Job ID = 14172390 SRX = SRX3292994 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: 00:14:11 24780645 reads; of these: 24780645 (100.00%) were unpaired; of these: 2627892 (10.60%) aligned 0 times 18047288 (72.83%) aligned exactly 1 time 4105465 (16.57%) aligned >1 times 89.40% overall alignment rate Time searching: 00:14:11 Overall time: 00:14:11 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] 3617896 / 22152753 = 0.1633 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 15:41:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3292994/SRX3292994.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3292994/SRX3292994.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3292994/SRX3292994.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3292994/SRX3292994.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 15:41:49: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:41:49: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:42:00: 1000000 INFO @ Sat, 11 Dec 2021 15:42:12: 2000000 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 15:42:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3292994/SRX3292994.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3292994/SRX3292994.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3292994/SRX3292994.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3292994/SRX3292994.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 15:42:19: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:42:19: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:42:23: 3000000 INFO @ Sat, 11 Dec 2021 15:42:29: 1000000 INFO @ Sat, 11 Dec 2021 15:42:35: 4000000 INFO @ Sat, 11 Dec 2021 15:42:38: 2000000 BedGraph に変換中... INFO @ Sat, 11 Dec 2021 15:42:46: 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 15:42:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3292994/SRX3292994.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3292994/SRX3292994.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3292994/SRX3292994.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3292994/SRX3292994.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 15:42:49: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:42:49: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:42:49: 3000000 INFO @ Sat, 11 Dec 2021 15:42:59: 6000000 INFO @ Sat, 11 Dec 2021 15:42:59: 4000000 INFO @ Sat, 11 Dec 2021 15:43:02: 1000000 INFO @ Sat, 11 Dec 2021 15:43:10: 5000000 INFO @ Sat, 11 Dec 2021 15:43:11: 7000000 INFO @ Sat, 11 Dec 2021 15:43:15: 2000000 INFO @ Sat, 11 Dec 2021 15:43:21: 6000000 INFO @ Sat, 11 Dec 2021 15:43:25: 8000000 INFO @ Sat, 11 Dec 2021 15:43:27: 3000000 INFO @ Sat, 11 Dec 2021 15:43:31: 7000000 INFO @ Sat, 11 Dec 2021 15:43:37: 9000000 INFO @ Sat, 11 Dec 2021 15:43:41: 4000000 INFO @ Sat, 11 Dec 2021 15:43:42: 8000000 INFO @ Sat, 11 Dec 2021 15:43:51: 10000000 INFO @ Sat, 11 Dec 2021 15:43:53: 9000000 INFO @ Sat, 11 Dec 2021 15:43:54: 5000000 INFO @ Sat, 11 Dec 2021 15:44:03: 10000000 INFO @ Sat, 11 Dec 2021 15:44:04: 11000000 INFO @ Sat, 11 Dec 2021 15:44:07: 6000000 INFO @ Sat, 11 Dec 2021 15:44:13: 11000000 INFO @ Sat, 11 Dec 2021 15:44:17: 12000000 INFO @ Sat, 11 Dec 2021 15:44:20: 7000000 INFO @ Sat, 11 Dec 2021 15:44:24: 12000000 INFO @ Sat, 11 Dec 2021 15:44:30: 13000000 INFO @ Sat, 11 Dec 2021 15:44:34: 8000000 INFO @ Sat, 11 Dec 2021 15:44:34: 13000000 INFO @ Sat, 11 Dec 2021 15:44:44: 14000000 INFO @ Sat, 11 Dec 2021 15:44:45: 14000000 INFO @ Sat, 11 Dec 2021 15:44:47: 9000000 INFO @ Sat, 11 Dec 2021 15:44:56: 15000000 INFO @ Sat, 11 Dec 2021 15:44:58: 15000000 INFO @ Sat, 11 Dec 2021 15:45:00: 10000000 INFO @ Sat, 11 Dec 2021 15:45:07: 16000000 INFO @ Sat, 11 Dec 2021 15:45:11: 16000000 INFO @ Sat, 11 Dec 2021 15:45:13: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 15:45:17: 17000000 INFO @ Sat, 11 Dec 2021 15:45:24: 17000000 INFO @ Sat, 11 Dec 2021 15:45:26: 12000000 INFO @ Sat, 11 Dec 2021 15:45:27: 18000000 INFO @ Sat, 11 Dec 2021 15:45:33: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 15:45:33: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 15:45:33: #1 total tags in treatment: 18534857 INFO @ Sat, 11 Dec 2021 15:45:33: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:45:33: #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 15:45:34: #1 tags after filtering in treatment: 18534714 INFO @ Sat, 11 Dec 2021 15:45:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 15:45:34: #1 finished! INFO @ Sat, 11 Dec 2021 15:45:34: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:45:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:45:35: #2 number of paired peaks: 461 WARNING @ Sat, 11 Dec 2021 15:45:35: Fewer paired peaks (461) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 461 pairs to build model! INFO @ Sat, 11 Dec 2021 15:45:35: start model_add_line... INFO @ Sat, 11 Dec 2021 15:45:35: start X-correlation... INFO @ Sat, 11 Dec 2021 15:45:35: end of X-cor INFO @ Sat, 11 Dec 2021 15:45:35: #2 finished! INFO @ Sat, 11 Dec 2021 15:45:35: #2 predicted fragment length is 102 bps INFO @ Sat, 11 Dec 2021 15:45:35: #2 alternative fragment length(s) may be 4,102 bps INFO @ Sat, 11 Dec 2021 15:45:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3292994/SRX3292994.10_model.r WARNING @ Sat, 11 Dec 2021 15:45:35: #2 Since the d (102) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 15:45:35: #2 You may need to consider one of the other alternative d(s): 4,102 WARNING @ Sat, 11 Dec 2021 15:45:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 