Job ID = 14170998 SRX = SRX8174953 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: 00:13:54 37135388 reads; of these: 37135388 (100.00%) were unpaired; of these: 886523 (2.39%) aligned 0 times 26725439 (71.97%) aligned exactly 1 time 9523426 (25.65%) aligned >1 times 97.61% overall alignment rate Time searching: 00:13:54 Overall time: 00:13:54 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 16 files... [bam_rmdupse_core] 5977632 / 36248865 = 0.1649 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 09:33:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8174953/SRX8174953.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8174953/SRX8174953.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8174953/SRX8174953.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8174953/SRX8174953.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 09:33:20: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:33:20: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:33:26: 1000000 INFO @ Sat, 11 Dec 2021 09:33:33: 2000000 INFO @ Sat, 11 Dec 2021 09:33:39: 3000000 INFO @ Sat, 11 Dec 2021 09:33:45: 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 09:33:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8174953/SRX8174953.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8174953/SRX8174953.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8174953/SRX8174953.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8174953/SRX8174953.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 09:33:49: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:33:49: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:33:53: 5000000 INFO @ Sat, 11 Dec 2021 09:33:58: 1000000 INFO @ Sat, 11 Dec 2021 09:34:01: 6000000 INFO @ Sat, 11 Dec 2021 09:34:06: 2000000 INFO @ Sat, 11 Dec 2021 09:34:09: 7000000 INFO @ Sat, 11 Dec 2021 09:34:15: 3000000 INFO @ Sat, 11 Dec 2021 09:34:17: 8000000 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 09:34:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8174953/SRX8174953.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8174953/SRX8174953.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8174953/SRX8174953.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8174953/SRX8174953.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 09:34:19: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:34:19: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:34:23: 4000000 INFO @ Sat, 11 Dec 2021 09:34:25: 9000000 INFO @ Sat, 11 Dec 2021 09:34:29: 1000000 INFO @ Sat, 11 Dec 2021 09:34:32: 5000000 INFO @ Sat, 11 Dec 2021 09:34:34: 10000000 INFO @ Sat, 11 Dec 2021 09:34:38: 2000000 INFO @ Sat, 11 Dec 2021 09:34:40: 6000000 INFO @ Sat, 11 Dec 2021 09:34:42: 11000000 INFO @ Sat, 11 Dec 2021 09:34:47: 3000000 INFO @ Sat, 11 Dec 2021 09:34:48: 7000000 INFO @ Sat, 11 Dec 2021 09:34:50: 12000000 INFO @ Sat, 11 Dec 2021 09:34:56: 4000000 INFO @ Sat, 11 Dec 2021 09:34:57: 8000000 INFO @ Sat, 11 Dec 2021 09:34:59: 13000000 INFO @ Sat, 11 Dec 2021 09:35:05: 5000000 INFO @ Sat, 11 Dec 2021 09:35:05: 9000000 INFO @ Sat, 11 Dec 2021 09:35:07: 14000000 INFO @ Sat, 11 Dec 2021 09:35:14: 10000000 INFO @ Sat, 11 Dec 2021 09:35:14: 6000000 INFO @ Sat, 11 Dec 2021 09:35:15: 15000000 INFO @ Sat, 11 Dec 2021 09:35:22: 11000000 INFO @ Sat, 11 Dec 2021 09:35:23: 7000000 INFO @ Sat, 11 Dec 2021 09:35:24: 16000000 INFO @ Sat, 11 Dec 2021 09:35:31: 12000000 INFO @ Sat, 11 Dec 2021 09:35:32: 8000000 INFO @ Sat, 11 Dec 2021 09:35:32: 17000000 INFO @ Sat, 11 Dec 2021 09:35:39: 13000000 INFO @ Sat, 11 Dec 2021 09:35:40: 18000000 INFO @ Sat, 11 Dec 2021 09:35:41: 9000000 INFO @ Sat, 11 Dec 2021 09:35:47: 14000000 INFO @ Sat, 11 Dec 2021 09:35:49: 19000000 INFO @ Sat, 11 Dec 2021 09:35:50: 10000000 INFO @ Sat, 11 Dec 2021 09:35:56: 15000000 INFO @ Sat, 11 Dec 2021 09:35:57: 20000000 INFO @ Sat, 11 Dec 2021 09:35:59: 11000000 INFO @ Sat, 11 Dec 2021 09:36:04: 16000000 INFO @ Sat, 11 Dec 2021 09:36:05: 21000000 INFO @ Sat, 11 Dec 2021 09:36:08: 12000000 INFO @ Sat, 11 Dec 2021 09:36:13: 17000000 INFO @ Sat, 11 Dec 2021 09:36:14: 22000000 INFO @ Sat, 11 Dec 2021 09:36:17: 13000000 INFO @ Sat, 11 Dec 2021 09:36:21: 18000000 