Job ID = 6529751 SRX = SRX4669058 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: 00:00:01 Multiseed full-index search: 00:06:08 26147445 reads; of these: 26147445 (100.00%) were unpaired; of these: 1132584 (4.33%) aligned 0 times 22044262 (84.31%) aligned exactly 1 time 2970599 (11.36%) aligned >1 times 95.67% overall alignment rate Time searching: 00:06:09 Overall time: 00:06:09 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] 4753692 / 25014861 = 0.1900 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 03:44:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669058/SRX4669058.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669058/SRX4669058.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669058/SRX4669058.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669058/SRX4669058.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 @ Tue, 30 Jun 2020 03:44:10: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:44:10: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:44:17: 1000000 INFO @ Tue, 30 Jun 2020 03:44:23: 2000000 INFO @ Tue, 30 Jun 2020 03:44:30: 3000000 INFO @ Tue, 30 Jun 2020 03:44:36: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 03:44:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669058/SRX4669058.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669058/SRX4669058.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669058/SRX4669058.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669058/SRX4669058.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 @ Tue, 30 Jun 2020 03:44:40: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:44:40: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:44:43: 5000000 INFO @ Tue, 30 Jun 2020 03:44:47: 1000000 INFO @ Tue, 30 Jun 2020 03:44:49: 6000000 INFO @ Tue, 30 Jun 2020 03:44:54: 2000000 INFO @ Tue, 30 Jun 2020 03:44:56: 7000000 INFO @ Tue, 30 Jun 2020 03:45:00: 3000000 INFO @ Tue, 30 Jun 2020 03:45:03: 8000000 INFO @ Tue, 30 Jun 2020 03:45:07: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 03:45:10: 9000000 INFO @ Tue, 30 Jun 2020 03:45:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669058/SRX4669058.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669058/SRX4669058.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669058/SRX4669058.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669058/SRX4669058.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 @ Tue, 30 Jun 2020 03:45:10: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:45:10: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:45:14: 5000000 INFO @ Tue, 30 Jun 2020 03:45:17: 1000000 INFO @ Tue, 30 Jun 2020 03:45:17: 10000000 INFO @ Tue, 30 Jun 2020 03:45:21: 6000000 INFO @ Tue, 30 Jun 2020 03:45:23: 2000000 INFO @ Tue, 30 Jun 2020 03:45:23: 11000000 INFO @ Tue, 30 Jun 2020 03:45:28: 7000000 INFO @ Tue, 30 Jun 2020 03:45:29: 3000000 INFO @ Tue, 30 Jun 2020 03:45:30: 12000000 INFO @ Tue, 30 Jun 2020 03:45:35: 8000000 INFO @ Tue, 30 Jun 2020 03:45:35: 4000000 INFO @ Tue, 30 Jun 2020 03:45:37: 13000000 INFO @ Tue, 30 Jun 2020 03:45:42: 5000000 INFO @ Tue, 30 Jun 2020 03:45:42: 9000000 INFO @ Tue, 30 Jun 2020 03:45:44: 14000000 INFO @ Tue, 30 Jun 2020 03:45:48: 6000000 INFO @ Tue, 30 Jun 2020 03:45:49: 10000000 INFO @ Tue, 30 Jun 2020 03:45:51: 15000000 INFO @ Tue, 30 Jun 2020 03:45:54: 7000000 INFO @ Tue, 30 Jun 2020 03:45:56: 11000000 INFO @ Tue, 30 Jun 2020 03:45:58: 16000000 INFO @ Tue, 30 Jun 2020 03:46:00: 8000000 INFO @ Tue, 30 Jun 2020 03:46:03: 12000000 INFO @ Tue, 30 Jun 2020 03:46:06: 17000000 INFO @ Tue, 30 Jun 2020 03:46:07: 9000000 INFO @ Tue, 30 Jun 2020 03:46:10: 13000000 INFO @ Tue, 30 Jun 2020 03:46:13: 18000000 INFO @ Tue, 30 Jun 2020 03:46:13: 10000000 INFO @ Tue, 30 Jun 2020 03:46:17: 14000000 INFO @ Tue, 30 Jun 2020 03:46:20: 19000000 INFO @ Tue, 30 Jun 2020 03:46:20: 11000000 INFO @ Tue, 30 Jun 2020 03:46:24: 15000000 INFO @ Tue, 30 Jun 2020 03:46:26: 12000000 INFO @ Tue, 30 Jun 2020 03:46:27: 20000000 INFO @ Tue, 30 Jun 2020 03:46:29: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:46:29: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:46:29: #1 total tags in treatment: 20261169 INFO @ Tue, 30 Jun 2020 03:46:29: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:46:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 03:46:30: #1 tags after filtering in treatment: 20261143 INFO @ Tue, 30 Jun 2020 03:46:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:46:30: #1 finished! INFO @ Tue, 30 Jun 2020 03:46:30: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:46:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:46:30: 16000000 INFO @ Tue, 30 Jun 2020 03:46:31: #2 number of paired peaks: 100 WARNING @ Tue, 30 Jun 2020 03:46:31: Fewer paired peaks (100) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 100 pairs to build model! INFO @ Tue, 30 Jun 2020 03:46:31: start model_add_line... INFO @ Tue, 30 Jun 2020 03:46:31: start X-correlation... INFO @ Tue, 30 Jun 2020 03:46:31: end of X-cor INFO @ Tue, 30 Jun 2020 03:46:31: #2 finished! INFO @ Tue, 30 Jun 2020 03:46:31: #2 predicted fragment length is 45 bps INFO @ Tue, 30 Jun 2020 03:46:31: #2 alternative fragment length(s) may be 2,45 bps INFO @ Tue, 30 Jun 2020 03:46:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669058/SRX4669058.05_model.r WARNING @ Tue, 30 Jun 2020 03:46:31: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:46:31: #2 You may need to consider one of the other alternative d(s): 2,45 WARNING @ Tue, 30 Jun 2020 03:46:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 03:46:31: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:46:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:46:33: 