Job ID = 14167879 SRX = SRX8688920 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: 00:03:26 13097216 reads; of these: 13097216 (100.00%) were unpaired; of these: 413412 (3.16%) aligned 0 times 9940606 (75.90%) aligned exactly 1 time 2743198 (20.94%) aligned >1 times 96.84% overall alignment rate Time searching: 00:03:26 Overall time: 00:03:26 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_sort_core] merging from 8 files... [bam_rmdupse_core] 1778205 / 12683804 = 0.1402 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 @ Fri, 10 Dec 2021 13:43:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688920/SRX8688920.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688920/SRX8688920.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688920/SRX8688920.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688920/SRX8688920.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 @ Fri, 10 Dec 2021 13:43:36: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:43:36: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:43:41: 1000000 INFO @ Fri, 10 Dec 2021 13:43:47: 2000000 INFO @ Fri, 10 Dec 2021 13:43:53: 3000000 INFO @ Fri, 10 Dec 2021 13:43:58: 4000000 INFO @ Fri, 10 Dec 2021 13:44:04: 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 @ Fri, 10 Dec 2021 13:44:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688920/SRX8688920.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688920/SRX8688920.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688920/SRX8688920.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688920/SRX8688920.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 @ Fri, 10 Dec 2021 13:44:06: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:44:06: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:44:10: 6000000 INFO @ Fri, 10 Dec 2021 13:44:14: 1000000 INFO @ Fri, 10 Dec 2021 13:44:18: 7000000 INFO @ Fri, 10 Dec 2021 13:44:22: 2000000 INFO @ Fri, 10 Dec 2021 13:44:25: 8000000 INFO @ Fri, 10 Dec 2021 13:44:30: 3000000 INFO @ Fri, 10 Dec 2021 13:44:33: 9000000 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 @ Fri, 10 Dec 2021 13:44:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688920/SRX8688920.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688920/SRX8688920.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688920/SRX8688920.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688920/SRX8688920.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 @ Fri, 10 Dec 2021 13:44:36: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:44:36: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:44:37: 4000000 INFO @ Fri, 10 Dec 2021 13:44:40: 10000000 INFO @ Fri, 10 Dec 2021 13:44:43: 1000000 INFO @ Fri, 10 Dec 2021 13:44:45: 5000000 INFO @ Fri, 10 Dec 2021 13:44:47: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 13:44:47: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 13:44:47: #1 total tags in treatment: 10905599 INFO @ Fri, 10 Dec 2021 13:44:47: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:44:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 13:44:47: #1 tags after filtering in treatment: 10905484 INFO @ Fri, 10 Dec 2021 13:44:47: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 13:44:47: #1 finished! INFO @ Fri, 10 Dec 2021 13:44:47: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:44:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:44:48: #2 number of paired peaks: 599 WARNING @ Fri, 10 Dec 2021 13:44:48: Fewer paired peaks (599) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 599 pairs to build model! INFO @ Fri, 10 Dec 2021 13:44:48: start model_add_line... INFO @ Fri, 10 Dec 2021 13:44:48: start X-correlation... INFO @ Fri, 10 Dec 2021 13:44:48: end of X-cor INFO @ Fri, 10 Dec 2021 13:44:48: #2 finished! INFO @ Fri, 10 Dec 2021 13:44:48: #2 predicted fragment length is 55 bps INFO @ Fri, 10 Dec 2021 13:44:48: #2 alternative fragment length(s) may be 55 bps INFO @ Fri, 10 Dec 2021 13:44:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688920/SRX8688920.05_model.r WARNING @ Fri, 10 Dec 2021 13:44:48: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 13:44:48: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Fri, 10 Dec 2021 13:44:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 13:44:48: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:44:48: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 13:44:50: 2000000 INFO @ Fri, 10 Dec 2021 13:44:53: 6000000 INFO @ Fri, 10 Dec 2021 13:44:58: 3000000 INFO @ Fri, 10 Dec 2021 13:45:02: 7000000 INFO @ Fri, 10 Dec 2021 13:45:05: 4000000 INFO @ Fri, 10 Dec 2021 13:45:10: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:45:10: 8000000 INFO @ Fri, 10 Dec 2021 13:45:12: 5000000 INFO @ Fri, 10 Dec 2021 13:45:19: 9000000 INFO @ Fri, 10 Dec 2021 13:45:19: 6000000 INFO @ Fri, 10 Dec 2021 13:45:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688920/SRX8688920.05_peaks.xls INFO @ Fri, 10 Dec 2021 13:45:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688920/SRX8688920.