INFO @ Sat, 11 Dec 2021 09:36:22: 23000000 INFO @ Sat, 11 Dec 2021 09:36:26: 14000000 INFO @ Sat, 11 Dec 2021 09:36:30: 24000000 INFO @ Sat, 11 Dec 2021 09:36:30: 19000000 INFO @ Sat, 11 Dec 2021 09:36:35: 15000000 INFO @ Sat, 11 Dec 2021 09:36:39: 25000000 INFO @ Sat, 11 Dec 2021 09:36:39: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 09:36:44: 16000000 INFO @ Sat, 11 Dec 2021 09:36:48: 26000000 INFO @ Sat, 11 Dec 2021 09:36:48: 21000000 INFO @ Sat, 11 Dec 2021 09:36:53: 17000000 INFO @ Sat, 11 Dec 2021 09:36:56: 27000000 INFO @ Sat, 11 Dec 2021 09:36:57: 22000000 INFO @ Sat, 11 Dec 2021 09:37:02: 18000000 INFO @ Sat, 11 Dec 2021 09:37:04: 28000000 INFO @ Sat, 11 Dec 2021 09:37:06: 23000000 INFO @ Sat, 11 Dec 2021 09:37:11: 19000000 INFO @ Sat, 11 Dec 2021 09:37:13: 29000000 INFO @ Sat, 11 Dec 2021 09:37:15: 24000000 INFO @ Sat, 11 Dec 2021 09:37:20: 20000000 INFO @ Sat, 11 Dec 2021 09:37:21: 30000000 INFO @ Sat, 11 Dec 2021 09:37:24: #1 tag size is determined as 75 bps INFO @ Sat, 11 Dec 2021 09:37:24: #1 tag size = 75 INFO @ Sat, 11 Dec 2021 09:37:24: #1 total tags in treatment: 30271233 INFO @ Sat, 11 Dec 2021 09:37:24: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:37:24: #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 09:37:24: 25000000 INFO @ Sat, 11 Dec 2021 09:37:25: #1 tags after filtering in treatment: 30271232 INFO @ Sat, 11 Dec 2021 09:37:25: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:37:25: #1 finished! INFO @ Sat, 11 Dec 2021 09:37:25: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:37:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:37:27: #2 number of paired peaks: 264 WARNING @ Sat, 11 Dec 2021 09:37:27: Fewer paired peaks (264) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 264 pairs to build model! INFO @ Sat, 11 Dec 2021 09:37:27: start model_add_line... INFO @ Sat, 11 Dec 2021 09:37:27: start X-correlation... INFO @ Sat, 11 Dec 2021 09:37:27: end of X-cor INFO @ Sat, 11 Dec 2021 09:37:27: #2 finished! INFO @ Sat, 11 Dec 2021 09:37:27: #2 predicted fragment length is 47 bps INFO @ Sat, 11 Dec 2021 09:37:27: #2 alternative fragment length(s) may be 2,47,591 bps INFO @ Sat, 11 Dec 2021 09:37:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8174953/SRX8174953.05_model.r WARNING @ Sat, 11 Dec 2021 09:37:27: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:37:27: #2 You may need to consider one of the other alternative d(s): 2,47,591 WARNING @ Sat, 11 Dec 2021 09:37:27: #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 09:37:27: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:37:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:37:29: 21000000 INFO @ Sat, 11 Dec 2021 09:37:33: 26000000 INFO @ Sat, 11 Dec 2021 09:37:38: 22000000 INFO @ Sat, 11 Dec 2021 09:37:41: 27000000 INFO @ Sat, 11 Dec 2021 09:37:47: 23000000 INFO @ Sat, 11 Dec 2021 09:37:50: 28000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 09:37:56: 24000000 INFO @ Sat, 11 Dec 2021 09:37:59: 29000000 INFO @ Sat, 11 Dec 2021 09:38:05: 25000000 INFO @ Sat, 11 Dec 2021 09:38:07: 30000000 INFO @ Sat, 11 Dec 2021 09:38:10: #1 tag size is determined as 75 bps INFO @ Sat, 11 Dec 2021 09:38:10: #1 tag size = 75 INFO @ Sat, 11 Dec 2021 09:38:10: #1 total tags in treatment: 30271233 INFO @ Sat, 11 Dec 2021 09:38:10: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:38:10: #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 09:38:11: #1 tags after filtering in treatment: 30271232 INFO @ Sat, 11 Dec 2021 09:38:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:38:11: #1 finished! INFO @ Sat, 11 Dec 2021 09:38:11: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:38:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:38:12: #2 number of paired peaks: 264 WARNING @ Sat, 11 Dec 2021 09:38:12: Fewer paired peaks (264) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 264 pairs to build model! INFO @ Sat, 11 Dec 2021 09:38:12: start model_add_line... INFO @ Sat, 11 Dec 2021 09:38:12: start X-correlation... INFO @ Sat, 11 Dec 2021 09:38:12: end of X-cor INFO @ Sat, 11 Dec 2021 09:38:12: #2 finished! INFO @ Sat, 11 Dec 2021 09:38:12: #2 predicted fragment length is 47 bps INFO @ Sat, 