15:45:35: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:45:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:45:38: 18000000 INFO @ Sat, 11 Dec 2021 15:45:39: 13000000 INFO @ Sat, 11 Dec 2021 15:45:45: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 15:45:45: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 15:45:45: #1 total tags in treatment: 18534857 INFO @ Sat, 11 Dec 2021 15:45:45: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:45:45: #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 15:45:46: #1 tags after filtering in treatment: 18534714 INFO @ Sat, 11 Dec 2021 15:45:46: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 15:45:46: #1 finished! INFO @ Sat, 11 Dec 2021 15:45:46: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:45:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:45:47: #2 number of paired peaks: 461 WARNING @ Sat, 11 Dec 2021 15:45:47: Fewer paired peaks (461) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 461 pairs to build model! INFO @ Sat, 11 Dec 2021 15:45:47: start model_add_line... INFO @ Sat, 11 Dec 2021 15:45:47: start X-correlation... INFO @ Sat, 11 Dec 2021 15:45:47: end of X-cor INFO @ Sat, 11 Dec 2021 15:45:47: #2 finished! INFO @ Sat, 11 Dec 2021 15:45:47: #2 predicted fragment length is 102 bps INFO @ Sat, 11 Dec 2021 15:45:47: #2 alternative fragment length(s) may be 4,102 bps INFO @ Sat, 11 Dec 2021 15:45:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3292994/SRX3292994.05_model.r WARNING @ Sat, 11 Dec 2021 15:45:47: #2 Since the d (102) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 15:45:47: #2 You may need to consider one of the other alternative d(s): 4,102 WARNING @ Sat, 11 Dec 2021 15:45:47: #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 15:45:47: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:45:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:45:52: 14000000 INFO @ Sat, 11 Dec 2021 15:46:05: 15000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 15:46:11: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:46:18: 16000000 INFO @ Sat, 11 Dec 2021 15:46:24: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:46:30: 17000000 INFO @ Sat, 11 Dec 2021 15:46:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3292994/SRX3292994.10_peaks.xls INFO @ Sat, 11 Dec 2021 15:46:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3292994/SRX3292994.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:46:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3292994/SRX3292994.10_summits.bed INFO @ Sat, 11 Dec 2021 15:46:31: Done! pass1 - making usageList (455 chroms): 2 millis pass2 - checking and writing primary data (1120 records, 4 fields): 35 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:46:43: 18000000 INFO @ Sat, 11 Dec 2021 15:46:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3292994/SRX3292994.05_peaks.xls INFO @ Sat, 11 Dec 2021 15:46:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3292994/SRX3292994.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:46:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3292994/SRX3292994.05_summits.bed INFO @ Sat, 11 Dec 2021 15:46:44: Done! pass1 - making usageList (491 chroms): 1 millis pass2 - checking and writing primary data (1790 records, 4 fields): 33 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:46:50: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 15:46:50: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 15:46:50: #1 total tags in treatment: 18534857 INFO @ Sat, 11 Dec 2021 15:46:50: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:46:50: #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 15:46:51: #1 tags after filtering in treatment: 18534714 INFO @ Sat, 11 Dec 2021 15:46:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 15:46:51: #1 finished! INFO @ Sat, 11 Dec 2021 15:46:51: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:46:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:46:52: #2 number of paired peaks: 461 WARNING @ Sat, 11 Dec 2021 15:46:52: Fewer paired peaks (461) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 461 pairs to build model! INFO @ Sat, 11 Dec 2021 15:46:52: start model_add_line... INFO @ Sat, 11 Dec 2021 15:46:52: start X-correlation... INFO @ Sat, 11 Dec 2021 15:46:52: end of X-cor INFO @ Sat, 11 Dec 2021 15:46:52: #2 finished! INFO @ Sat, 11 Dec 2021 15:46:52: #2 predicted fragment length is 102 bps INFO @ Sat, 11 Dec 2021 15:46:52: #2 alternative fragment length(s) may be 4,102 bps INFO @ Sat, 11 Dec 2021 15:46:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3292994/SRX3292994.20_model.r WARNING @ Sat, 11 Dec 2021 15:46:52: #2 Since the d (102) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 15:46:52: #2 You may need to consider one of the other alternative d(s): 4,102 WARNING @ Sat, 11 Dec 2021 15:46:52: #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 15:46:52: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:46:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:47:28: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:47:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3292994/SRX3292994.20_peaks.xls INFO @ Sat, 11 Dec 2021 15:47:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3292994/SRX3292994.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:47:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3292994/SRX3292994.20_summits.bed INFO @ Sat, 11 Dec 2021 15:47:48: Done! pass1 - making usageList (396 chroms): 2 millis pass2 - checking and writing primary data (915 records, 4 fields): 32 millis CompletedMACS2peakCalling