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:45:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688920/SRX8688920.05_summits.bed INFO @ Fri, 10 Dec 2021 13:45:21: Done! pass1 - making usageList (570 chroms): 1 millis pass2 - checking and writing primary data (2685 records, 4 fields): 19 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 13:45:26: 7000000 INFO @ Fri, 10 Dec 2021 13:45:27: 10000000 INFO @ Fri, 10 Dec 2021 13:45:34: 8000000 INFO @ Fri, 10 Dec 2021 13:45:35: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 13:45:35: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 13:45:35: #1 total tags in treatment: 10905599 INFO @ Fri, 10 Dec 2021 13:45:35: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:45:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 13:45:36: #1 tags after filtering in treatment: 10905484 INFO @ Fri, 10 Dec 2021 13:45:36: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 13:45:36: #1 finished! INFO @ Fri, 10 Dec 2021 13:45:36: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:45:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:45:36: #2 number of paired peaks: 599 WARNING @ Fri, 10 Dec 2021 13:45:36: Fewer paired peaks (599) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 599 pairs to build model! INFO @ Fri, 10 Dec 2021 13:45:36: start model_add_line... INFO @ Fri, 10 Dec 2021 13:45:37: start X-correlation... INFO @ Fri, 10 Dec 2021 13:45:37: end of X-cor INFO @ Fri, 10 Dec 2021 13:45:37: #2 finished! INFO @ Fri, 10 Dec 2021 13:45:37: #2 predicted fragment length is 55 bps INFO @ Fri, 10 Dec 2021 13:45:37: #2 alternative fragment length(s) may be 55 bps INFO @ Fri, 10 Dec 2021 13:45:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688920/SRX8688920.10_model.r WARNING @ Fri, 10 Dec 2021 13:45:37: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 13:45:37: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Fri, 10 Dec 2021 13:45:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 13:45:37: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:45:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 13:45:40: 9000000 INFO @ Fri, 10 Dec 2021 13:45:46: 10000000 INFO @ Fri, 10 Dec 2021 13:45:51: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 13:45:51: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 13:45:51: #1 total tags in treatment: 10905599 INFO @ Fri, 10 Dec 2021 13:45:51: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:45:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 13:45:52: #1 tags after filtering in treatment: 10905484 INFO @ Fri, 10 Dec 2021 13:45:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 13:45:52: #1 finished! INFO @ Fri, 10 Dec 2021 13:45:52: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:45:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:45:53: #2 number of paired peaks: 599 WARNING @ Fri, 10 Dec 2021 13:45:53: Fewer paired peaks (599) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 599 pairs to build model! INFO @ Fri, 10 Dec 2021 13:45:53: start model_add_line... INFO @ Fri, 10 Dec 2021 13:45:53: start X-correlation... INFO @ Fri, 10 Dec 2021 13:45:53: end of X-cor INFO @ Fri, 10 Dec 2021 13:45:53: #2 finished! INFO @ Fri, 10 Dec 2021 13:45:53: #2 predicted fragment length is 55 bps INFO @ Fri, 10 Dec 2021 13:45:53: #2 alternative fragment length(s) may be 55 bps INFO @ Fri, 10 Dec 2021 13:45:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688920/SRX8688920.20_model.r WARNING @ Fri, 10 Dec 2021 13:45:53: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 13:45:53: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Fri, 10 Dec 2021 13:45:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 13:45:53: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:45:53: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 13:46:00: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:46:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688920/SRX8688920.10_peaks.xls INFO @ Fri, 10 Dec 2021 13:46:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688920/SRX8688920.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:46:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688920/SRX8688920.10_summits.bed INFO @ Fri, 10 Dec 2021 13:46:11: Done! pass1 - making usageList (408 chroms): 1 millis pass2 - checking and writing primary data (1140 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 13:46:15: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:46:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688920/SRX8688920.20_peaks.xls INFO @ Fri, 10 Dec 2021 13:46:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688920/SRX8688920.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:46:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688920/SRX8688920.20_summits.bed INFO @ Fri, 10 Dec 2021 13:46:27: Done! pass1 - making usageList (187 chroms): 1 millis pass2 - checking and writing primary data (367 records, 4 fields): 9 millis CompletedMACS2peakCalling