11 Dec 2021 09:38:12: #2 alternative fragment length(s) may be 2,47,591 bps INFO @ Sat, 11 Dec 2021 09:38:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8174953/SRX8174953.10_model.r WARNING @ Sat, 11 Dec 2021 09:38:12: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:38:12: #2 You may need to consider one of the other alternative d(s): 2,47,591 WARNING @ Sat, 11 Dec 2021 09:38:12: #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 09:38:12: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:38:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:38:13: 26000000 INFO @ Sat, 11 Dec 2021 09:38:19: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:38:22: 27000000 INFO @ Sat, 11 Dec 2021 09:38:30: 28000000 INFO @ Sat, 11 Dec 2021 09:38:38: 29000000 INFO @ Sat, 11 Dec 2021 09:38:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8174953/SRX8174953.05_peaks.xls INFO @ Sat, 11 Dec 2021 09:38:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8174953/SRX8174953.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:38:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8174953/SRX8174953.05_summits.bed INFO @ Sat, 11 Dec 2021 09:38:44: Done! pass1 - making usageList (815 chroms): 2 millis pass2 - checking and writing primary data (3408 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:38:46: 30000000 INFO @ Sat, 11 Dec 2021 09:38:48: #1 tag size is determined as 75 bps INFO @ Sat, 11 Dec 2021 09:38:48: #1 tag size = 75 INFO @ Sat, 11 Dec 2021 09:38:48: #1 total tags in treatment: 30271233 INFO @ Sat, 11 Dec 2021 09:38:48: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:38:48: #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 09:38:49: #1 tags after filtering in treatment: 30271232 INFO @ Sat, 11 Dec 2021 09:38:49: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:38:49: #1 finished! INFO @ Sat, 11 Dec 2021 09:38:49: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:38:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:38:51: #2 number of paired peaks: 264 WARNING @ Sat, 11 Dec 2021 09:38:51: Fewer paired peaks (264) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 264 pairs to build model! INFO @ Sat, 11 Dec 2021 09:38:51: start model_add_line... INFO @ Sat, 11 Dec 2021 09:38:51: start X-correlation... INFO @ Sat, 11 Dec 2021 09:38:51: end of X-cor INFO @ Sat, 11 Dec 2021 09:38:51: #2 finished! INFO @ Sat, 11 Dec 2021 09:38:51: #2 predicted fragment length is 47 bps INFO @ Sat, 11 Dec 2021 09:38:51: #2 alternative fragment length(s) may be 2,47,591 bps INFO @ Sat, 11 Dec 2021 09:38:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8174953/SRX8174953.20_model.r WARNING @ Sat, 11 Dec 2021 09:38:51: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:38:51: #2 You may need to consider one of the other alternative d(s): 2,47,591 WARNING @ Sat, 11 Dec 2021 09:38:51: #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 09:38:51: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:38:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:38:59: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:39:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8174953/SRX8174953.10_peaks.xls INFO @ Sat, 11 Dec 2021 09:39:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8174953/SRX8174953.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:39:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8174953/SRX8174953.10_summits.bed INFO @ Sat, 11 Dec 2021 09:39:21: Done! pass1 - making usageList (697 chroms): 2 millis pass2 - checking and writing primary data (2346 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:39:37: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:39:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8174953/SRX8174953.20_peaks.xls INFO @ Sat, 11 Dec 2021 09:39:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8174953/SRX8174953.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:39:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8174953/SRX8174953.20_summits.bed INFO @ Sat, 11 Dec 2021 09:39:59: Done! pass1 - making usageList (517 chroms): 2 millis pass2 - checking and writing primary data (1385 records, 4 fields): 14 millis CompletedMACS2peakCalling