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:10:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:10:19: #2 number of paired peaks: 413 WARNING @ Sat, 11 Dec 2021 09:10:19: Fewer paired peaks (413) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 413 pairs to build model! INFO @ Sat, 11 Dec 2021 09:10:19: start model_add_line... INFO @ Sat, 11 Dec 2021 09:10:19: start X-correlation... INFO @ Sat, 11 Dec 2021 09:10:19: end of X-cor INFO @ Sat, 11 Dec 2021 09:10:19: #2 finished! INFO @ Sat, 11 Dec 2021 09:10:19: #2 predicted fragment length is 57 bps INFO @ Sat, 11 Dec 2021 09:10:19: #2 alternative fragment length(s) may be 4,57,558 bps INFO @ Sat, 11 Dec 2021 09:10:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689042/SRX8689042.20_model.r WARNING @ Sat, 11 Dec 2021 09:10:19: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:10:19: #2 You may need to consider one of the other alternative d(s): 4,57,558 WARNING @ Sat, 11 Dec 2021 09:10:19: #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 09:10:19: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:10:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:10:34: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 09:10:46: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:10:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689042/SRX8689042.10_peaks.xls INFO @ Sat, 11 Dec 2021 09:10:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689042/SRX8689042.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:10:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689042/SRX8689042.10_summits.bed INFO @ Sat, 11 Dec 2021 09:10:50: Done! pass1 - making usageList (588 chroms): 1 millis pass2 - checking and writing primary data (1618 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:11:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689042/SRX8689042.20_peaks.xls INFO @ Sat, 11 Dec 2021 09:11:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689042/SRX8689042.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:11:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689042/SRX8689042.20_summits.bed INFO @ Sat, 11 Dec 2021 09:11:00: Done! pass1 - making usageList (268 chroms): 1 millis pass2 - checking and writing primary data (521 records, 4 fields): 9 millis CompletedMACS2peakCalling