13000000 INFO @ Tue, 30 Jun 2020 03:46:38: 17000000 INFO @ Tue, 30 Jun 2020 03:46:39: 14000000 INFO @ Tue, 30 Jun 2020 03:46:44: 18000000 INFO @ Tue, 30 Jun 2020 03:46:45: 15000000 INFO @ Tue, 30 Jun 2020 03:46:51: 19000000 INFO @ Tue, 30 Jun 2020 03:46:51: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:46:58: 20000000 INFO @ Tue, 30 Jun 2020 03:46:58: 17000000 INFO @ Tue, 30 Jun 2020 03:47:00: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:47:00: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:47:00: #1 total tags in treatment: 20261169 INFO @ Tue, 30 Jun 2020 03:47:00: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:47:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 03:47:01: #1 tags after filtering in treatment: 20261143 INFO @ Tue, 30 Jun 2020 03:47:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:47:01: #1 finished! INFO @ Tue, 30 Jun 2020 03:47:01: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:47:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:47:03: #2 number of paired peaks: 100 WARNING @ Tue, 30 Jun 2020 03:47:03: Fewer paired peaks (100) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 100 pairs to build model! INFO @ Tue, 30 Jun 2020 03:47:03: start model_add_line... INFO @ Tue, 30 Jun 2020 03:47:03: start X-correlation... INFO @ Tue, 30 Jun 2020 03:47:03: end of X-cor INFO @ Tue, 30 Jun 2020 03:47:03: #2 finished! INFO @ Tue, 30 Jun 2020 03:47:03: #2 predicted fragment length is 45 bps INFO @ Tue, 30 Jun 2020 03:47:03: #2 alternative fragment length(s) may be 2,45 bps INFO @ Tue, 30 Jun 2020 03:47:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669058/SRX4669058.10_model.r WARNING @ Tue, 30 Jun 2020 03:47:03: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:47:03: #2 You may need to consider one of the other alternative d(s): 2,45 WARNING @ Tue, 30 Jun 2020 03:47:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 03:47:03: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:47:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:47:05: 18000000 INFO @ Tue, 30 Jun 2020 03:47:08: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:47:11: 19000000 INFO @ Tue, 30 Jun 2020 03:47:17: 20000000 INFO @ Tue, 30 Jun 2020 03:47:19: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:47:19: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:47:19: #1 total tags in treatment: 20261169 INFO @ Tue, 30 Jun 2020 03:47:19: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:47:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 03:47:20: #1 tags after filtering in treatment: 20261143 INFO @ Tue, 30 Jun 2020 03:47:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:47:20: #1 finished! INFO @ Tue, 30 Jun 2020 03:47:20: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:47:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:47:22: #2 number of paired peaks: 100 WARNING @ Tue, 30 Jun 2020 03:47:22: Fewer paired peaks (100) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 100 pairs to build model! INFO @ Tue, 30 Jun 2020 03:47:22: start model_add_line... INFO @ Tue, 30 Jun 2020 03:47:22: start X-correlation... INFO @ Tue, 30 Jun 2020 03:47:22: end of X-cor INFO @ Tue, 30 Jun 2020 03:47:22: #2 finished! INFO @ Tue, 30 Jun 2020 03:47:22: #2 predicted fragment length is 45 bps INFO @ Tue, 30 Jun 2020 03:47:22: #2 alternative fragment length(s) may be 2,45 bps INFO @ Tue, 30 Jun 2020 03:47:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669058/SRX4669058.20_model.r WARNING @ Tue, 30 Jun 2020 03:47:22: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:47:22: #2 You may need to consider one of the other alternative d(s): 2,45 WARNING @ Tue, 30 Jun 2020 03:47:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 03:47:22: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:47:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:47:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669058/SRX4669058.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:47:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669058/SRX4669058.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:47:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669058/SRX4669058.05_summits.bed INFO @ Tue, 30 Jun 2020 03:47:28: Done! pass1 - making usageList (368 chroms): 2 millis pass2 - checking and writing primary data (1270 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:47:39: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:47:58: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:47:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669058/SRX4669058.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:47:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669058/SRX4669058.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:47:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669058/SRX4669058.10_summits.bed INFO @ Tue, 30 Jun 2020 03:47:59: Done! pass1 - making usageList (192 chroms): 1 millis pass2 - checking and writing primary data (405 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:48:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669058/SRX4669058.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:48:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669058/SRX4669058.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:48:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669058/SRX4669058.20_summits.bed INFO @ Tue, 30 Jun 2020 03:48:18: Done! pass1 - making usageList (82 chroms): 1 millis pass2 - checking and writing primary data (152 records, 4 fields): 6 millis CompletedMACS2peakCalling